[med-svn] [qualimap] 01/02: Imported Upstream version 2.1.3+dfsg
Andreas Tille
tille at debian.org
Tue Nov 17 13:54:00 UTC 2015
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository qualimap.
commit 9d68a06fbba8985018a1938c4fae40a185b40ffb
Author: Andreas Tille <tille at debian.org>
Date: Tue Nov 17 14:42:32 2015 +0100
Imported Upstream version 2.1.3+dfsg
---
.classpath | 8 +
.gitignore | 13 +
.project | 30 +
.settings/org.eclipse.jdt.core.prefs | 6 +
.settings/org.eclipse.m2e.core.prefs | 5 +
.settings/org.hibernate.eclipse.console.prefs | 4 +
.settings/org.maven.ide.eclipse.prefs | 9 +
BUILD | 41 +
LICENSE | 339 +
build_html.sh | 17 +
build_tar.sh | 21 +
cli/HISTORY | 190 +
cli/qualimap | 89 +
cli/qualimap.bat | 3 +
cli/scripts/countsQC.r | 396 +
cli/scripts/init.r | 11 +
cli/scripts/installDependencies.r | 34 +
cli/scripts/paintLocation.r | 108 +
cli/scripts/parseConfig.r | 233 +
cli/scripts/qualimapRfunctions.r | 1637 +
cli/scripts/qualimapRscript.r | 735 +
cli/scripts/utils.r | 226 +
cli/species/human.ens68.txt | 55076 +++++++++++++++++++
cli/species/mouse.ens68.txt | 37316 +++++++++++++
doc/Makefile | 161 +
doc/README | 22 +
doc/_templates/layout.html | 18 +
doc/analysis.rst | 555 +
doc/command_line.rst | 310 +
doc/conf.py | 253 +
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doc/workflow.rst | 64 +
pom.xml | 203 +
src/etc/header.txt | 19 +
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.../qc/qualimap/beans/BamDetailedGenomeWindow.java | 165 +
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.../ngs/qc/qualimap/gui/images/minus_blue.png | Bin 0 -> 734 bytes
.../bioinfo/ngs/qc/qualimap/gui/images/mpiib.jpeg | Bin 0 -> 7345 bytes
.../ngs/qc/qualimap/gui/images/open_folder.png | Bin 0 -> 875 bytes
.../ngs/qc/qualimap/gui/images/pdf_title.png | Bin 0 -> 7051 bytes
.../qualimap/gui/images/qualimap_logo_medium.png | Bin 0 -> 7229 bytes
.../bioinfo/ngs/qc/qualimap/gui/images/report.png | Bin 0 -> 649 bytes
.../ngs/qc/qualimap/gui/images/save_pdf.png | Bin 0 -> 742 bytes
.../ngs/qc/qualimap/gui/images/save_zip.png | Bin 0 -> 829 bytes
.../bioinfo/ngs/qc/qualimap/gui/images/tick.png | Bin 0 -> 537 bytes
.../ngs/qc/qualimap/gui/images/world_go.png | Bin 0 -> 944 bytes
.../org/bioinfo/ngs/qc/qualimap/help/main-help.txt | 15 +
.../ngs/qc/qualimap/scripts/qualimapRfunctions.r | 1419 +
.../ngs/qc/qualimap/scripts/qualimapRscript.r | 609 +
.../qualimap/species/human.61.genes.biotypes.txt | 53515 ++++++++++++++++++
.../qc/qualimap/species/human.biotypes.groups.txt | 31 +
.../qualimap/species/human.hg19.gc_histogram.txt | 1002 +
.../qualimap/species/mouse.61.genes.biotypes.txt | 36817 +++++++++++++
.../qc/qualimap/species/mouse.biotypes.groups.txt | 31 +
.../qualimap/species/mouse.mm10.gc_histogram.txt | 1002 +
.../qc/qualimap/species/mouse.mm9.gc_histogram.txt | 1002 +
.../bioinfo/ngs/qc/qualimap/test/BamQCTest.java | 145 +
.../bioinfo/ngs/qc/qualimap/test/Environment.java | 79 +
.../ngs/qc/qualimap/test/HistogramTest.java | 59 +
.../qc/qualimap/test/JunctionLocationMapTest.java | 62 +
.../ngs/qc/qualimap/test/ReadCountsTest.java | 234 +
.../bioinfo/ngs/qc/qualimap/test/RnaSeqTest.java | 60 +
.../bioinfo/ngs/qc/qualimap/test/TestConfig.java | 87 +
.../org/bioinfo/ngs/qc/qualimap/test/TestEjml.java | 84 +
test/bamqc/results/pl.props | 44 +
test/bamqc/results/pl_1_and_2.props | 44 +
test/bamqc/results/pl_1_and_2_inside.props | 46 +
test/bamqc/results/test001.bam.props | 19 +
test/bamqc/test001.txt | 4 +
test/bamqc/test002.txt | 4 +
test/bamqc/test003.txt | 6 +
test/bamqc/test004.txt | 6 +
test/bamqc/test005.txt | 5 +
test/bamqc/test006.txt | 6 +
test/bamqc/test007.txt | 8 +
test/common_data/gambusino_chr1.gff | 2 +
test/common_data/gambusino_reads.sorted.bam | Bin 0 -> 3397 bytes
test/common_data/pl_1_and_2.bam | Bin 0 -> 22607258 bytes
test/common_data/test_region_01.gff | 1 +
test/common_data/test_region_01_bed | 1 +
test/common_data/transcripts.gtf | 8 +
test/count-reads/external/test001.txt | 5 +
test/count-reads/external/test002.txt | 6 +
test/count-reads/external/test003.txt | 7 +
test/count-reads/external/test004.txt | 6 +
test/count-reads/external/test005.txt | 6 +
test/count-reads/external/test006.txt | 7 +
test/count-reads/reads_001.coord_sort.bam | Bin 0 -> 399 bytes
test/count-reads/reads_001.sam | 10 +
test/count-reads/results/test001.result | 8 +
test/count-reads/results/test002.result | 8 +
test/count-reads/results/test003.result | 8 +
test/count-reads/results/test004.result | 8 +
test/count-reads/test001.txt | 7 +
test/count-reads/test002.txt | 9 +
test/count-reads/test003.txt | 10 +
test/count-reads/test004.txt | 10 +
test/count-reads/test005.txt | 10 +
update_version_howto.txt | 31 +
util/createPreCalculatedGCContentHistogram.py | 96 +
util/createQualimapInfoFile.py | 130 +
435 files changed, 339067 insertions(+)
diff --git a/.classpath b/.classpath
new file mode 100644
index 0000000..ce8af6a
--- /dev/null
+++ b/.classpath
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+ <classpathentry kind="src" path="src/main/java"/>
+ <classpathentry kind="src" path="src/main/resources"/>
+ <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6"/>
+ <classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER"/>
+ <classpathentry kind="output" path="target/classes"/>
+</classpath>
diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..ba036ef
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,13 @@
+.idea
+build
+*.settings
+*.project
+*.user*
+*.swp
+*.swo
+*.obj
+target/*
+*~
+*.ebwt
+*.bt2
+*.log
diff --git a/.project b/.project
new file mode 100644
index 0000000..a31f9b3
--- /dev/null
+++ b/.project
@@ -0,0 +1,30 @@
+<projectDescription>
+ <name>qualimap</name>
+ <comment>NO_M2ECLIPSE_SUPPORT: Project files created with the maven-eclipse-plugin are not supported in M2Eclipse.</comment>
+ <projects>
+ <project>bioinfo-chart</project>
+ <project>bioinfo-commons</project>
+ <project>bioinfo-formats</project>
+ <project>bioinfo-graphics</project>
+ <project>bioinfo-math</project>
+ <project>bioinfo-ngs</project>
+ <project>bioinfo-report</project>
+ <project>bioinfo-tool</project>
+ </projects>
+ <buildSpec>
+ <buildCommand>
+ <name>org.eclipse.jdt.core.javabuilder</name>
+ </buildCommand>
+ <buildCommand>
+ <name>org.maven.ide.eclipse.maven2Builder</name>
+ </buildCommand>
+ <buildCommand>
+ <name>org.eclipse.m2e.core.maven2Builder</name>
+ </buildCommand>
+ </buildSpec>
+ <natures>
+ <nature>org.eclipse.m2e.core.maven2Nature</nature>
+ <nature>org.eclipse.jdt.core.javanature</nature>
+ <nature>org.maven.ide.eclipse.maven2Nature</nature>
+ </natures>
+</projectDescription>
\ No newline at end of file
diff --git a/.settings/org.eclipse.jdt.core.prefs b/.settings/org.eclipse.jdt.core.prefs
new file mode 100644
index 0000000..4240507
--- /dev/null
+++ b/.settings/org.eclipse.jdt.core.prefs
@@ -0,0 +1,6 @@
+#Wed Feb 23 16:11:11 CET 2011
+eclipse.preferences.version=1
+org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.6
+org.eclipse.jdt.core.compiler.compliance=1.6
+org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
+org.eclipse.jdt.core.compiler.source=1.6
diff --git a/.settings/org.eclipse.m2e.core.prefs b/.settings/org.eclipse.m2e.core.prefs
new file mode 100644
index 0000000..79e3ddb
--- /dev/null
+++ b/.settings/org.eclipse.m2e.core.prefs
@@ -0,0 +1,5 @@
+#Thu Apr 07 18:01:26 CEST 2011
+activeProfiles=
+eclipse.preferences.version=1
+resolveWorkspaceProjects=false
+version=1
diff --git a/.settings/org.hibernate.eclipse.console.prefs b/.settings/org.hibernate.eclipse.console.prefs
new file mode 100644
index 0000000..78bbada
--- /dev/null
+++ b/.settings/org.hibernate.eclipse.console.prefs
@@ -0,0 +1,4 @@
+#Tue Mar 15 13:04:46 CET 2011
+default.configuration=
+eclipse.preferences.version=1
+hibernate3.enabled=false
diff --git a/.settings/org.maven.ide.eclipse.prefs b/.settings/org.maven.ide.eclipse.prefs
new file mode 100644
index 0000000..53c670b
--- /dev/null
+++ b/.settings/org.maven.ide.eclipse.prefs
@@ -0,0 +1,9 @@
+#Thu Apr 07 16:47:26 CEST 2011
+activeProfiles=
+eclipse.preferences.version=1
+fullBuildGoals=process-test-resources
+includeModules=false
+resolveWorkspaceProjects=false
+resourceFilterGoals=process-resources resources\:testResources
+skipCompilerPlugin=true
+version=1
diff --git a/BUILD b/BUILD
new file mode 100644
index 0000000..275ad64
--- /dev/null
+++ b/BUILD
@@ -0,0 +1,41 @@
+Building Qualimap from source code
+----------------------------------
+
+1) Prepare environment
+
+Install jdk-6 (both Sun and OpenJDK should work) and maven2
+
+Add required picard-1.70.jar and sam-1.70.jar to maven repo:
+They can be found in directory "external"
+Alternatevly one can download picard-tools v1.70 from http://sourceforge.net/projects/picard/files/
+
+mvn install:install-file -DgroupId=net.sf.picard -DartifactId=picard -Dversion=1.70 -Dpackaging=jar -Dfile=/path/to/picard-tools-1.70/picard-1.70.jar
+
+mvn install:install-file -DgroupId=net.sf.samtools -DartifactId=samtools -Dversion=1.70 -Dpackaging=jar -Dfile=/path/to/picard-tools-1.70/sam-1.70.jar
+
+mvn install:install-file -DgroupId=org.ejml -DartifactId=ejml -Dversion=0.24 -Dpackaging=jar -Dfile=ejml-0.24.jar
+
+
+2) Build Qualimap
+
+Use maven2 command:
+
+mvn install
+
+Upon first build all dependencies will be downloaded to the repo, this may require some time.
+
+3) Run Qualimap
+
+The built jar can be found in target/install subdir of sources folder.
+
+
+4) Develop Qualimap
+
+You can use your favorite Java IDE to work on Qualimap.
+However, we recommend (and use) IntelliJ IdeA Community Edition.
+
+5) Troubleshouting
+
+If you have problems building Qualimap, please refer to google-groups:
+http://groups.google.com/group/qualimap
+
diff --git a/LICENSE b/LICENSE
new file mode 100644
index 0000000..a43ea21
--- /dev/null
+++ b/LICENSE
@@ -0,0 +1,339 @@
+ GNU GENERAL PUBLIC LICENSE
+ Version 2, June 1991
+
+ Copyright (C) 1989, 1991 Free Software Foundation, Inc.
+ 675 Mass Ave, Cambridge, MA 02139, USA
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+ Preamble
+
+ The licenses for most software are designed to take away your
+freedom to share and change it. By contrast, the GNU General Public
+License is intended to guarantee your freedom to share and change free
+software--to make sure the software is free for all its users. This
+General Public License applies to most of the Free Software
+Foundation's software and to any other program whose authors commit to
+using it. (Some other Free Software Foundation software is covered by
+the GNU Library General Public License instead.) You can apply it to
+your programs, too.
+
+ When we speak of free software, we are referring to freedom, not
+price. Our General Public Licenses are designed to make sure that you
+have the freedom to distribute copies of free software (and charge for
+this service if you wish), that you receive source code or can get it
+if you want it, that you can change the software or use pieces of it
+in new free programs; and that you know you can do these things.
+
+ To protect your rights, we need to make restrictions that forbid
+anyone to deny you these rights or to ask you to surrender the rights.
+These restrictions translate to certain responsibilities for you if you
+distribute copies of the software, or if you modify it.
+
+ For example, if you distribute copies of such a program, whether
+gratis or for a fee, you must give the recipients all the rights that
+you have. You must make sure that they, too, receive or can get the
+source code. And you must show them these terms so they know their
+rights.
+
+ We protect your rights with two steps: (1) copyright the software, and
+(2) offer you this license which gives you legal permission to copy,
+distribute and/or modify the software.
+
+ Also, for each author's protection and ours, we want to make certain
+that everyone understands that there is no warranty for this free
+software. If the software is modified by someone else and passed on, we
+want its recipients to know that what they have is not the original, so
+that any problems introduced by others will not reflect on the original
+authors' reputations.
+
+ Finally, any free program is threatened constantly by software
+patents. We wish to avoid the danger that redistributors of a free
+program will individually obtain patent licenses, in effect making the
+program proprietary. To prevent this, we have made it clear that any
+patent must be licensed for everyone's free use or not licensed at all.
+
+ The precise terms and conditions for copying, distribution and
+modification follow.
+
+ GNU GENERAL PUBLIC LICENSE
+ TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
+
+ 0. This License applies to any program or other work which contains
+a notice placed by the copyright holder saying it may be distributed
+under the terms of this General Public License. The "Program", below,
+refers to any such program or work, and a "work based on the Program"
+means either the Program or any derivative work under copyright law:
+that is to say, a work containing the Program or a portion of it,
+either verbatim or with modifications and/or translated into another
+language. (Hereinafter, translation is included without limitation in
+the term "modification".) Each licensee is addressed as "you".
+
+Activities other than copying, distribution and modification are not
+covered by this License; they are outside its scope. The act of
+running the Program is not restricted, and the output from the Program
+is covered only if its contents constitute a work based on the
+Program (independent of having been made by running the Program).
+Whether that is true depends on what the Program does.
+
+ 1. You may copy and distribute verbatim copies of the Program's
+source code as you receive it, in any medium, provided that you
+conspicuously and appropriately publish on each copy an appropriate
+copyright notice and disclaimer of warranty; keep intact all the
+notices that refer to this License and to the absence of any warranty;
+and give any other recipients of the Program a copy of this License
+along with the Program.
+
+You may charge a fee for the physical act of transferring a copy, and
+you may at your option offer warranty protection in exchange for a fee.
+
+ 2. You may modify your copy or copies of the Program or any portion
+of it, thus forming a work based on the Program, and copy and
+distribute such modifications or work under the terms of Section 1
+above, provided that you also meet all of these conditions:
+
+ a) You must cause the modified files to carry prominent notices
+ stating that you changed the files and the date of any change.
+
+ b) You must cause any work that you distribute or publish, that in
+ whole or in part contains or is derived from the Program or any
+ part thereof, to be licensed as a whole at no charge to all third
+ parties under the terms of this License.
+
+ c) If the modified program normally reads commands interactively
+ when run, you must cause it, when started running for such
+ interactive use in the most ordinary way, to print or display an
+ announcement including an appropriate copyright notice and a
+ notice that there is no warranty (or else, saying that you provide
+ a warranty) and that users may redistribute the program under
+ these conditions, and telling the user how to view a copy of this
+ License. (Exception: if the Program itself is interactive but
+ does not normally print such an announcement, your work based on
+ the Program is not required to print an announcement.)
+
+These requirements apply to the modified work as a whole. If
+identifiable sections of that work are not derived from the Program,
+and can be reasonably considered independent and separate works in
+themselves, then this License, and its terms, do not apply to those
+sections when you distribute them as separate works. But when you
+distribute the same sections as part of a whole which is a work based
+on the Program, the distribution of the whole must be on the terms of
+this License, whose permissions for other licensees extend to the
+entire whole, and thus to each and every part regardless of who wrote it.
+
+Thus, it is not the intent of this section to claim rights or contest
+your rights to work written entirely by you; rather, the intent is to
+exercise the right to control the distribution of derivative or
+collective works based on the Program.
+
+In addition, mere aggregation of another work not based on the Program
+with the Program (or with a work based on the Program) on a volume of
+a storage or distribution medium does not bring the other work under
+the scope of this License.
+
+ 3. You may copy and distribute the Program (or a work based on it,
+under Section 2) in object code or executable form under the terms of
+Sections 1 and 2 above provided that you also do one of the following:
+
+ a) Accompany it with the complete corresponding machine-readable
+ source code, which must be distributed under the terms of Sections
+ 1 and 2 above on a medium customarily used for software interchange; or,
+
+ b) Accompany it with a written offer, valid for at least three
+ years, to give any third party, for a charge no more than your
+ cost of physically performing source distribution, a complete
+ machine-readable copy of the corresponding source code, to be
+ distributed under the terms of Sections 1 and 2 above on a medium
+ customarily used for software interchange; or,
+
+ c) Accompany it with the information you received as to the offer
+ to distribute corresponding source code. (This alternative is
+ allowed only for noncommercial distribution and only if you
+ received the program in object code or executable form with such
+ an offer, in accord with Subsection b above.)
+
+The source code for a work means the preferred form of the work for
+making modifications to it. For an executable work, complete source
+code means all the source code for all modules it contains, plus any
+associated interface definition files, plus the scripts used to
+control compilation and installation of the executable. However, as a
+special exception, the source code distributed need not include
+anything that is normally distributed (in either source or binary
+form) with the major components (compiler, kernel, and so on) of the
+operating system on which the executable runs, unless that component
+itself accompanies the executable.
+
+If distribution of executable or object code is made by offering
+access to copy from a designated place, then offering equivalent
+access to copy the source code from the same place counts as
+distribution of the source code, even though third parties are not
+compelled to copy the source along with the object code.
+
+ 4. You may not copy, modify, sublicense, or distribute the Program
+except as expressly provided under this License. Any attempt
+otherwise to copy, modify, sublicense or distribute the Program is
+void, and will automatically terminate your rights under this License.
+However, parties who have received copies, or rights, from you under
+this License will not have their licenses terminated so long as such
+parties remain in full compliance.
+
+ 5. You are not required to accept this License, since you have not
+signed it. However, nothing else grants you permission to modify or
+distribute the Program or its derivative works. These actions are
+prohibited by law if you do not accept this License. Therefore, by
+modifying or distributing the Program (or any work based on the
+Program), you indicate your acceptance of this License to do so, and
+all its terms and conditions for copying, distributing or modifying
+the Program or works based on it.
+
+ 6. Each time you redistribute the Program (or any work based on the
+Program), the recipient automatically receives a license from the
+original licensor to copy, distribute or modify the Program subject to
+these terms and conditions. You may not impose any further
+restrictions on the recipients' exercise of the rights granted herein.
+You are not responsible for enforcing compliance by third parties to
+this License.
+
+ 7. If, as a consequence of a court judgment or allegation of patent
+infringement or for any other reason (not limited to patent issues),
+conditions are imposed on you (whether by court order, agreement or
+otherwise) that contradict the conditions of this License, they do not
+excuse you from the conditions of this License. If you cannot
+distribute so as to satisfy simultaneously your obligations under this
+License and any other pertinent obligations, then as a consequence you
+may not distribute the Program at all. For example, if a patent
+license would not permit royalty-free redistribution of the Program by
+all those who receive copies directly or indirectly through you, then
+the only way you could satisfy both it and this License would be to
+refrain entirely from distribution of the Program.
+
+If any portion of this section is held invalid or unenforceable under
+any particular circumstance, the balance of the section is intended to
+apply and the section as a whole is intended to apply in other
+circumstances.
+
+It is not the purpose of this section to induce you to infringe any
+patents or other property right claims or to contest validity of any
+such claims; this section has the sole purpose of protecting the
+integrity of the free software distribution system, which is
+implemented by public license practices. Many people have made
+generous contributions to the wide range of software distributed
+through that system in reliance on consistent application of that
+system; it is up to the author/donor to decide if he or she is willing
+to distribute software through any other system and a licensee cannot
+impose that choice.
+
+This section is intended to make thoroughly clear what is believed to
+be a consequence of the rest of this License.
+
+ 8. If the distribution and/or use of the Program is restricted in
+certain countries either by patents or by copyrighted interfaces, the
+original copyright holder who places the Program under this License
+may add an explicit geographical distribution limitation excluding
+those countries, so that distribution is permitted only in or among
+countries not thus excluded. In such case, this License incorporates
+the limitation as if written in the body of this License.
+
+ 9. The Free Software Foundation may publish revised and/or new versions
+of the General Public License from time to time. Such new versions will
+be similar in spirit to the present version, but may differ in detail to
+address new problems or concerns.
+
+Each version is given a distinguishing version number. If the Program
+specifies a version number of this License which applies to it and "any
+later version", you have the option of following the terms and conditions
+either of that version or of any later version published by the Free
+Software Foundation. If the Program does not specify a version number of
+this License, you may choose any version ever published by the Free Software
+Foundation.
+
+ 10. If you wish to incorporate parts of the Program into other free
+programs whose distribution conditions are different, write to the author
+to ask for permission. For software which is copyrighted by the Free
+Software Foundation, write to the Free Software Foundation; we sometimes
+make exceptions for this. Our decision will be guided by the two goals
+of preserving the free status of all derivatives of our free software and
+of promoting the sharing and reuse of software generally.
+
+ NO WARRANTY
+
+ 11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY
+FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN
+OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES
+PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED
+OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
+MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS
+TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE
+PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING,
+REPAIR OR CORRECTION.
+
+ 12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
+WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR
+REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES,
+INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING
+OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED
+TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY
+YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER
+PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE
+POSSIBILITY OF SUCH DAMAGES.
+
+ END OF TERMS AND CONDITIONS
+
+ Appendix: How to Apply These Terms to Your New Programs
+
+ If you develop a new program, and you want it to be of the greatest
+possible use to the public, the best way to achieve this is to make it
+free software which everyone can redistribute and change under these terms.
+
+ To do so, attach the following notices to the program. It is safest
+to attach them to the start of each source file to most effectively
+convey the exclusion of warranty; and each file should have at least
+the "copyright" line and a pointer to where the full notice is found.
+
+ <one line to give the program's name and a brief idea of what it does.>
+ Copyright (C) 19yy <name of author>
+
+ This program is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 2 of the License, or
+ (at your option) any later version.
+
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program; if not, write to the Free Software
+ Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.
+
+Also add information on how to contact you by electronic and paper mail.
+
+If the program is interactive, make it output a short notice like this
+when it starts in an interactive mode:
+
+ Gnomovision version 69, Copyright (C) 19yy name of author
+ Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
+ This is free software, and you are welcome to redistribute it
+ under certain conditions; type `show c' for details.
+
+The hypothetical commands `show w' and `show c' should show the appropriate
+parts of the General Public License. Of course, the commands you use may
+be called something other than `show w' and `show c'; they could even be
+mouse-clicks or menu items--whatever suits your program.
+
+You should also get your employer (if you work as a programmer) or your
+school, if any, to sign a "copyright disclaimer" for the program, if
+necessary. Here is a sample; alter the names:
+
+ Yoyodyne, Inc., hereby disclaims all copyright interest in the program
+ `Gnomovision' (which makes passes at compilers) written by James Hacker.
+
+ <signature of Ty Coon>, 1 April 1989
+ Ty Coon, President of Vice
+
+This General Public License does not permit incorporating your program into
+proprietary programs. If your program is a subroutine library, you may
+consider it more useful to permit linking proprietary applications with the
+library. If this is what you want to do, use the GNU Library General
+Public License instead of this License.
diff --git a/build_html.sh b/build_html.sh
new file mode 100755
index 0000000..b32c43f
--- /dev/null
+++ b/build_html.sh
@@ -0,0 +1,17 @@
+#/bin/bash
+
+export QUALIMAP_HTML_DOCS=doc_html
+
+mkdir $QUALIMAP_HTML_DOCS
+
+make -C doc html
+cp -vr doc/_build/html/* $QUALIMAP_HTML_DOCS
+
+zip -r doc.zip $QUALIMAP_HTML_DOCS
+
+#cleanup
+rm -rf $QUALIMAP_HTML_DOCS
+
+
+
+
diff --git a/build_tar.sh b/build_tar.sh
new file mode 100755
index 0000000..87078f4
--- /dev/null
+++ b/build_tar.sh
@@ -0,0 +1,21 @@
+#/bin/bash
+
+export QUALIMAP_DIR=qualimap-build-`date +%d-%m-%y`
+
+mvn install
+mkdir $QUALIMAP_DIR
+cp -vR target/install/* $QUALIMAP_DIR
+
+make -C doc latexpdf
+cp -v doc/_build/latex/QualimapManual.pdf $QUALIMAP_DIR
+
+tar -cf $QUALIMAP_DIR.tar $QUALIMAP_DIR
+gzip -f $QUALIMAP_DIR.tar
+#scp $QUALIMAP_DIR.tar.gz genome:/data/qualimapLatestBuild/
+
+#cleanup
+#rm -rf $QUALIMAP_DIR
+
+
+
+
diff --git a/cli/HISTORY b/cli/HISTORY
new file mode 100644
index 0000000..e0ed399
--- /dev/null
+++ b/cli/HISTORY
@@ -0,0 +1,190 @@
+Version Release History
+=======================
+
+
+Version 2.1.2 - September 23, 2015
+----------------------------------
+
+ * BAM QC: added an option to analyze overlapping paired-end read alignments (suggested by Eva Koenig)
+ * BAM QC: fixed processing of incorrect alignments (reported by Alexander Peltzer)
+ * BAM QC: improved paired reads statistics description (suggested by Jochen Singer)
+ * RNA-seq QC: fixed issue with transcript high coverage (reported by Daniel Barrel)
+ * RNA-seq QC: added to statistcs number of intronic/intergenic reads overlapping exons
+ * RNA-seq QC: minor fix of coverage plot
+ * Counts QC: fixed an issue due to update of NOISeq package
+ * Multisample BAM QC: corrected labels in coverage and GC-content plots (reported by Franziska Singer)
+ * Multisample BAM QC: fixed issue with min X-value in insert size plots (reported by Roland Schmucki)
+ * Improved PDF format output
+ * Documentation: update BAM QC, RNA-seq QC descriptions
+
+
+Version 2.1.1 - June 15, 2015
+-----------------------------
+
+ * BAM QC: added chromosome names when drawing chromosome limits
+ * BAM QC: fixed fail when no mapped reads; add warning
+ * BAM QC: fixed computing coverage standard deviation (reported by Charlotte Peeters)
+ * BAM QC: by default duplicates (secondary alignments) are skipped if marked
+ * BAM QC: added report for "OutOfMemory" error
+ * RNA-seq QC: added support for computing number of read pairs
+ * Counts QC: fix fail when sample name starts from number (reported by Alena Dobiasova)
+ * Documentation: updated BAM QC, RNA-seq QC
+ * Documentation: added special solution regarding DISPLAY issue on Linux server (suggested by Roberto Spreafico)
+
+
+Version 2.1 - March 19, 2015
+----------------------------
+
+ * BAM QC: added percentage of mapped reads with at least one insertion or deletion
+ * BAM QC: added an option to skip duplicates when running analysis (suggested by Johan Dalberg)
+ * RNA-seq QC: add text report of results (suggested by Lorena Pantano)
+ * BAM QC: fixed issue with inRegionReferenceSize outside of regions (reported by Tristan Carland)
+ * comp-counts: fixed bug when output file path is wrong (reported by Stephane Plaisance)
+ * RNA-seq QC: fixed issue with no-sorting required, improved statistics and input description (thanks to Priyanka Jain for report)
+ * RNA-seq QC: fixed issue when num reads equals zero
+ * RNA-seq QC: improved logging (implemented by Lorena Pantano)
+ * Feature reader: improved exception processing
+ * Fixed an issue with output folder when outformat is PDF
+
+
+Version 2.0.2 - February 10, 2015
+---------------------------------
+
+ * Compute counts: fixed issue with GTF file analysis and added support for single-end reads strand specificity (thanks to Roberto Spreafico for reports)
+ * BAM QC: added support of mismatches and indels in the text report (thanks to Nils for report)
+ * RNA-seq QC: fixed issue with loading GTF files with strange names (thanks to Haroon Kalam for report)
+ * RNA-seq QC: fixed crash when there are no junctions detected (thanks to François Lefebvre and Larry Willhelm for reports)
+ * Multi-BamQC: fixed issue with max coverage of BAM file supported
+
+
+Version 2.0.1 - Januar 6, 2015
+------------------------------
+
+ * BAM QC: fixed problem with nucleotide content (thanks to Travis Collier)
+ * RNA-seq QC: fixed issue with chromosomes
+ * RNA-seq QC: add support for paired-end reads
+ * countsQC: fixed bug when population less than sample size
+ * Fixed issue with default outdir name
+
+
+Version 2.0 - August 27, 2014
+-----------------------------
+
+ * New mode: multi-sample BAM QC
+ * Counts QC: completely redesigned, add support for multi-sample input
+ * RNA-seq QC: add new plots (coverage across genebody, reads genomic origin, junction analysis)
+ * Command line interface improved
+ * BAM QC: changed order of plots
+ * BAM QC: fix insert size overflow
+ * BAM QC: add insert size info to plain text report
+ * BAM QC: fix bug with stats inside of regions
+ * BAM QC: performance improved for long genomes
+ * RNA-seq QC: fix default protocol
+ * Add utility script to create species annotations for Counts QC
+ * Add condtion to exit on error in main script (suggestion from Johan Dahlberg)
+ * Fix coverage quota in plain text report (bugfix from John Budde)
+ * Major documentation update
+
+A number of renamings in command line interface were introduced.
+
+common:
+ -rscriptpath => -R or --rscriptpath
+bamqc:
+ -outcov => -oc or --output-genome-coverage
+rnaseq:
+ -counts => -oc
+ -algorithm => -a or --algorithm
+ -protocol => -p or --sequencing-protocol
+comp-counts
+ -sorted => -s or --sorted
+ -paired => -pe or --paired
+ -algorithm => -a or --algorithm
+ -protocol => -p or --sequencing-protocol
+
+
+Version 1.0 - May 29, 2014
+--------------------------
+
+ * BAM QC: add computation of mismatches and error rate
+ * BAM QC: add new metrics for insert size
+ * BAM QC: contig coverage added to text report (patch from Johan Dahlberg)
+ * BAM QC: add option to output per-base coverage
+ * Compute counts: add full support for paired-end reads
+ * RNA-seq QC: add new plots and statistics
+ * Updated documentation
+
+
+Version 0.8.1 - May 5, 2014
+---------------------------
+
+ * Fixed bug with CountsQC and R version 3
+ * Fixed bug with double reference size computation
+
+Version 0.8 - March 5, 2014
+------------------------------
+
+ * Added new analysis mode "RNA-seq QC"
+ * Added PDF output path
+ * Fixed bug with R-version recognition
+ * Fixed bug with per-chromosome standard deviation calculation
+ * Fixed integer overflow in number of reads
+ * Fixed crash with insert size
+ * Fixed bug with empty SAMRecord
+
+Version 0.7.1 - April 19, 2013
+------------------------------
+
+ * Fixed bug with "Coverage Across Reference" plot
+ * Fixed bug in BAM QC when regions don't have any coverage
+
+
+Version 0.7 - April 10, 2013
+----------------------------
+
+ * Fixed bug in per chromosome coverage report (https://groups.google.com/d/msg/qualimap/AO_6111Gg1E/21SdvEWeAfUJ)
+ * Deletions are now properly computed when calculating coverage
+ * Fixed bug in renaming of tabs
+ * Added global parameter to set Rscript path
+ * Minor fixes in command line tools argument parsing
+ * Improved handling of discordant regions between the BED/GFF and BAM files in BAM QC
+ * Updated documentation
+
+Version 0.6 - October 30, 2012
+--------------------------
+
+ * Fixed bug with small homopolymer indels estimation
+ * Fixed bug with EQ and X SAM format tags in BAM QC
+ * BAM QC: added option to set minimum homopolymer size
+ * BAM QC: added option to open SAM files along with BAM files from GUI
+
+Version 0.5 - July 25, 2012
+--------------------------
+
+ * BED format is now supported throughout application
+ * Raw data from BAM QC and Counts QC plots can be exported
+ * BAM QC: Added homopolymer indels estimation
+ * BAM QC: Added strand specificity calculation
+ * BAM QC: Added clipping profile and number of clipped reads statistics
+ * Compute counts: Added 5' to 3' prime bias calculation
+ * Allow to set java memory size from launching script
+ * Fixed problem with upperCoverageBound in Coverage Across Reference chart
+ * Fixed issue with insert size limits
+ * Added missing qualimap.bat to launch application on MS Windows
+
+Version 0.4 - June 4, 2012
+--------------------------
+
+ * Fixed problem with chromsome limits in Insert Size chart
+ * Fixed issue with "compute counts" when regions are having several
+ intersecting reads
+ * Fixed crash with Coverage Histogram 0-50X for high coverage samples
+ * Fixed Coverage Histogram when minimal coverage is more than zero
+ * Fixed issue with GFF files, containing empty lines
+
+
+Version 0.3 - May 18,2012
+-------------------------
+
+ First public release.
+
+
diff --git a/cli/qualimap b/cli/qualimap
new file mode 100755
index 0000000..08d266e
--- /dev/null
+++ b/cli/qualimap
@@ -0,0 +1,89 @@
+#!/bin/bash
+
+# This script launches Qualimap on Linux and MacOS
+
+# Change default memory settings here
+
+JAVA_MEM_DEFAULT_SIZE="1200M"
+
+# Check for special argument controlling memory size
+
+ARGS=()
+for p in "$@"
+do
+ if [[ "$p" = "--java-mem-size="* ]]; then
+ # skip argument to prevent propogating and get its value
+ JAVA_MEM_SIZE=`echo $p | cut -d \= -f 2`
+ else
+ # collect arguments
+ ARGS+=($p)
+ fi
+
+ if [[ "$p" = *"help"* || "$p" = *"-h" ]]; then
+ OUTPUT_ADDITIONAL_HELP="1"
+ fi
+
+done
+
+if [ "$JAVA_MEM_SIZE" = "" ]; then
+ # Setting default memory size
+ JAVA_MEM_SIZE=$JAVA_MEM_DEFAULT_SIZE
+fi
+
+echo "Java memory size is set to $JAVA_MEM_SIZE"
+echo "Launching application..."
+echo
+
+if [ "$JAVA_OPTS" != "" ]
+then
+ java_options=$JAVA_OPTS
+ echo "detected environment java options $java_options"
+else
+ java_options="-Xms32m -Xmx$JAVA_MEM_SIZE -XX:MaxPermSize=1024m"
+fi
+
+
+CLASSPATH=""
+
+prg=$0
+
+# check if symbolic link
+
+while [ -h "$prg" ] ; do
+ ls=`ls -ld "$prg"`
+ link=`expr "$ls" : '.*-> \(.*\)$'`
+ if expr "$link" : '.*/.*' > /dev/null; then
+ prg="$link"
+ else
+ prg="`dirname $prg`/$link"
+ fi
+done
+
+
+shell_path=`dirname "$prg"`;
+absolute=`echo $shell_path | grep "^/"`;
+
+if [ -z $absolute ]
+then
+ export QUALIMAP_HOME="`pwd`/$shell_path"
+else
+ export QUALIMAP_HOME="$shell_path"
+fi
+
+# For debug purposes
+
+#echo $QUALIMAP_HOME
+#echo "ARGS are ${ARGS[@]}"
+
+set -o errexit
+
+java $java_options -classpath $QUALIMAP_HOME/qualimap.jar:$QUALIMAP_HOME/lib/* org.bioinfo.ngs.qc.qualimap.main.NgsSmartMain "${ARGS[@]}"
+
+if [ -n "$OUTPUT_ADDITIONAL_HELP" ]; then
+ echo "Special arguments: "
+ echo
+ echo " --java-mem-size Use this argument to set Java memory heap size. Example:"
+ echo " qualimap bamqc -bam very_large_alignment.bam --java-mem-size=4G"
+ echo
+fi
+
diff --git a/cli/qualimap.bat b/cli/qualimap.bat
new file mode 100644
index 0000000..05b7b8c
--- /dev/null
+++ b/cli/qualimap.bat
@@ -0,0 +1,3 @@
+
+REM The qualimap.jar has to be unpacked
+start java -Xms32m -Xmx1G -classpath ".\qualimap.jar;.\lib\*" org.bioinfo.ngs.qc.qualimap.main.NgsSmartMain
\ No newline at end of file
diff --git a/cli/scripts/countsQC.r b/cli/scripts/countsQC.r
new file mode 100644
index 0000000..6f008f5
--- /dev/null
+++ b/cli/scripts/countsQC.r
@@ -0,0 +1,396 @@
+#!/usr/bin/env Rscript
+
+suppressPackageStartupMessages(library(optparse))
+suppressPackageStartupMessages(library(NOISeq))
+
+option_list <- list(
+ make_option(c("-c", "--compare"), action="store_true",
+ dest="compare", help="Compare conditions"),
+ make_option(c("--input"), type="character", action="store",
+ help="REQUIRED. File describing the input samples.",default=NULL,
+ metavar="input_desc"),
+ make_option(c("--info"), type="character", action="store",
+ help="Optional. Table summarizing gene annotations.
+ Table must include the following: gene name, biotype, length,
+ gc, chromosome, start pos, end pos",default=NULL, metavar="file_info"),
+ #make_option(c("--groups"), type="character", action="store",
+ # help="Optional. File with groups for the --info file." , default=NULL, metavar="file_groups"),
+ make_option(c("-k", "--threshold"), type="integer", action="store",
+ help="Optional. Threshold for the number of counts.",default=0,
+ metavar="counts_threshold"),
+ make_option(c("-o", "--dirOut"), type="character", action="store",
+ help="Optional. Output folder.",default="./counts_qc",
+ metavar="folder_output"),
+ make_option("--homedir", type="character", action="store",
+ help="DEVELOPMENTAL. NOT TO BE USED IN THIS VERSION", default="./",
+ metavar="home_src folder")
+)
+
+opt <- parse_args(OptionParser(option_list=option_list))
+HOMESRC <- opt$homedir
+source(file.path(HOMESRC, "qualimapRfunctions.r"))
+
+input.desc <- opt$input
+if(is.null(input.desc)){
+ stop("--input is a REQUIRED argument")
+}
+
+if(!file.exists(opt$dirOut)){
+ dir.create(opt$dirOut, recursive=TRUE)
+}
+
+# cutoff for the number of counts to consider a biological feature as detected
+k <- opt$threshold
+
+if (is.null(opt$compare)) {
+ compare.conditions <- FALSE
+} else {
+ compare.conditions <- opt$compare
+}
+
+cm <- 1.5 # cex.main
+cl <- 1.2 # cex.lab
+ca <- 1 # cex.axis
+cc <- 1.2 # cex
+
+image.width <- 3*480
+image.height <- 3*480
+point.size <- 3*12
+
+init.png <- function(path, width = image.width, height = image.height) {
+ png(path, width, height,
+ pointsize = point.size,
+ type="cairo")
+}
+
+# took it from http://gettinggeneticsdone.blogspot.de/2011/07/scatterplot-matrices-in-r.html
+
+panel.cor <- function(x, y, digits=2, prefix="", cex.cor, ...)
+{
+ usr <- par("usr"); on.exit(par(usr))
+ par(usr = c(0, 1, 0, 1))
+ r <- abs(cor(x, y))
+ txt <- format(c(r, 0.123456789), digits=digits)[1]
+ txt <- paste(prefix, txt, sep="")
+ if(missing(cex.cor)) cex.cor <- 0.8/strwidth(txt)
+ text(0.5, 0.5, txt, cex = cex.cor * r)
+}
+
+# LOAD DATA
+
+cat("Reading input data using input description from", input.desc, "\n")
+counts <- load.counts.data(input.desc)
+
+num_samples <- ncol(counts)
+cat("Loaded counts for ", nrow(counts), " features\n")
+cat("Num samples:", num_samples, "\n")
+
+expr.factors <- data.frame(Conditions = attr(counts, "factors"))
+
+#expr.factors <- data.frame(Conditions = gl(2, num_samples/2, labels = c("C1","C2") ))
+#factors <- data.frame(Tissue = c("Kidney", "Liver", "Kidney", "Liver","Kidney", "Liver","Kidney", "Liver","Kidney", "Liver"))
+cat("Conditions:\n")
+expr.factors
+cat("\n")
+
+cat("Compare conditions ", compare.conditions, "\n")
+if ( compare.conditions == TRUE) {
+ if (num_samples < 2) {
+ stop("Need at least 2 samples to compare conditions")
+ }
+
+ if (nlevels(expr.factors[,1]) != 2) {
+ stop("Comparison can be performed only for 2 different conditions.")
+ }
+}
+
+# LOAD ANNOTATIONS
+
+info.available <- FALSE
+gene.biotypes <- NULL
+gene.length <- NULL
+gene.gc <- NULL
+gene.loc <- NULL
+
+if (!is.null(opt$info)){
+ cat("Loading annotations from ", opt$info,"\n")
+ #ann.data <- read.csv(opt$info, row.names = 1, sep = "\t")
+ ann.data <- read.csv(opt$info, sep = "\t")
+ cat("Loaded annoations for ",nrow(ann.data), "genes\n")
+ gene.biotypes <- ann.data[1]
+
+ #cat("Gene lentgh head:", str(head(gene.length)), "\n")
+ #cat(str(head(gene.biotypes)))
+ gene.length <- ann.data[2]
+ gene.gc <- ann.data[3]
+
+ #gene.loc <- ann.data[c(4,5,6)]
+ info.available <- TRUE
+
+} else {
+ print("Annotation data is not available.")
+}
+
+if (info.available) {
+ gene.names <- rownames(counts)
+ ann.names <- rownames(ann.data)
+ intersection <- intersect(ann.names, gene.names)
+ if (length(intersection) == 0) {
+ warning("The gene names from counts do not correspond to the names from annotation file.")
+ str(gene.names)
+ str(ann.names)
+ cat("Annotation based analysis is deactivated\n")
+ info.available <- FALSE
+ gene.biotypes <- NULL
+ gene.length <- NULL
+ gene.gc <- NULL
+ } else {
+ #str(gene.names)
+ #str(ann.names)
+ cat(length(intersection),"out of",length(gene.names),"annotations from counts file found in annotations file\n")
+ }
+}
+str(counts)
+dim(counts)
+
+cat("Init NOISeq data...\n")
+ns.data <- readData(data = counts, length = gene.length, gc = gene.gc, biotype = gene.biotypes,
+ chromosome = gene.loc, factors = expr.factors )
+
+
+
+###############################################################################
+
+#### GLOBAL
+
+
+cat("\nDraw global plots...\n")
+
+# Counts Density
+
+cat("Compute counts density...\n")
+
+init.png( paste(opt$dirOut, "00_Counts_Density.png",sep="/") )
+
+par(mar=c(5, 4, 4, 8) + 0.1, xpd=TRUE)
+
+transformed.counts <- log2(counts + 0.5)
+
+d.max <- 0
+dens_data <- vector("list", num_samples)
+
+for (i in 1:num_samples) {
+ idx <- transformed.counts[,i] >= 1
+ d <- density((transformed.counts[idx,i]))
+ y.max <- max(d$y)
+ if (y.max > d.max) {
+ d.max <- y.max
+ }
+ dens_data[[i]] <- d
+}
+
+
+for (i in 1:num_samples) {
+ d <- dens_data[[i]]
+ if (i == 1) {
+ plot( d , type='l', col = i, lwd=2, ylim=c(0,d.max),
+ main="Counts density", xlab="Log2(Counts)", ylab="Density")
+ } else {
+ lines(d, type='l', col = i, lwd=2)
+ }
+}
+
+legend("right", title="Samples", fill=1:num_samples, legend=colnames(counts))
+garbage <- dev.off()
+
+# Correlation matrix
+
+if (num_samples > 1) {
+
+ cat("Compute scatterplots..\n")
+
+ init.png( paste(opt$dirOut, "01_Scatterplot_Matrix.png",sep="/") )
+
+
+ sample.size <- 5000
+ if ( sample.size > nrow(transformed.counts) ) {
+ sample.size <- nrow(transformed.counts)
+ }
+
+ s <- sample(1:nrow(transformed.counts), sample.size, replace=FALSE)
+ counts.sample <- transformed.counts[s,]
+ pairs(counts.sample, lower.panel = panel.smooth, upper.panel = panel.cor, main = "Scatterplot Matrix")
+
+ garbage <- dev.off()
+} else {
+ cat("Only one sample is provide, skipping sample comparison counts scatterplot matrix...\n")
+}
+
+
+# Global saturation
+
+cat("Compute saturation..\n")
+mysaturation <- dat(ns.data, k = k, ndepth = 8, type = "saturation")
+
+init.png(paste(opt$dirOut, "02_Saturation.png", sep = "/") )
+explo.plot(mysaturation, toplot = 1, samples = 1:num_samples)
+garbage <- dev.off()
+
+cat("Compute counts per biotype..\n")
+counts.bio <- dat(ns.data, factor = NULL, type = "countsbio")
+
+if (num_samples > 1) { # Workaround for 1-sample bug
+
+# Global feature distribution plot
+init.png(paste(opt$dirOut, "03_Counts_Distribution.png",sep="/"))
+explo.plot(counts.bio, toplot=1, samples = NULL, plottype = "boxplot")
+garbage <- dev.off()
+
+# Global features with low count
+init.png(paste(opt$dirOut, "04_Features_With_Low_Counts.png", sep="/"))
+explo.plot(counts.bio, toplot=1, samples = NULL, plottype = "barplot")
+garbage <- dev.off()
+
+}
+
+# TODO: should we include also global estimators for selected groups?
+
+###############################################################################
+#### PER SAMPLE ANALYSIS
+
+cat("Draw per sample plots...\n\n")
+
+if (info.available) {
+ cat("Compute bio detection per sample ...\n")
+ bio.detection <- dat(ns.data, k = k, type = "biodetection", factor = NULL)
+ cat("Compute length bias per sample ...\n")
+ length.bias <- dat(ns.data, factor = NULL, type = "lengthbias")
+ cat("Compute GC bias per sample ...\n")
+ gc.bias <- dat(ns.data, factor = NULL, type = "GCbias")
+}
+
+for (i in 1:num_samples) {
+
+ sample.name <- colnames(counts)[i]
+ cat("Processing sample",sample.name,"\n")
+
+ sample.outDir <- paste(opt$dirOut, sample.name, sep = "/")
+ if(!file.exists(sample.outDir)){
+ dir.create(sample.outDir, recursive=TRUE)
+ }
+
+ # Saturation
+
+ init.png(paste(sample.outDir,"01_Saturation.png",sep="/"))
+ explo.plot(mysaturation, toplot = 1, samples = i)
+ garbage <- dev.off()
+
+ if (info.available) {
+
+ init.png(paste(sample.outDir, "02_Bio_Detection.png", sep="/"))
+ explo.plot(bio.detection, samples = i)
+ garbage <- dev.off()
+
+ if (num_samples > 1) { # workaround form 1-sample bug
+ init.png(paste(sample.outDir, "03_Counts_Per_Biotype.png",sep="/"))
+ explo.plot(counts.bio, toplot=1, samples = i, plottype = "boxplot")
+ garbage <- dev.off()
+ }
+
+ init.png(paste(sample.outDir, "04_Length_Bias.png", sep="/"))
+ explo.plot(length.bias, samples = i, toplot = 1)
+ garbage <- dev.off()
+
+ init.png(paste(sample.outDir, "05_GC_Bias.png", sep="/"))
+ explo.plot(gc.bias, samples = i, toplot = 1)
+ garbage <- dev.off()
+
+ }
+
+}
+
+
+###############################################################################
+
+#### PER CONDITION ANALYSIS
+
+
+if (compare.conditions == TRUE) {
+
+ cat ("\nPerforming comparison for conditions\n")
+
+ cmp.outDir <- paste(opt$dirOut, "Comparison", sep = "/")
+ if(!file.exists(cmp.outDir)){
+ dir.create(cmp.outDir, recursive=TRUE)
+ }
+
+ cat("Compute counts per biotype for conditions..\n")
+ counts.bio <- dat(ns.data, factor = "Conditions", type = "countsbio")
+
+ init.png(paste(cmp.outDir, "01_Counts_Distribution.png",sep="/"))
+ explo.plot(counts.bio, toplot=1, samples = NULL, plottype = "boxplot")
+ garbage <- dev.off()
+
+ init.png(paste(cmp.outDir, "02_Features_With_Low_Counts.png", sep="/"))
+ explo.plot(counts.bio, toplot=1, samples = NULL, plottype = "barplot")
+ garbage <- dev.off()
+
+ if (info.available) {
+
+ cat("Compute bio detection for conditions ...\n")
+ bio.detection <- dat(ns.data, k = k, type = "biodetection", factor = "Conditions")
+
+ init.png(paste(cmp.outDir, "03_Bio_Detection.png", sep="/"), width = 2*image.width)
+ par(mfrow = c(1,2))
+ explo.plot(bio.detection, samples = c(1,2))
+ garbage <- dev.off()
+
+ #init.png(paste(sample.outDir, "03_Counts_Per_Biotype.png",sep="/"))
+ #explo.plot(counts.bio, toplot=1, samples = i, plottype = "boxplot")
+ #garbage <- dev.off()
+
+ cat("Compute length bias for conditions ...\n")
+ length.bias <- dat(ns.data, factor = "Conditions", type = "lengthbias")
+
+ init.png(paste(cmp.outDir, "04_Length_Bias.png", sep="/"), width = 2*image.width)
+ explo.plot(length.bias, samples = NULL, toplot = 1)
+ garbage <- dev.off()
+
+ cat("Compute GC bias for conditions ...\n")
+ gc.bias <- dat(ns.data, factor = "Conditions", type = "GCbias")
+ init.png(paste(cmp.outDir, "05_GC_Bias.png", sep="/"), width = 2*image.width)
+ explo.plot(gc.bias, samples = NULL, toplot = 1)
+ garbage <- dev.off()
+
+ }
+
+
+# #### CORRELATION PLOT
+#
+#
+# if (!is.null(misdatos2)) {
+#
+# png(paste(opt$dirOut, "correlation_plot.png", sep = ""),
+# width = 3*480, height = 3*480, pointsize = 3*12)
+#
+# cor.plot.2D(misdatos1, misdatos2, noplot = 0.001, log.scale = TRUE,
+# xlab = paste("log2(", nom1, "+1)", sep = ""),
+# ylab = paste("log2(", nom2, "+1)", sep = ""))
+#
+# garbage <- dev.off()
+#
+# }
+#
+
+}
+
+cat("CountsQC is successfully finished!\n")
+
+
+
+
+
+
+
+
+
diff --git a/cli/scripts/init.r b/cli/scripts/init.r
new file mode 100755
index 0000000..0bd62a4
--- /dev/null
+++ b/cli/scripts/init.r
@@ -0,0 +1,11 @@
+
+is.installed <- function(mypkg) is.element(mypkg, installed.packages()[,1])
+
+required.packages <- c('optparse', 'NOISeq', 'XML', 'Rsamtools', 'Repitools', 'rtracklayer' )
+
+for (package in required.packages) {
+ if (!is.installed(package)) {
+ print (paste("ERROR! Package :", package, ": is missing!"))
+ }
+}
+
diff --git a/cli/scripts/installDependencies.r b/cli/scripts/installDependencies.r
new file mode 100644
index 0000000..9bbc69b
--- /dev/null
+++ b/cli/scripts/installDependencies.r
@@ -0,0 +1,34 @@
+#installing deps
+
+# CountsQC
+
+if(!require("optparse")) {
+ install.packages("optparse", repos = "http://cran.r-project.org")
+}
+
+if(!require("NOISeq")) {
+ source("http://bioconductor.org/biocLite.R")
+ biocLite("NOISeq")
+}
+
+# Epigenetics
+
+if(!require("XML")) {
+ install.packages("XML", repos = "http://cran.r-project.org")
+}
+
+if(!require("Repitools")) {
+ source("http://bioconductor.org/biocLite.R")
+ biocLite("Repitools")
+}
+
+if(!require("Rsamtools")) {
+ source("http://bioconductor.org/biocLite.R")
+ biocLite("Rsamtools")
+}
+
+if(!require("rtracklayer")) {
+ source("http://bioconductor.org/biocLite.R")
+ biocLite("rtracklayer")
+}
+
diff --git a/cli/scripts/paintLocation.r b/cli/scripts/paintLocation.r
new file mode 100755
index 0000000..f863cb3
--- /dev/null
+++ b/cli/scripts/paintLocation.r
@@ -0,0 +1,108 @@
+#if(!require("optparse")) { install.packages("optparse", repos = "http://cran.r-project.org") }
+#if(!require("XML")) { install.packages("XML", repos = "http://cran.r-project.org") }
+
+suppressPackageStartupMessages(library("optparse"))
+#if(!require("Repitools")) {
+ #source("http://bioconductor.org/biocLite.R")
+ #biocLite("Repitools")
+#}
+#if(!require("Rsamtools")) {
+ #source("http://bioconductor.org/biocLite.R")
+ #biocLite("Rsamtools")
+#}
+suppressPackageStartupMessages(library(Repitools))
+suppressPackageStartupMessages(library(Rsamtools))
+suppressPackageStartupMessages(library(XML))
+
+option_list <- list(
+ make_option(c("-v", "--verbose"), action="store_true", default=TRUE,
+ help="Print extra output [default]"),
+ make_option(c("-q", "--quietly"), action="store_false",
+ dest="verbose", help="Print little output"),
+ make_option(c("--fileConfig"), type="character", action="store",
+ help="REQUIRED. Path to configuartion file.",
+ metavar="file_counts"),
+ make_option(c("--vizType"), type="character", action="store",
+ help="Visualization type. Supported values are heatmap or line", default="heatmap",
+ metavar="file_counts"),
+ make_option("--homedir", type="character", action="store",
+ help="Option allows to launch the script from external tools.", default="./",
+ metavar="home_dir folder")
+ )
+
+opt <- parse_args(OptionParser(option_list=option_list))
+
+HOMEDIR <- opt$homedir
+viz.type <- opt$viz
+
+source(file.path(HOMEDIR, "parseConfig.r"))
+source(file.path(HOMEDIR, "utils.r"))
+#opt$fileConfig <- c("../../qualimapEpi/src/configs/config.test.xml")
+
+
+print("STATUS:Parsing arguments:")
+
+args <- parseConfig(opt$fileConfig)
+#print(colnames(args))
+#print(args[[1,"microarray"]])
+
+#print("STATUS : Parsed arguments successfully");
+
+sample1 <- unParseDF(args[[1,"sample1"]], c("medips","input","sample.name","replicate.name"))
+#print(sample1)
+#print(class(sample1))
+#sample2 <- unParseDF(args[[1,"sample2"]], c("medips","input","sample.name","replicate.name"))
+#print(sample2)
+geneSelection <- if(!is.na(args[[1,"geneSelection"]])) unParseDF(args[[1,"geneSelection"]], c("file","column")) else NULL
+#print(geneSelection)
+regions <- unParseDF(args[[1,"regions"]], c("regions"))[1,1] # [1,1] because it has only one value
+#print(regions)
+ma <- if(!is.na(args[[1,"microarray"]])) unParseDF(args[[1,"microarray"]],c("file","threshold")) else NULL
+ma.file <- if(!is.null(ma)) as.character(ma[1,"file"]) else NULL
+ma.threshold <- if(!is.null(ma)) as.numeric(ma[,"threshold"]) else c(0)
+#print(ma)
+clusters <- if(!is.na(args[[1,"clusters"]])) unParseDF(args[[1,"clusters"]],c("num")) else c(25) # Default 23 clusters
+#print(clusters)
+dirOut <- if(!is.na(args[[1,"dirOut"]])) unParseDF(args[[1,"dirOut"]], c("dirOut"))[1,1] else NULL # [1,1] because it has only one value
+#print(dirOut)
+dir.create(dirOut,showWarnings = FALSE)
+
+expID <- if(!is.na(args[[1,"expID"]])) unParseDF(args[[1,"expID"]], c("expID"))[1,1] else "Clustering Profile" # [1,1] because it has only one value. Default "location"
+#print(expID)
+
+#print("location")
+#print(args[[1,"location"]])
+
+up=if(!is.na(args[[1,"location"]])) as.numeric(unParseDF(args[[1,"location"]],c("up"))[1,1]) else 2000
+#print("up")
+#print(up)
+
+down=if(!is.na(args[[1,"location"]])) as.numeric(unParseDF(args[[1,"location"]],c("down"))[1,1]) else 500
+#print("down")
+#print(down)
+
+freq=if(!is.na(args[[1,"location"]])) as.numeric(unParseDF(args[[1,"location"]],c("freq"))[1,1]) else 100
+#print("freq")
+#print(freq)
+
+#print("fragment")
+#print(args[[1,"fragment"]])
+fragment=if(!is.na(args[[1,"fragment"]])) as.numeric(unParseDF(args[[1,"fragment"]],c("fragment"))[1,1]) else 300
+#print("fragment")
+#print(fragment)
+
+print("STATUS:Building annotations:")
+annot <- buildAnnotation(regions=regions)
+#annot <- buildAnnotation()
+
+#print(c(as.character(sample1[,"medips"]), as.character(sample2[1,"medips"])))
+#annot <- 1
+#print("STATUS:Building features scores:")
+fs <- buildFeatureScores(sample1=sample1,sample2=NULL,annot=annot,up=up,down=down,freq=freq,s.width=fragment)
+#fs <- buildFeatureScores(grl.stored="/data/medips/analysis/location/Rdata/GRangesList.48.Rdata",annot=annot)
+#cl.from.fs <- heatmapCluster(featureScores=fs,ma.file=ma.file,expr.threshold=c(as.numeric(ma.threshold)),n.clusters=c(as.numeric(clusters[1,])),dirOut=dirOut,expName=expID,up=up,down=down,freq=freq,s.width=fragment)
+print("STATUS:Perform clustering:")
+cl.from.fs <- heatmapCluster(featureScores=fs,ma.file=ma.file,expr.threshold=c(as.numeric(ma.threshold)),n.clusters=c(as.numeric(clusters[1,])),dirOut=dirOut,expName=expID,plot.type=viz.type)
+
+#fs <- buildFeatureScores2(sample1=sa:mple1,sample2=sample2,annot=annot)
+
diff --git a/cli/scripts/parseConfig.r b/cli/scripts/parseConfig.r
new file mode 100644
index 0000000..f16b5b2
--- /dev/null
+++ b/cli/scripts/parseConfig.r
@@ -0,0 +1,233 @@
+#if(!require("XML",quietly=T)) { install.packages("XML", repos = "http://cran.r-project.org") }
+
+suppressPackageStartupMessages(library("XML",quietly=T))
+
+checkChild <- function(node,name, fileXML="fileConfig"){
+ if(is.null(node[[name]])){ stop(paste("Node <", as.character(xmlName(node)), "> does not have a child <", name, "> in ", fileXML,sep="")) }
+
+}
+
+#hasChild <- function(node, name, fileXML="fileConfig") {
+# if (is.null(node[[name]])) {
+# return TRUE;
+# } else {
+# return FALSE;
+# }
+#}
+
+parseReplicate <- function(replicate){
+ checkChild(replicate, "medips")
+ medips = as.character(xmlValue(replicate[["medips"]]))
+ input = as.character(xmlValue(replicate[["input"]]))
+ name = as.character(xmlValue(replicate[["name"]]))
+ d <- data.frame(medips=medips,input=input,name=name)
+ d
+}
+
+parseSample <- function(sample,ord.sample=0){
+ #print(xmlName(sample))
+ sample.name <- if(!is.null(xmlAttrs(sample)["name"])) as.character(xmlAttrs(sample)["name"]) else paste("","")
+ #print(sample.name)
+ checkChild(sample, "replicate")
+ parsedMedips <- c()
+ parsedInput <- c()
+ parsedName <- c()
+ i <- 1
+ for(curRep in xmlChildren(sample)){
+ if(xmlName(curRep) == "replicate"){
+ d <- parseReplicate(curRep)
+ #print(as.character(d$medips))
+ #print(as.character(d$input))
+ parsedMedips <- c(parsedMedips,as.character(d$medips))
+ parsedInput <- c(parsedInput,as.character(d$input))
+ parsedName <- if(!is.na(d$name)) c(parsedName,as.character(d$name)) else c(parsedName, paste(sample.name,as.character(i),sep="_"))
+ i <- i + 1
+ }
+ }
+ parsed <- data.frame(medips=parsedMedips, input=parsedInput, sample.name=sample.name, replicate.name=parsedName)
+ parsed
+}
+
+parseLocation <- function(pos){
+ ch.pos <- xmlChildren(pos)
+
+ #threshold <- if (!is.null(ch.ma[["threshold"]])) xmlValue(ch.ma[["threshold"]]) else NA
+ up <- if (!is.null(ch.pos[["up"]])) xmlValue(ch.pos[["up"]]) else 2000
+ down <- if (!is.null(ch.pos[["down"]])) xmlValue(ch.pos[["down"]]) else 500
+ freq <- if (!is.null(ch.pos[["freq"]])) xmlValue(ch.pos[["freq"]]) else 100
+
+ d <- data.frame(up=up, down=down, freq=freq)
+ d
+}
+
+parseMicroarray <- function(ma){
+ #print(xmlName(ma))
+ checkChild(ma, "file")
+ ch.ma <- xmlChildren(ma)
+
+ parsedTh <- c()
+ for(th in xmlChildren(ma)){
+ if(xmlName(th)=="threshold"){
+ parsedTh <- c(parsedTh, xmlValue(th))
+ }
+
+ }
+
+ #threshold <- if (!is.null(ch.ma[["threshold"]])) xmlValue(ch.ma[["threshold"]]) else NA
+ threshold <- if (!is.null(ch.ma[["threshold"]])) parsedTh else NA
+ d <- data.frame(file=xmlValue(ch.ma[["file"]]), threshold=threshold)
+ d
+}
+
+parseGeneSelection <- function(node){
+ checkChild(node, "file")
+ ch.node <-xmlChildren(node)
+
+ column <- if (!is.null(ch.node[["column"]])) xmlValue(ch.node[["column"]]) else 1
+
+ d <- data.frame(file=xmlValue(ch.node[["file"]]), column=column)
+ d
+}
+
+parseDirOut <- function(node){
+ d <- data.frame(dirOut=xmlValue(node))
+ d
+}
+
+parseRegions <- function(node){
+ d <- data.frame(regions=xmlValue(node))
+ d
+}
+
+
+parseFragment <- function(node){
+ d <- data.frame(fragment=xmlValue(node))
+ d
+}
+
+parseExpID <- function(node){
+ d <- data.frame(expID=xmlValue(node))
+ d
+}
+
+parseClusters <- function(cls){
+ checkChild(cls,"num")
+ parsedNums <- c()
+ for(cl in xmlChildren(cls)){
+ if(xmlName(cl)=="num"){
+ parsedNums <- c(parsedNums, xmlValue(cl))
+ }
+
+ }
+
+ d <- data.frame(num=parsedNums)
+ #print(d)
+ d
+}
+
+parseConfig <- function(fileXML){
+ if(!file.exists(fileXML)){
+ stop(paste("fileConfig ", fileXML, "does not exist"))
+ }
+
+ r <- xmlRoot(xmlTreeParse(fileXML))
+
+ checkChild(r,"samples",fileXML)
+
+ l.param <- xmlChildren(r)
+
+
+ samples <-l.param[["samples"]]
+ checkChild(samples,"sample1",fileXML)
+
+ l.samples <- xmlChildren(samples)
+
+ #if (hasChild(samples,"sample2",fileXML)) {
+ # df.sample2 <- parseSample(l.samples[["sample2"]],ord.sample=2)
+ #}
+
+
+ df.sample1 <- parseSample(l.samples[["sample1"]],ord.sample=1)
+
+ #print(df.sample1$medips)
+ #print(df.sample1$input)
+
+ #print(df.sample2$medips)
+ #print(df.sample2$input)
+
+ l.microarray <- l.param[["microarray"]]
+ df.microarray <- if(!is.null(l.microarray)) parseMicroarray(l.microarray) else NULL
+
+ l.geneSelection <- l.param[["geneSelection"]]
+ df.geneSelection <- if(!is.null(l.geneSelection)) parseGeneSelection(l.geneSelection) else NULL
+
+ checkChild(r,"regions",fileXML)
+ l.regions <- l.param[["regions"]]
+ df.regions <- if(!is.null(l.regions)) parseRegions(l.regions) else NULL
+
+ l.dirOut <- l.param[["dirOut"]]
+ df.dirOut <- if(!is.null(l.dirOut)) parseDirOut(l.dirOut) else NULL
+
+ l.expID <- l.param[["expID"]]
+ df.expID <- if(!is.null(l.expID)) parseExpID(l.expID) else NULL
+
+ if(!is.null(l.param[["clusters"]])){
+ clusters <- l.param[["clusters"]]
+
+ l.clusters <- xmlChildren(clusters)
+ df.clusters <- parseClusters(clusters)
+ }else{
+ df.clusters <- NULL
+ }
+
+ l.location <- l.param[["location"]]
+ df.location <- if(!is.null(l.location)) parseLocation(l.location) else NULL
+
+ l.fragment <- l.param[["fragment"]]
+ df.fragment <- if(!is.null(l.fragment)) parseFragment(l.fragment) else NULL
+
+
+ parsed <- matrix(list(), nrow=1, ncol=10)
+ #colnames(parsed) <- c("sample1", "sample2", "clusters", "microarray","geneSelection","dirOut","expID","location","fragment")
+ colnames(parsed) <- c("sample1", "mr.empty", "clusters", "microarray","geneSelection","dirOut","expID","location","fragment","regions")
+ #print(df.geneSelection)
+ parsed[[1,"sample1"]] <- df.sample1
+ #parsed[[1,"sample2"]] <- df.sample2
+ parsed[[1,"clusters"]] <- if (!is.null(df.clusters)) df.clusters else NA
+ parsed[[1,"microarray"]] <- if (!is.null(df.microarray)) df.microarray else NA
+ parsed[[1,"regions"]] <- df.regions
+ parsed[[1,"geneSelection"]] <- if(!is.null(df.geneSelection)) df.geneSelection else NA
+ parsed[[1,"dirOut"]] <- if(!is.null(df.dirOut)) df.dirOut else NA
+ parsed[[1,"expID"]] <- if(!is.null(df.expID)) df.expID else NA
+ parsed[[1,"location"]] <- if(!is.null(df.location)) df.location else NA
+ parsed[[1,"fragment"]] <- if(!is.null(df.fragment)) df.fragment else NA
+
+ #parsed <- data.frame(sample1=df.sample1, sample2=df.sample2,microarray=microarray)
+ parsed
+}
+
+
+unParseDF <- function(d,names){
+ # d is a data.frame. For example args[[1,"sample1"]]
+ # names is a list of fields to be unparsed. For example c("medips","input","name")
+ # Returns a matrix with as many rows as values and as many column as fields
+ # Example: sample1 <- unParseDF(args[[1,"sample1"]], c("medips","input","name"))
+
+ mat <- t(apply(d,1,unParseDataFrameLine,names)) # transposition to have rows as samples and columns as "medips","input","name"
+
+ mat
+}
+
+
+
+unParseDataFrameLine <- function(l,names){
+ # Auxiliar function used by unParseDF so one can use it in apply()
+ # It interrogates the columns selected in names of the line l and creates a list with them
+ ret <- c()
+ for(i in 1:length(names)){
+ ret <- c(ret,l[names[i]])
+ }
+ ret
+}
+
+
diff --git a/cli/scripts/qualimapRfunctions.r b/cli/scripts/qualimapRfunctions.r
new file mode 100644
index 0000000..d524819
--- /dev/null
+++ b/cli/scripts/qualimapRfunctions.r
@@ -0,0 +1,1637 @@
+####################################################################
+################### Qualimap R Functions ####################
+####################################################################
+
+# By Sonia Tarazona, Fernando Garcia-Alcalde and Konstantin Okonechnikov
+#
+
+
+
+# This function creates input data based on the description file
+
+load.counts.data <- function(input.desc) {
+
+ input.data <- read.table(input.desc, sep= "\t", stringsAsFactors=FALSE)
+
+ sample.names <- character()
+ conditions <- character()
+ counts <- data.frame()
+ gene.names <- NULL
+ for (i in 1:nrow(input.data)) {
+ sample.names <- c(sample.names, input.data[i,1])
+ conditions <- c(conditions, input.data[i,2])
+ path <- input.data[i,3]
+ data.column <- as.numeric(input.data[i,4])
+ sample.counts <- read.table(path, sep = "\t")
+ if (is.null(gene.names)) {
+ gene.names <- as.character(sample.counts[,1])
+ head(gene.names)
+ counts <- sample.counts[data.column]
+ } else {
+ counts <- cbind(counts, sample.counts[,data.column])
+ }
+ }
+ head(counts)
+ head(gene.names)
+ rownames(counts) <- gene.names
+ colnames(counts) <- sample.names
+
+ attr(counts, "factors") <- as.factor(conditions)
+
+ counts
+
+
+}
+
+
+#****************************************************************************#
+
+
+## Function to intersect multiple sets
+
+int.mult <- function(lista, todos = NULL) {
+
+ if(is.null(todos)) {
+ todos <- unlist(lista)
+ }
+
+ comunes <- todos
+
+ for(i in 1:length(lista)) {
+ comunes <- intersect(comunes, lista[[i]])
+ }
+
+ comunes
+}
+
+
+
+
+#****************************************************************************#
+
+
+
+
+## To count number of non-zero elements
+
+noceros <- function (x, num = TRUE, k = 0) {
+
+ nn <- length(which(x > k))
+
+ if (num) {
+ nn
+
+ } else {
+ if(nn > 0) { which(x > k) } else { NULL }
+ }
+}
+
+
+
+
+#***************************************************************************#
+
+
+
+
+
+## Saturation Plot (GLOBAL)
+
+
+satur.plot <- function (datos1, datos2, ylim = NULL, k = 0, tit = "Saturation",
+ cex.main = cex.main, cex.lab = cex.lab,
+ cex.axis = cex.axis, cex = cex,
+ legend = c(deparse(substitute(datos1)),
+ deparse(substitute(datos2)))) {
+
+
+# For datos1
+ n1 <- ncol(as.matrix(datos1))
+
+
+ if (n1 > 1) {
+
+ muestra1 <- as.list(1:n1)
+ for (i in 2:n1) {
+
+ combi1 <- combn(n1, i, simplify = FALSE)
+
+ if( length(combi1) > 20 ) {
+ sub20 <- sample(1:length(combi1), size = 20, replace = FALSE)
+ combi1 <- combi1[sub20]
+ }
+
+ muestra1 <- append(muestra1, combi1)
+ }
+
+ varias1 <- vector("list", length = length(muestra1))
+ names(varias1) <- sapply(muestra1, function(x) {
+ paste("C1.", x, collapse = "", sep = "")})
+
+ for (i in 1:length(muestra1)) {
+ varias1[[i]] <- apply(as.matrix(datos1[,muestra1[[i]]]), 1, sum)
+ }
+
+ satura1 <- data.frame("muestra" = names(varias1),
+ "seq.depth" = sapply(varias1, sum),
+ "noceros" = sapply(varias1, noceros, k = k))
+ }
+
+
+
+ if (n1 == 1) {
+
+ total1 <- sum(datos1)
+ satura1 <- NULL
+
+ for (i in 1:9) { # 10%, 20%, ..., 90% reads (apart 100% is calculated)
+ muestra1 <- rmultinom(10, size = round(total1*i/10,0), prob = datos1)
+ detec1 <- mean(apply(muestra1, 2, noceros, k = k))
+ satura1 <- rbind(satura1, c(round(total1*i/10,0), detec1))
+ }
+ satura1 <- rbind(satura1, c(total1, noceros(datos1, k = k)))
+ colnames(satura1) <- c("seq.depth", "noceros")
+ satura1 <- as.data.frame(satura1)
+ }
+
+
+
+
+# For datos2
+
+ if (!is.null(datos2)) {
+
+ n2 <- ncol(as.matrix(datos2))
+
+ if (n2 > 1) {
+
+ if (n1 == n2) {
+ muestra2 <- muestra1
+
+ } else {
+
+ muestra2 <- as.list(1:n2)
+
+ for (i in 2:n2) {
+
+ combi2 <- combn(n2, i, simplify = FALSE)
+
+ if (length(combi2) > 20) {
+ sub20 <- sample(1:length(combi2), size = 20, replace = FALSE)
+ combi2 <- combi2[sub20]
+ }
+
+ muestra2 <- append(muestra2, combi2)
+
+ }
+ }
+
+ varias2 <- vector("list", length = length(muestra2))
+ names(varias2) <- sapply(muestra2, function(x) {
+ paste("C2.", x, collapse = "", sep = "")})
+
+ for (i in 1:length(muestra2)) {
+ varias2[[i]] <- apply(as.matrix(datos2[,muestra2[[i]]]), 1, sum)
+ }
+
+ satura2 <- data.frame("muestra" = names(varias2),
+ "seq.depth" = sapply(varias2, sum),
+ "noceros" = sapply(varias2, noceros, k = k))
+ }
+
+
+ if (n2 == 1) {
+
+ total2 <- sum(datos2)
+ satura2 <- NULL
+
+ for (i in 1:9) { # 10%, 20%, ..., 90% reads (apart 100% is calculated)
+
+ muestra2 <- rmultinom(10, size = round(total2*i/10,0), prob = datos2)
+ detec2 <- mean(apply(muestra2, 2, noceros, k = k))
+ satura2 <- rbind(satura2, c(round(total2*i/10,0), detec2))
+ }
+
+ satura2 <- rbind(satura2, c(total2, noceros(datos2, k = k)))
+ colnames(satura2) <- c("seq.depth", "noceros")
+ satura2 <- as.data.frame(satura2)
+ }
+
+
+ if (is.null(ylim)) {
+ ylim <- c(0, NROW(datos1))
+ }
+
+ SS1 <- range(satura1$seq.depth/10^6)
+ SS2 <- range(satura2$seq.depth/10^6)
+
+ xM <- max(SS1[2], SS2[2])
+ xm <- min(SS1[1], SS2[1])
+
+ par(xpd=TRUE, mar=par()$mar+c(0,0,2,0), bg = "#e6e6e6")
+
+ plot(satura1$seq.depth/10^6, satura1$noceros, pch = 16, col = 2,
+ ylim = ylim, xlim = c(xm, xM), main = tit, type = "o",
+ xlab = "Sequencing Depth (million reads)",
+ ylab = paste("Number of features with reads >", k), cex = 1.5, las = 1,
+ cex.main = cex.main, cex.lab = cex.lab, cex.axis = cex.axis)
+
+ rect(par("usr")[1], par("usr")[3], par("usr")[2], par("usr")[4],
+ col = "white")
+
+ points(satura1$seq.depth/10^6, satura1$noceros, pch = 16, col = 2,
+ type = "o", cex = 1.5)
+
+ points(satura2$seq.depth/10^6, satura2$noceros, pch = 16, col = 4,
+ type = "o", cex = 1.5)
+
+ legend(x = (xm+xM)/2, y = ylim[2]+0.15*diff(ylim),
+ legend = legend, text.col = c(2,4), bty = "n", xjust = 0.5,
+ lty = 1, lwd = 2, col = c(2, 4), cex = cex, horiz = TRUE)
+
+ par(mar=c(5, 4, 4, 2) + 0.1)
+
+
+ } else {
+
+ if (is.null(ylim)) {
+ ylim <- c(0, NROW(datos1))
+ }
+
+ xlim <- range(satura1$seq.depth/10^6)
+
+ par(bg = "#e6e6e6")
+
+ plot(satura1$seq.depth/10^6, satura1$noceros, pch = 16, col = 2,
+ ylim = ylim, xlim = xlim, main = tit, type = "o",
+ xlab = "Sequencing Depth (million reads)",
+ ylab = paste("Number of features with reads >", k), cex = 1.5, las = 1,
+ cex.main = cex.main, cex.lab = cex.lab, cex.axis = cex.axis)
+
+ rect(par("usr")[1], par("usr")[3], par("usr")[2], par("usr")[4],
+ col = "white")
+
+ points(satura1$seq.depth/10^6, satura1$noceros, pch = 16, col = 2,
+ type = "o", cex = 1.5)
+
+ }
+
+}
+
+
+
+
+
+#***************************************************************************#
+
+
+
+
+
+
+
+###############################################################################
+###############################################################################
+
+
+## Data for saturation plot with different biotypes
+
+
+saturbio.dat <- function (datos1, datos2, k = 0, infobio, biotypes, nsim = 5) {
+
+ # infobio = vector containing biotype for each gene in "datos"
+ # biotypes = list containing groups of biotypes to be studied
+
+ biog <- lapply(biotypes, function(x) { which(is.element(infobio, x)) })
+
+ satura1 <- satura2 <- vector("list", length = length(biotypes))
+ names(satura1) <- names(satura2) <- names(biotypes)
+
+ newdet1 <- newdet2 <- vector("list", length = length(biotypes))
+ names(newdet1) <- names(newdet2) <- names(biotypes)
+
+
+ # datos1
+ n1 <- NCOL(datos1)
+
+
+ if (n1 > 1) { # when replicates are available in condition 1
+
+ varias1 <- vector("list", length = n1) # counts for each sequencing depth
+ names(varias1) <- paste(1:n1, "rep", sep = "")
+
+ for(i in 1:n1) {
+
+ muestra1 <- combn(n1, i, simplify = FALSE)
+
+ if (length(muestra1) > 20) {
+ sub20 <- sample(1:length(muestra1), size = 20, replace = FALSE)
+ muestra1 <- muestra1[sub20]
+ }
+
+ sumrepli <- NULL
+
+ for (com in 1:length(muestra1)) {
+ sumrepli <- cbind(sumrepli, rowSums(as.matrix(datos1[,muestra1[[com]]])))
+ }
+
+ varias1[[i]] <- as.matrix(sumrepli)
+
+ }
+ }
+
+
+ if (n1 == 1) { # simulating replicates for datos1
+
+ varias1 <- vector("list", length = nsim) # counts for each sequencing depth
+ names(varias1) <- paste("dp", 1:nsim, sep = "")
+
+ total1 <- sum(datos1)
+
+ for (i in 1:(nsim-1)) { # total1*i/nbox reads (100% is calculated apart)
+
+ muestra1 <- rmultinom(10, size = round(total1*i/nsim,0), prob = datos1)
+
+ varias1[[i]] <- muestra1
+ }
+
+ varias1[[nsim]] <- as.matrix(datos1)
+ }
+
+ seq.depth1 <- sapply(varias1, function(x) { mean(colSums(x)) })
+
+ # computing saturation for each biotype (datos1)
+ for (j in 1:length(satura1)) {
+
+ conbio1 <- lapply(varias1, function(x) { as.matrix(x[biog[[j]],]) })
+
+ satura1[[j]] <- sapply(conbio1,
+ function(x) { mean(apply(x, 2, noceros, k = k)) })
+ }
+
+
+ ## computing detection increasing per million reads: condition 1
+ for (j in 1:length(newdet1)) {
+
+ puntos1 <- data.frame("x" = seq.depth1, "y" = satura1[[j]])
+
+ pendi <- NULL
+
+ for(i in 2:nrow(puntos1)) {
+
+ nuevo <- max(0, (puntos1$y[i]-puntos1$y[i-1])/
+ (puntos1$x[i]-puntos1$x[i-1]))
+
+ pendi <- c(pendi, nuevo)
+ }
+
+ pendimil1 <- c(NA, pendi)*1000000
+
+ newdet1[[j]] <- pendimil1
+
+ }
+
+
+
+
+ #### datos2
+ if (!is.null(datos2)) {
+
+ n2 <- NCOL(datos2)
+
+ if (n2 > 1) { # when replicates are available in condition 2
+
+ varias2 <- vector("list", length = n2) # counts for each sequencing depth
+ names(varias2) <- paste(1:n2, "rep", sep = "")
+
+ for(i in 1:n2) {
+
+ muestra2 <- combn(n2, i, simplify = FALSE)
+
+ if (length(muestra2) > 20) {
+ sub20 <- sample(1:length(muestra2), size = 20, replace = FALSE)
+ muestra2 <- muestra2[sub20]
+ }
+
+ sumrepli <- NULL
+
+ for (com in 1:length(muestra2)) {
+ sumrepli <- cbind(sumrepli,
+ rowSums(as.matrix(datos2[,muestra2[[com]]])))
+ }
+
+ varias2[[i]] <- as.matrix(sumrepli)
+
+ }
+ }
+
+
+ if (n2 == 1) { # replicates have to be simulated
+
+ varias2 <- vector("list", length = nsim) # counts for each seq depth
+ names(varias2) <- paste("dp", 1:nsim, sep = "")
+
+ total2 <- sum(datos2)
+
+ for (i in 1:(nsim-1)) { # total1*i/nbox reads (100% is calculated apart)
+
+ muestra2 <- rmultinom(10, size = round(total2*i/nsim,0), prob = datos2)
+
+ varias2[[i]] <- muestra2
+ }
+
+ varias2[[nsim]] <- as.matrix(datos2)
+ }
+
+ seq.depth2 <- sapply(varias2, function(x) { mean(colSums(x)) })
+
+ # computing saturation for each biotype (datos2)
+ for (j in 1:length(satura2)) {
+
+ conbio2 <- lapply(varias2, function(x) { as.matrix(x[biog[[j]]]) })
+
+ satura2[[j]] <- sapply(conbio2,
+ function(x) { mean(apply(x, 2, noceros, k = k)) })
+ }
+
+
+ # computing detection increasing per million reads: condition 2
+ for (j in 1:length(newdet2)) {
+
+ puntos2 <- data.frame("x" = seq.depth2, "y" = satura2[[j]])
+
+ pendi <- NULL
+
+ for(i in 2:nrow(puntos2)) {
+
+ nuevo <- max(0, (puntos2$y[i]-puntos2$y[i-1])/
+ (puntos2$x[i]-puntos2$x[i-1]))
+
+ pendi <- c(pendi, nuevo)
+ }
+
+ pendimil2 <- c(NA, pendi)*1000000
+
+ newdet2[[j]] <- pendimil2
+ }
+
+ satura <- list("cond1" = satura1, "cond2" = satura2,
+ "bionum" = sapply(biog, length),
+ "depth1" = seq.depth1, "depth2" = seq.depth2,
+ "newdet1" = newdet1, "newdet2" = newdet2)
+
+
+ } else {
+
+ satura <- list("cond1" = satura1, "cond2" = satura2,
+ "bionum" = sapply(biog, length),
+ "depth1" = seq.depth1, "depth2" = NULL,
+ "newdet1" = newdet1, "newdet2" = NULL)
+ }
+
+
+ ### Results
+
+ satura
+
+}
+
+
+
+
+
+#*****************************************************************************#
+
+
+
+
+
+
+## Saturation plot with different biotypes
+
+saturbio.plot <- function(depth1, depth2 = NULL, sat1, sat2 = NULL, bionum,
+ newdet1 = NULL, newdet2 = NULL,
+ xlim = NULL, yleftlim = NULL, yrightlim = NULL,
+ main = "Saturation per biotype", lwdL = 2, lwdR = 20,
+ legend = c("sample1", "sample2"),
+ ylabL = "Number of detected features",
+ ylabR = "New detections per million reads",
+ cex.main = 1, cex.lab = 1, cex.axis = 1, cex = 1) {
+
+
+ if (bionum > 0) {
+
+ if (!is.null(depth2)) {
+
+ # yleftlim for plot and plot.y2
+ if (is.null(yleftlim)) {
+ yleftlim <- c(min(c(sat1, sat2)), max(c(sat1, sat2)))
+ }
+
+ # xlim for plot
+ if (is.null(xlim)) {
+ SS1 <- range(depth1/10^6)
+ SS2 <- range(depth2/10^6)
+
+ xM <- max(SS1[2], SS2[2])
+ xm <- min(SS1[1], SS2[1])
+
+ xlim <- c(xm, xM)
+ }
+
+ percen1 <- round(100*max(sat1)/bionum, 1)
+ percen2 <- round(100*max(sat2)/bionum, 1)
+
+
+ if(is.null(newdet1)) {
+
+ # PLOT for detections
+ #par(bg = "#e6e6e6")
+
+ plot(depth1/10^6, sat1, pch = 16, col = 2, ylim = yleftlim, lwd = lwdL,
+ xlim = xlim, main = main, type = "o",
+ xlab = "Sequencing Depth (million reads)",
+ ylab = ylabL, cex.main = cex.main, cex.lab = cex.lab, las = 1,
+ cex.axis = cex.axis, cex = 1.5)
+
+ rect(par("usr")[1], par("usr")[3], par("usr")[2], par("usr")[4],
+ col = "white")
+
+ points(depth1/10^6, sat1, pch = 16, col = 2, lwd = lwdL,
+ type = "o", cex = 1.5)
+
+ points(depth2/10^6, sat2, pch = 16, col = 4, lwd = lwdL,
+ type = "o", cex = 1.5)
+
+ legend("top",
+ legend = paste(legend, ": ",
+ c(percen1, percen2), "% detected", sep = ""),
+ text.col = c(2,4), bty = "n", lty = 1, lwd = lwdL,
+ col = c(2, 4), cex = 0.9)
+
+ } else {
+
+ # yrightlim for plot.y2
+ if (is.null(yrightlim)) {
+ maxi <- max(na.omit(c(newdet1, newdet2)))
+ if (maxi < 10) {
+ yrightlim <- c(0, max(10,maxi))
+ } else {
+ yrightlim <- c(0, maxi*1.1)
+ }
+ }
+
+ # PLOT with 2 axis
+ plot.y2(x = depth1/10^6, yright = newdet1, yleft = sat1,
+ type = c("h", "o"), lwd = c(lwdR, lwdL),
+ xlab = "Sequencing depth (million reads)", xlim = xlim,
+ yrightlim = yrightlim, yleftlim = yleftlim,
+ yylab = c(ylabR, ylabL), pch = c(1,19), col = c("pink",2),
+ main = main, x2 = depth2/10^6, yright2 = newdet2, yleft2 = sat2,
+ col2 = c("lightblue1",4), cex.main = cex.main,
+ cex.lab = cex.lab, cex.axis = cex.axis, cex2 = c(1.5,1.5))
+
+ legend.text <- c(paste(legend[1], "(left)"),
+ paste(legend[2], "(left)"),
+ paste(legend[1], "(right)"),
+ paste(legend[2], "(right)"),
+ paste(percen1,"% detected"),
+ paste(percen2,"% detected"))
+
+ legend.pch <- c(16, 16, 15, 15, 1, 1)
+
+ legend.col <- c(2, 4, "pink", "lightblue1", 0, 0)
+
+ legend("top",
+ legend = legend.text, pch = legend.pch,
+ col = legend.col, ncol = 3, bty = "n", cex = 0.9)
+ }
+
+ } else {
+
+
+
+
+ ### Only for 1 sample
+
+ # yleftlim for plot and plot.y2
+ if (is.null(yleftlim)) {
+ yleftlim <- range(sat1)
+ }
+
+ # xlim for plot
+ if (is.null(xlim)) {
+ xlim <- range(depth1/10^6)
+ }
+
+ percen1 <- round(100*max(sat1)/bionum, 1)
+
+
+ if(is.null(newdet1)) {
+
+ # PLOT for detections
+ #par(bg = "#e6e6e6")
+
+ plot(depth1/10^6, sat1, pch = 16, col = 4, ylim = yleftlim, lwd = lwdL,
+ xlim = xlim, main = main, type = "o",
+ xlab = "Sequencing Depth (million reads)",
+ ylab = ylabL, cex.main = cex.main, cex.lab = cex.lab, las = 1,
+ cex.axis = cex.axis, cex = 1.5)
+
+ rect(par("usr")[1], par("usr")[3], par("usr")[2], par("usr")[4],
+ col = "white")
+
+ points(depth1/10^6, sat1, pch = 16, col = 2, lwd = lwdL,
+ type = "o", cex = 1.5)
+
+ legend("top",
+ legend = paste(legend, ": ", percen1, "% detected", sep = ""),
+ text.col = 2, bty = "n", lty = 1, lwd = lwdL,
+ col = 4, cex = 0.9)
+
+ } else {
+
+ # yrightlim for plot.y2
+ if (is.null(yrightlim)) {
+ maxi <- max(na.omit(newdet1))
+ if (maxi < 10) {
+ yrightlim <- c(0, max(10,maxi))
+ } else {
+ yrightlim <- c(0, maxi*1.1)
+ }
+ }
+
+ # PLOT with 2 axis
+ plot.y2(x = depth1/10^6, yright = newdet1, yleft = sat1,
+ type = c("h", "o"),
+ lwd = c(lwdR, lwdL),
+ xlab = "Sequencing depth (million reads)", xlim = xlim,
+ yrightlim = yrightlim, yleftlim = yleftlim,
+ yylab = c(ylabR, ylabL), pch = c(1,19),
+ main = main, col = c("pink",2), cex.main = cex.main,
+ cex.lab = cex.lab, cex.axis = cex.axis, cex2 = c(1.5,1.5))
+
+ legend.text <- c("Left axis", "Right axis",
+ paste(percen1,"%detected"))
+
+ legend.pch = c(16, 15, 1)
+
+ legend.col = c(2, "pink", 0)
+
+ legend("top",
+ legend = legend.text, pch = legend.pch,
+ col = legend.col, ncol = 3, cex = 0.9)
+ }
+ }
+
+ } else {
+
+ print("Biotype not found in this dataset")
+ }
+}
+
+
+
+
+
+
+
+#*****************************************************************************#
+
+
+
+
+
+
+
+## Counts for detected genes Plot according to BIOTYPES
+
+
+countsbio.dat <- function (datos1, datos2, k = 0, infobio, biotypes, nbox = 5)
+ {
+
+ # infobio = vector containing biotype for each gene in "datos"
+ # biotypes = list containing groups of biotypes to be studied
+ # nbox = number of different depths to be plotted (only for simulated data)
+
+
+ biog <- lapply(biotypes, function(x) { which(is.element(infobio, x)) })
+ # which genes belong to each biotype
+
+ satura1 <- satura2 <- vector("list", length = length(biotypes))
+ names(satura1) <- names(satura2) <- names(biotypes)
+
+
+ ### DATOS 1
+ n1 <- NCOL(datos1)
+
+ ## replicates available for condition 1
+ if (n1 > 1) {
+
+ varias1 <- vector("list", length = n1) # counts for each sequencing depth
+ names(varias1) <- paste(1:n1, "rep", sep = "")
+
+ for(i in 1:n1) {
+
+ muestra1 <- combn(n1, i, simplify = FALSE)
+
+ if (length(muestra1) > 20) {
+ sub20 <- sample(1:length(muestra1), size = 20, replace = FALSE)
+ muestra1 <- muestra1[sub20]
+ }
+
+ sumrepli <- NULL
+
+ for (com in 1:length(muestra1)) {
+ sumrepli <- cbind(sumrepli, rowSums(as.matrix(datos1[,muestra1[[com]]])))
+ }
+
+ varias1[[i]] <- rowMeans(sumrepli)
+ }
+ }
+
+
+ ## replicates simulated for condition 1
+ if (n1 == 1) { # replicates have to be simulated
+
+ varias1 <- vector("list", length = nbox) # counts for each sequencing depth
+ names(varias1) <- paste("dp", 1:nbox, sep = "")
+
+ total1 <- sum(datos1)
+
+ if (nbox > 1) {
+
+ for (i in 1:(nbox-1)) { # total1*i/nbox reads (100% is calculated apart)
+
+ muestra1 <- rmultinom(10, size = round(total1*i/nbox,0), prob = datos1)
+
+ varias1[[i]] <- rowMeans(muestra1)
+ }
+ }
+
+ varias1[[nbox]] <- datos1
+ }
+
+ seq.depth1 <- sapply(varias1, sum) # sequencing depth for each new sample
+
+
+
+ ## selecting detected genes for each biotype (datos1)
+ for (j in 1:length(satura1)) {
+
+ satura1[[j]] <- vector("list", length = length(varias1))
+ names(satura1[[j]]) <- names(varias1)
+
+ # selecting genes in bioclass j for each sample
+ conbio1 <- lapply(varias1, function(x) { x[biog[[j]]] })
+
+ for (i in 1:length(conbio1)) {
+
+ # selecting the genes with counts > k
+ noK <- noceros(conbio1[[i]], k = k, num = FALSE)
+
+ if (is.null(noK)) {
+ satura1[[j]][[i]] <- NA
+ } else {
+ satura1[[j]][[i]] <- conbio1[[i]][noK]
+ }
+ }
+ }
+
+
+
+ #### DATOS 2
+
+ if (!is.null(datos2)) {
+
+ n2 <- NCOL(datos2)
+
+ ## replicates available for condition 2
+ if (n2 > 1) {
+
+ varias2 <- vector("list", length = n2)
+ names(varias2) <- paste(1:n2, "rep", sep = "")
+
+ for (i in 1:n2) {
+
+ muestra2 <- combn(n2, i, simplify = FALSE)
+
+ if (length(muestra2) > 20) {
+ sub20 <- sample(1:length(muestra2), size = 20, replace = FALSE)
+ muestra2 <- muestra2[sub20]
+ }
+
+ sumrepli2 <- NULL
+
+ for (com in 1:length(muestra2)) {
+ sumrepli2 <- cbind(sumrepli2,
+ rowSums(as.matrix(datos2[,muestra2[[com]]])))
+ }
+
+ varias2[[i]] <- rowMeans(sumrepli2)
+ }
+ }
+
+
+ ## replicates simulated for condition 2
+ if (n2 == 1) { # replicates have to be simulated
+
+ varias2 <- vector("list", length = nbox) # counts for each seq depth
+ names(varias2) <- paste("dp", 1:nbox, sep = "")
+
+ total2 <- sum(datos2)
+
+ if (nbox > 1) {
+
+ for (i in 1:(nbox-1)) { # total1*i/nbox reads (100% is calculated apart)
+
+ muestra2 <- rmultinom(10,
+ size = round(total2*i/nbox,0), prob = datos2)
+
+ varias2[[i]] <- rowMeans(muestra2)
+ }
+ }
+
+ varias2[[nbox]] <- datos2
+ }
+
+ seq.depth2 <- sapply(varias2, sum) # sequencing depth for each new sample
+
+
+ ## selecting detected genes for each biotype (datos2)
+ for (j in 1:length(satura2)) {
+
+ satura2[[j]] <- vector("list", length = length(varias2))
+ names(satura2[[j]]) <- names(varias2)
+
+ # selecting genes in bioclass j for each sample
+ conbio2 <- lapply(varias2, function(x) { x[biog[[j]]] })
+
+ for (i in 1:length(conbio2)) {
+
+ # selecting the genes with counts > k
+ noK <- noceros(conbio2[[i]], k = k, num = FALSE)
+
+ if (is.null(noK)) {
+ satura2[[j]][[i]] <- NA
+ } else {
+ satura2[[j]][[i]] <- conbio2[[i]][noK]
+ }
+ }
+ }
+
+ ## results
+ satura <- list("cond1" = satura1, "cond2" = satura2,
+ "bionum" = sapply(biog, length),
+ "depth1" = seq.depth1, "depth2" = seq.depth2)
+ } else {
+
+ ## results
+ satura <- list("cond1" = satura1, "cond2" = satura2,
+ "bionum" = sapply(biog, length),
+ "depth1" = seq.depth1, "depth2" = NULL)
+
+ }
+
+ satura
+
+}
+
+
+
+
+#****************************************************************************#
+
+
+
+
+
+## PLOT: Mean length for detected genes Plot according to BIOTYPES
+
+countbio.plot <- function (depth1, depth2, sat1, sat2, bionum,
+ legend = c("sample1", "sample2"), main = "",
+ ylab = "# counts of detected features",
+ xlab = "Sequencing Depth", ylim = NULL, las = 0,
+ cex.main = 1, cex.lab = 1, cex.axis = 1, cex = 1) {
+
+ if (bionum == 0) {
+
+ print("Biotype not found in this dataset")
+
+ } else {
+
+ if (!is.null(depth2)) {
+
+ # ylim for plot
+ if (is.null(ylim)) {
+
+ #maxi <- sapply(c(sat1,sat2), max, na.rm = TRUE)
+ q75 <- sapply(c(sat1,sat2), quantile, probs = 0.75, na.rm = TRUE)
+
+ #limis <- q75 + 0.2*(maxi - q75)
+
+ #ylim <- c(0, max(limis, na.rm = TRUE))
+ ylim <- c(0, suppressWarnings(max(q75, na.rm = TRUE))*1.3)
+ }
+
+ # boxplots data
+
+ depth <- c(depth1, depth2)
+ depth <- round(depth/10^6, 1)
+ d.sort <- sort(depth)
+ d.order <- order(depth)
+
+ n1 <- length(depth1)
+ n2 <- length(depth2)
+
+ databox <- vector("list", length = n1+n2)
+ names(databox) <- d.sort
+
+ colo <- NULL
+
+ for (i in 1:(n1+n2)) {
+
+ if ( d.order[i] > n1 ) {
+
+ dd <- d.order[i] - n1
+ databox[[i]] <- sat2[[dd]]
+ colo <- c(colo, 4)
+
+ } else {
+
+ dd <- d.order[i]
+ databox[[i]] <- sat1[[dd]]
+ colo <- c(colo, 2)
+ }
+ }
+ } else {
+
+ #### only DATOS1
+
+ # ylim for plot
+ if (is.null(ylim)) {
+
+ #maxi <- sapply(sat1, max, na.rm = TRUE)
+ q75 <- sapply(sat1, quantile, probs = 0.75, na.rm = TRUE)
+
+ #limis <- q75 + 0.001*(maxi - q75)
+
+ #ylim <- c(0, max(limis, na.rm = TRUE))
+ ylim <- c(0, suppressWarnings(max(q75, na.rm = TRUE))*1.3)
+ }
+
+ # boxplots data
+
+ depth <- round(depth1/10^6,1)
+
+ n1 <- length(depth1)
+
+ databox <- sat1
+
+ colo <- rep(2, n1)
+
+ }
+
+ numNA <- sapply(databox, function(x) { length(which(is.na(x))) })
+ cuantos <- sapply(databox, length)
+
+ if (sum(cuantos-numNA) != 0) {
+
+ # BOXPLOT
+ par(bg = "#e6e6e6")
+
+ boxplot(databox, col = colo, ylim = ylim, main = main,
+ type = "b", xlab = xlab, ylab = ylab, names = depth,
+ cex.main = cex.main, cex.lab = cex.lab, cex.axis = cex.axis)
+
+ rect(par("usr")[1], par("usr")[3], par("usr")[2], par("usr")[4], col = "white")
+
+ boxplot(databox, col = colo, ylim = ylim, main = main,
+ type = "b", xlab = xlab, ylab = ylab, names = depth,
+ cex.main = cex.main, cex.lab = cex.lab, cex.axis = cex.axis, add = TRUE)
+
+
+ if (!is.null(depth2)) {
+
+ legend("top",
+ legend = legend, text.col = c(2,4), bty = "o",
+ bg = "white", fill = c(2, 4), cex = cex, horiz = TRUE)
+ }
+
+ cuantos1 <- which(cuantos == 1)
+ sumant <- sapply(databox, sum, na.rm = TRUE)
+ sumant0 <- which(sumant == 0)
+ cuantosNA <- intersect(cuantos1, sumant0)
+
+ cuantos[cuantosNA] <- 0
+
+ mtext(cuantos, 3, at = 1:length(databox), cex = 0.7*cex, las = las)
+
+ } else {
+ mismar <- par()$mar
+ par(mar = c(2,2,4,2), bg = "#e6e6e6")
+ plot(1,1, col = "white", xlab = "", ylab = "", xaxt = "n", yaxt = "n", main = main)
+ rect(par("usr")[1], par("usr")[3], par("usr")[2], par("usr")[4], col = "white")
+ text(1,1, "No counts found for this class")
+ par(mar = mismar)
+ #print("No features detected for this biotype")
+ }
+ }
+}
+
+
+
+
+
+#*************************************************************************#
+
+
+
+#############################################################################
+############## Plot with 2 different Y axis (left and right) ############
+#############################################################################
+
+
+# By Ajay Shah (taken from [R] Plot 2 time series with different y axes
+# (left and right),
+# in https://stat.ethz.ch/pipermail/r-help/2004-March/047775.html)
+
+# Modified by: Sonia Tarazona
+
+### PARAMETERS (default):
+# x: data to be drawn on X-axis
+# yright: data to be drawn on Y right axis
+# yleft: data to be drawn on Y left axis
+# yrightlim (range(yright, na.rm = TRUE)): ylim for rigth Y-axis
+# yleftlim (range(yleft, na.rm = TRUE)): ylim for left Y-axis
+# xlab (NULL): Label for X-axis
+# yylab (c("","")): Labels for right and left Y-axis
+# pch (c(1,2)): Type of symbol for rigth and left data
+# col (c(1,2)): Color for rigth and left data
+# linky (TRUE): If TRUE, points are connected by lines.
+# smooth (0): Friedman's super smoothing
+# lwds (1): Line width for smoothed line
+# length (10): Number of tick-marks to be drawn on axis
+# ...: Other graphical parameters to be added by user (such as main, font, etc.)
+###
+
+
+
+plot.y2 <- function(x, yright, yleft, yrightlim = range(yright, na.rm = TRUE),
+ yleftlim = range(yleft, na.rm = TRUE),
+ xlim = range(x, na.rm = TRUE),
+ xlab = NULL, yylab = c("",""), lwd = c(2,2),
+ pch = c(1,2), col = c(1,2), type = c("o","o"),
+ linky = TRUE, smooth = 0, cex2 = c(1,1),
+ lwds = 1, length = 10, ...,
+ x2 = NULL, yright2 = NULL, yleft2 = NULL, col2 = c(3,4))
+{
+ #par(mar = c(5,2,4+2,2), oma = c(0,3,0,3))
+ #par(mar = c(5,4,4+2,4))
+
+ ## Plotting RIGHT axis data
+
+ #par(bg = "#e6e6e6")
+
+ plot(x, yright, ylim = yrightlim, axes = FALSE, ylab = "", xlab = xlab,
+ xlim = xlim,
+ pch = pch[1], type = type[1], lwd = lwd[1], col = col[1], ...)
+
+ rect(par("usr")[1], par("usr")[3], par("usr")[2], par("usr")[4],
+ col = "white")
+
+ points(x, yright, pch = pch[1], type = type[1], lwd = lwd[1],
+ col = col[1], cex = cex2[1], ...)
+
+ axis(4, pretty(yrightlim, length), col = 1, col.axis = 1, las = 1)
+
+ if (!is.null(yright2)) {
+ points(x2, yright2, type = type[1], pch = pch[1], lwd = lwd[1],
+ col = col2[1], cex = cex2[1], ...)
+ }
+
+ #if (linky) lines(x, yright, col = col[1], ...)
+
+ if (smooth != 0) lines(supsmu(x, yright, span = smooth), col = col[1],
+ lwd = lwds, ...)
+
+ if(yylab[1]=="") {
+ mtext(deparse(substitute(yright)), side = 4, outer = FALSE, line = 4,
+ col = 1, las = 3, ...)
+ } else {
+ mtext(yylab[1], side = 4, outer = FALSE, line = 4, col = 1, las = 3, ...)
+ }
+
+
+ par(new = TRUE)#, xpd = TRUE, mar = c(5,2,4+2,2), oma = c(0,3,0,3))
+
+ ## Plotting LEFT axis data
+
+ plot(x, yleft, ylim = yleftlim, axes = FALSE, ylab = "" , xlab = xlab,
+ xlim = xlim, cex = cex2[2],
+ pch = pch[2], type = type[2], lwd = lwd[2], col = col[2], ...)
+
+ box()
+
+ axis(2, pretty(yleftlim, length), col = 1, col.axis = 1, las = 1)
+
+ if (!is.null(yleft2)) {
+ points(x2, yleft2, type = type[2], pch = pch[2], lwd = lwd[2],
+ col = col2[2], cex = cex2[2], ...)
+ }
+
+
+ #if (linky) lines(x, yleft, col = col[2], ...)
+
+ if (smooth != 0) lines(supsmu(x, yleft, span = smooth), col = col[2],
+ lwd=lwds, ...)
+
+ if(yylab[2] == "") {
+ mtext(deparse(substitute(yleft)), side = 2, outer = FALSE, line = 4,
+ col = 1, las = 3,...)
+ } else {
+ mtext(yylab[2], side = 2, outer = FALSE, line = 4, col = 1, las = 3,...)
+ }
+
+
+ ## X-axis
+ axis(1, at = pretty(xlim, length))
+
+
+}
+
+
+
+
+
+
+###############################################################################
+###############################################################################
+
+
+
+
+
+## Global Saturation Plot including new detection per million reads
+
+
+satur.plot2 <- function (datos1, datos2, myoutput, yleftlim = NULL, yrightlim = NULL,
+ k = 0, tit = "Saturation", cex.main = cex.main,
+ cex.lab = cex.lab, cex.axis = cex.axis, cex = cex,
+ legend = c(deparse(substitute(datos1)),
+ deparse(substitute(datos2)))) {
+
+
+# For datos1
+ n1 <- ncol(as.matrix(datos1))
+
+
+ if (n1 > 1) {
+
+ muestra1 <- as.list(1:n1)
+ for (i in 2:n1) {
+
+ combi1 <- combn(n1, i, simplify = FALSE)
+
+ if( length(combi1) > 20 ) {
+ sub20 <- sample(1:length(combi1), size = 20, replace = FALSE)
+ combi1 <- combi1[sub20]
+ }
+
+ muestra1 <- append(muestra1, combi1)
+ }
+
+ varias1 <- vector("list", length = length(muestra1))
+ names(varias1) <- sapply(muestra1, function(x) {
+ paste("C1.", x, collapse = "", sep = "")})
+
+ for (i in 1:length(muestra1)) {
+ varias1[[i]] <- apply(as.matrix(datos1[,muestra1[[i]]]), 1, sum)
+ }
+
+ satura1 <- data.frame("muestra" = names(varias1),
+ "seq.depth" = sapply(varias1, sum),
+ "noceros" = sapply(varias1, noceros, k = k))
+ }
+
+
+
+ if (n1 == 1) {
+
+ total1 <- sum(datos1)
+ satura1 <- NULL
+
+ for (i in 1:9) { # 10%, 20%, ..., 90% reads (apart 100% is calculated)
+ muestra1 <- rmultinom(10, size = round(total1*i/10,0), prob = datos1)
+ detec1 <- mean(apply(muestra1, 2, noceros, k = k))
+ satura1 <- rbind(satura1, c(round(total1*i/10,0), detec1))
+ }
+ satura1 <- rbind(satura1, c(total1, noceros(datos1, k = k)))
+ colnames(satura1) <- c("seq.depth", "noceros")
+ satura1 <- as.data.frame(satura1)
+ }
+
+
+ # new detections (sample 1)
+
+ puntos1 <- data.frame("x" = satura1$seq.depth, "y" = satura1$noceros)
+
+ pendi <- NULL
+
+ for (i in 2:nrow(puntos1)) {
+
+ nuevo <- max(0, (puntos1$y[i]-puntos1$y[i-1])/
+ (puntos1$x[i]-puntos1$x[i-1]))
+
+ pendi <- c(pendi, nuevo)
+ }
+
+ newdet1 <- c(NA, pendi)*1000000
+
+
+
+
+
+# For datos2
+
+ if (!is.null(datos2)) {
+
+ n2 <- ncol(as.matrix(datos2))
+
+ if (n2 > 1) {
+
+ if (n1 == n2) {
+ muestra2 <- muestra1
+
+ } else {
+
+ muestra2 <- as.list(1:n2)
+
+ for (i in 2:n2) {
+
+ combi2 <- combn(n2, i, simplify = FALSE)
+
+ if (length(combi2) > 20) {
+ sub20 <- sample(1:length(combi2), size = 20, replace = FALSE)
+ combi2 <- combi2[sub20]
+ }
+
+ muestra2 <- append(muestra2, combi2)
+
+ }
+ }
+
+ varias2 <- vector("list", length = length(muestra2))
+ names(varias2) <- sapply(muestra2, function(x) {
+ paste("C2.", x, collapse = "", sep = "")})
+
+ for (i in 1:length(muestra2)) {
+ varias2[[i]] <- apply(as.matrix(datos2[,muestra2[[i]]]), 1, sum)
+ }
+
+ satura2 <- data.frame("muestra" = names(varias2),
+ "seq.depth" = sapply(varias2, sum),
+ "noceros" = sapply(varias2, noceros, k = k))
+ }
+
+
+ if (n2 == 1) {
+
+ total2 <- sum(datos2)
+ satura2 <- NULL
+
+ for (i in 1:9) { # 10%, 20%, ..., 90% reads (apart 100% is calculated)
+
+ muestra2 <- rmultinom(10, size = round(total2*i/10,0), prob = datos2)
+ detec2 <- mean(apply(muestra2, 2, noceros, k = k))
+ satura2 <- rbind(satura2, c(round(total2*i/10,0), detec2))
+ }
+
+ satura2 <- rbind(satura2, c(total2, noceros(datos2, k = k)))
+ colnames(satura2) <- c("seq.depth", "noceros")
+ satura2 <- as.data.frame(satura2)
+ }
+
+
+ # new detections (sample 2)
+
+ puntos2 <- data.frame("x" = satura2$seq.depth, "y" = satura2$noceros)
+
+ pendi <- NULL
+
+ for (i in 2:nrow(puntos2)) {
+
+ nuevo <- max(0, (puntos2$y[i]-puntos2$y[i-1])/
+ (puntos2$x[i]-puntos2$x[i-1]))
+
+ pendi <- c(pendi, nuevo)
+ }
+
+ newdet2 <- c(NA, pendi)*1000000
+
+
+
+
+ ## PLOT LIMITS
+
+ # yleftlim for plot.y2
+ if (is.null(yleftlim)) {
+ yleftlim <- c(0, NROW(datos1))
+ }
+
+
+ # xlim
+ SS1 <- range(satura1$seq.depth/10^6)
+ SS2 <- range(satura2$seq.depth/10^6)
+
+ xM <- max(SS1[2], SS2[2])
+ xm <- min(SS1[1], SS2[1])
+
+
+ # yrightlim for plot.y2
+ if (is.null(yrightlim)) {
+ maxi <- max(na.omit(c(newdet1, newdet2)))
+ if (maxi < 10) {
+ yrightlim <- c(0, max(10,maxi))
+ } else {
+ yrightlim <- c(0, maxi*1.1)
+ }
+ }
+
+
+
+ ## PLOT for SAMPLES 1 and 2
+
+ #par(xpd=TRUE, mar=par()$mar+c(0,0,2,0))
+
+ plot.y2(x = satura1$seq.depth/10^6, yright = newdet1,
+ yleft = satura1$noceros,
+ type = c("h", "o"), lwd = c(20,2), pch = c(1, 19),
+ yrightlim = yrightlim, yleftlim = yleftlim,
+ xlim = c(xm, xM), main = tit,
+ xlab = "Sequencing Depth (million reads)", col = c("pink", 2),
+ yylab = c("New detections per million reads",
+ paste("Number of features with reads >", k)),
+ cex2 = c(1.5,1.5),
+ cex.main = cex.main, cex.lab = cex.lab, cex.axis = cex.axis,
+ x2 = satura2$seq.depth/10^6, yright2 = newdet2,
+ yleft2 = satura2$noceros, col2 = c("lightblue1", 4))
+
+ legend.text <- c(paste(legend[1], "(left axis)"),
+ paste(legend[2], "(left axis)"),
+ paste(legend[1], "(right axis)"),
+ paste(legend[2], "(right axis)"))
+
+ legend.pch <- c(16, 16, 15, 15)
+
+ legend.col <- c(2, 4, "pink", "lightblue1")
+
+ legend("top",
+ legend = legend.text, pch = legend.pch,
+ col = legend.col, ncol = 2, bty = "n")
+
+ par(mar=c(5, 4, 4, 2) + 0.1)
+
+
+ # txt file for sample 1 and 2
+ mytxt <- cbind(satura1$seq.depth, satura1$noceros, newdet1,
+ satura2$seq.depth, satura2$noceros, newdet2)
+ colnames(mytxt) <- c("depth1", "detec1", "newdetec1",
+ "depth2", "detec2", "newdetec2")
+
+ write.table(mytxt, file = myoutput, quote = FALSE,
+ col.names = TRUE, row.names = FALSE, sep = "\t")
+
+
+ } else { ## 1 sample
+
+ ## PLOT LIMITS
+
+ # yleftlim for plot.y2
+ if (is.null(yleftlim)) {
+ yleftlim <- c(0, NROW(datos1))
+ }
+
+
+ # xlim
+ xlim <- range(satura1$seq.depth/10^6)
+
+
+ # yrightlim for plot.y2
+ if (is.null(yrightlim)) {
+ maxi <- max(na.omit(newdet1))
+ if (maxi < 10) {
+ yrightlim <- c(0, max(10,maxi))
+ } else {
+ yrightlim <- c(0, maxi*1.1)
+ }
+ }
+
+
+ ## PLOT for SAMPLE 1
+ plot.y2(x = satura1$seq.depth/10^6, yright = newdet1,
+ yleft = satura1$noceros,
+ type = c("h", "o"), lwd = c(20,2), pch = c(1, 19),
+ yrightlim = yrightlim, yleftlim = yleftlim,
+ xlim = xlim, main = tit,
+ xlab = "Sequencing Depth (million reads)", col = c("pink", 2),
+ yylab = c("New detections per million reads",
+ paste("Number of features with reads >", k)),
+ cex = c(1.5,1.5),
+ cex.main = cex.main, cex.lab = cex.lab, cex.axis = cex.axis)
+
+ legend.text <- c("Left axis", "Right axis")
+
+ legend.pch <- c(16, 15)
+
+ legend.col <- c(2, "pink")
+
+ legend("top",
+ legend = legend.text, pch = legend.pch,
+ col = legend.col, ncol = 2, bty = "n")
+
+
+ par(mar=c(5, 4, 4, 2) + 0.1)
+
+
+ # txt file for sample 1
+ mytxt <- cbind(satura1$seq.depth, satura1$noceros, newdet1)
+ colnames(mytxt) <- c("depth1", "detec1", "newdetec1")
+
+ write.table(mytxt, file = myoutput, quote = FALSE,
+ col.names = TRUE, row.names = FALSE, sep = "\t")
+
+
+ }
+
+}
+
+
+
+
+
+#***************************************************************************#
+
+
+
+
+
+
+
+## Correlation plot between two samples
+
+
+cor.plot <- function(datos1, datos2, log.scale = FALSE, ...) {
+
+ if (log.scale) {
+
+ datos1 <- log2(datos1 + 1)
+ datos2 <- log2(datos2 + 1)
+
+ }
+
+ plot(datos1, datos2,...)
+
+ coefLR <- summary(lm(datos2~datos1))$coefficients[,"Estimate"]
+
+ abline(a = coefLR[1], b = coefLR[2], col = 2, lwd = 2)
+
+ mycor <- cor(datos1, datos2)
+
+ myR2 <- round(100*mycor^2,2)
+
+ my.y <- min(datos2)+0.1*diff(range(datos2))
+
+ text(max(datos1), my.y, paste("y =", round(coefLR[1],3), "+", round(coefLR[2],3), "x"), col = 2, adj = 1)
+ text(max(datos1), my.y-0.05*diff(range(datos2)), paste("R2 =", myR2, "%"), col = 2, adj = 1)
+
+}
+
+
+
+
+
+## Function filled.contour with legend
+
+filled.contour <-
+function (x = seq(0, 1, length.out = nrow(z)), y = seq(0, 1,
+ length.out = ncol(z)), z, xlim = range(x, finite = TRUE),
+ ylim = range(y, finite = TRUE), zlim = range(z, finite = TRUE),
+ levels = pretty(zlim, nlevels), nlevels = 20, color.palette = cm.colors,
+ col = color.palette(length(levels) - 1), plot.title, plot.axes,
+ key.title, key.axes, asp = NA, xaxs = "i", yaxs = "i", las = 1,
+ axes = TRUE, frame.plot = axes, key.border = NA, ...)
+{
+ if (missing(z)) {
+ if (!missing(x)) {
+ if (is.list(x)) {
+ z <- x$z
+ y <- x$y
+ x <- x$x
+ }
+ else {
+ z <- x
+ x <- seq.int(0, 1, length.out = nrow(z))
+ }
+ }
+ else stop("no 'z' matrix specified")
+ }
+ else if (is.list(x)) {
+ y <- x$y
+ x <- x$x
+ }
+ if (any(diff(x) <= 0) || any(diff(y) <= 0))
+ stop("increasing 'x' and 'y' values expected")
+ mar.orig <- (par.orig <- par(c("mar", "las", "mfrow")))$mar
+ on.exit(par(par.orig))
+ w <- (3 + mar.orig[2L]) * par("csi") * 2.54
+ layout(matrix(c(2, 1), ncol = 2L), widths = c(1, lcm(w)))
+ par(las = las)
+ mar <- mar.orig
+ mar[4L] <- mar[2L]
+ mar[2L] <- 1
+ par(mar = mar)
+ plot.new()
+ plot.window(xlim = c(0, 1), ylim = range(levels), xaxs = "i",
+ yaxs = "i")
+ rect(0, levels[-length(levels)], 1, levels[-1L], col = col,
+ border=key.border)
+ if (missing(key.axes)) {
+ if (axes)
+ axis(4)
+ }
+ else key.axes
+ box()
+ if (!missing(key.title))
+ key.title
+ mar <- mar.orig
+ mar[4L] <- 1
+ par(mar = mar)
+ plot.new()
+ plot.window(xlim, ylim, "", xaxs = xaxs, yaxs = yaxs, asp = asp)
+ if (!is.matrix(z) || nrow(z) <= 1L || ncol(z) <= 1L)
+ stop("no proper 'z' matrix specified")
+ if (!is.double(z))
+ storage.mode(z) <- "double"
+
+ if (R.Version()$major > 2) {
+ .filled.contour(as.double(x), as.double(y), z, as.double(levels), col = col)
+ } else {
+ .Internal(filledcontour(as.double(x), as.double(y), z, as.double(levels),
+ col = col))
+ }
+
+ if (missing(plot.axes)) {
+ if (axes) {
+ title(main = "", xlab = "", ylab = "")
+ Axis(x, side = 1)
+ Axis(y, side = 2)
+ }
+ }
+ else plot.axes
+ if (frame.plot)
+ box()
+ if (missing(plot.title))
+ title(...)
+ else plot.title
+ invisible()
+}
+
+
+
+
+
+## Contour plot for correlation
+
+#library(colorRamps)
+
+cor.plot.2D <- function(datos1, datos2, noplot = 0.01,
+ log.scale = TRUE,...) {
+
+ nozeros <- which(rowSums(cbind(datos1, datos2)) > 0)
+
+ datos1 <- datos1[nozeros]
+ datos2 <- datos2[nozeros]
+
+ mycor <- round(cor(datos1, datos2),3)
+
+ if (log.scale) {
+
+ datos1 <- log2(datos1 + 1)
+ datos2 <- log2(datos2 + 1)
+
+ }
+
+ library(MASS)
+
+ limx <- quantile(datos1, c(noplot, 1-noplot))
+ limy <- quantile(datos2, c(noplot, 1-noplot))
+
+ d <- kde2d(datos1, datos2, n=100, lims=c(limx, limy))
+
+ filled.contour(d, color.palette = topo.colors,
+ main = paste("Pearson's correlation coefficient =", mycor),
+ n=100, key.title = title(main="Density"),
+ key.axes = axis(4),...)
+
+}
diff --git a/cli/scripts/qualimapRscript.r b/cli/scripts/qualimapRscript.r
new file mode 100644
index 0000000..d769110
--- /dev/null
+++ b/cli/scripts/qualimapRscript.r
@@ -0,0 +1,735 @@
+#!/usr/bin/env Rscript
+if(!require("optparse")) { install.packages("optparse", repos = "http://cran.r-project.org") }
+suppressPackageStartupMessages(library("optparse"))
+
+# Last modified: 14-VI-2012
+
+option_list <- list(
+ make_option(c("-v", "--verbose"), action="store_true", default=TRUE,
+ help="Print extra output [default]"),
+ make_option(c("-q", "--quietly"), action="store_false",
+ dest="verbose", help="Print little output"),
+ make_option(c("--data1"), type="character", action="store",
+ help="REQUIRED. First file with counts.",default=NULL,
+ metavar="file_counts"),
+ make_option(c("--data2"), type="character", action="store",
+ help="Optional. Second file with counts.",default=NULL,
+ metavar="file_counts"),
+ make_option(c("--name1"), type="character", action="store",
+ help="Optional. Name for the first sample",default="Sample 1",
+ metavar="sample_name"),
+ make_option(c("--name2"), type="character", action="store",
+ help="Optional. Name for the second sample.",default="Sample 2",
+ metavar="sample_name"),
+ make_option(c("--info"), type="character", action="store",
+ help="Optional. Info file.",default=NULL, metavar="file_info"),
+ make_option(c("--groups"), type="character", action="store",
+ help="Optional. File with groups for the --info file." , default=NULL, metavar="file_groups"),
+ make_option(c("-k", "--threshold"), type="integer", action="store",
+ help="Optional. Threshold for the number of counts.",default=5,
+ metavar="counts_threshold"),
+ make_option("--x11-disabled", action="store_true",
+ help="Do not use X11 to output plots",
+ dest="x11_disabled"),
+ make_option(c("-o", "--dirOut"), type="character", action="store",
+ help="Optional. Output folder.",default="./",
+ metavar="folder_output"),
+ make_option("--homesrc", type="character", action="store",
+ help="DEVELOPMENTAL. NOT TO BE USED IN THIS VERSION", default="./",
+ metavar="home_src folder")
+ )
+
+opt <- parse_args(OptionParser(option_list=option_list))
+
+#HOMESRC <- "/home/fdgarcia/qualimap/sonia"
+HOMESRC <- opt$homesrc
+source(file.path(HOMESRC, "qualimapRfunctions.r"))
+
+#datos1 <- "counts1.txt"
+datos1 <- opt$data1
+if(is.null(datos1)){
+ stop("--data1 is a REQUIRED argument")
+}
+datos2 <- opt$data2 # with the same features than datos1 and in the same order
+
+
+if(!file.exists(opt$dirOut)){
+ dir.create(opt$dirOut, recursive=TRUE)
+}
+
+# cutoff for the number of counts to consider a biological feature as detected
+k <- opt$threshold
+
+
+cm <- 1.5 # cex.main
+cl <- 1.2 # cex.lab
+ca <- 1 # cex.axis
+cc <- 1.2 # cex
+
+
+nom1 <- opt$name1
+nom2 <- opt$name2
+
+plot.png <- function(plot.name, height.factor = 1, width.factor = 1 ) {
+ #if (is.null(opt$x11_disabled)) {
+ # png(filename = file.path(opt$dirOut, plot.name),
+ # width = 3*480*width.factor, height = height.factor*3*480, units = "px", pointsize = 3*12)
+ #} else {
+ #cat("Can not plot ", plot.name, "!\nX11 mode is required.\n")
+ bitmap(file = file.path(opt$dirOut, plot.name),type="png16m",bg="white",
+ width = 3*480*width.factor, height = height.factor*3*480, units = "px", pointsize = 3*12)
+ #}
+
+}
+
+if (!is.null(opt$info)){
+#file including features ID in "datos1" and biotypes or other classification
+ infobio <- opt$info # NO header
+ if (!is.null(opt$groups)){
+ agru.biotype <- TRUE
+ # two columns file: 1) all biotypes in infobio 2) group for biotypes
+ file.agru <- opt$groups # NO header
+ }else{
+ file.agru <- NULL
+ agru.biotype <- FALSE
+ }
+}
+
+
+
+
+###########################################################################
+
+
+#### DATA
+
+fichero1 <- read.delim(datos1, header = FALSE, sep = "\t", as.is = TRUE)
+
+misdatos1 <- fichero1[,2]
+names(misdatos1) <- fichero1[,1]
+
+if (is.null(datos2)) {
+
+ misdatos2 <- NULL
+
+} else {
+
+ fichero2 <- read.delim(datos2, header = FALSE, sep = "\t", as.is = TRUE)
+
+ misdatos2 <- fichero2[,2]
+ names(misdatos2) <- fichero2[,1]
+}
+
+
+
+#### BIOTYPES
+if (!is.null(opt$info)) {
+
+ infofile <- read.delim(infobio, header = FALSE, sep = "\t", as.is = TRUE)
+ myinfo <- infofile[,2]
+ names(myinfo) <- infofile[,1]
+
+
+ ## Completing files: data & info
+
+ genes1 <- as.character(names(misdatos1))
+ genes2 <- as.character(names(misdatos2))
+ genesI <- as.character(names(myinfo))
+
+ if (length(genes2) > 0) {
+ allgenes <- union(genes1, genes2)
+ } else { allgenes <- genes1 }
+
+
+ # Completing myinfo
+ unknown <- setdiff(allgenes, genesI) # genes in data without biotype
+
+ if(length(unknown) > 0) {
+ unk <- rep("unknown", length(unknown))
+ names(unk) <- unknown
+ myinfo <- c(myinfo, unk) # adding unknown genes (without biotype)
+ write.table(unknown, file = file.path(opt$dirOut, "nogroup.txt"),
+ sep = "\t", row.names = FALSE,
+ col.names = FALSE, quote = FALSE) # file for unknown genes
+ }
+
+ genesII <- names(myinfo)
+
+
+ # Completing my data
+ notdet1 <- setdiff(genesII, genes1) # genes1 not in complete info -> counts=0
+ if (length(genes2) > 0) {
+ notdet2 <- setdiff(genesII, genes2)
+ # genes2 not in complete info -> counts=0
+ } else { notdet2 <- NULL }
+
+ if(length(notdet1) > 0) {
+ ceros1 <- rep(0, length(notdet1))
+ names(ceros1) <- notdet1
+ misdatos1 <- c(misdatos1, ceros1) # adding genes with 0s to data
+ nom <- paste(nom1, "nocounts.txt", sep = ".")
+ write.table(notdet1, file = file.path(opt$dirOut, nom),
+ sep = "\t", row.names = FALSE,
+ col.names = FALSE, quote = FALSE) # file for added genes
+ }
+
+ if(length(notdet2) > 0) {
+ ceros2 <- rep(0, length(notdet2))
+ names(ceros2) <- notdet2
+ misdatos2 <- c(misdatos2, ceros2) # adding genes with 0s to data
+ nom <- paste(nom2, "nocounts.txt", sep = ".")
+ write.table(notdet2, file = file.path(opt$dirOut, nom),
+ sep = "\t", row.names = FALSE,
+ col.names = FALSE, quote = FALSE) # file for added genes
+ }
+
+
+ # OK files
+ ok1 <- intersect(genes1, genesII) # genes1 with counts and biotype
+
+ nom <- paste(nom1, "OK.txt", sep = ".")
+ write.table(ok1, file = file.path(opt$dirOut, nom),
+ sep = "\t", row.names = FALSE,
+ col.names = FALSE, quote = FALSE) # file for added genes
+
+ if (!is.null(notdet2)) {
+
+ ok2 <- intersect(genes2, genesII) # genes2 with counts and biotype
+
+ nom <- paste(nom2, "OK.txt", sep = ".")
+ write.table(ok2, file = file.path(opt$dirOut, nom),
+ sep = "\t", row.names = FALSE,
+ col.names = FALSE, quote = FALSE) # file for added genes
+ }
+
+
+
+ ## Sorting files according to genes (all with the same genes)
+ misdatos1 <- misdatos1[genesII]
+
+ if(!is.null(misdatos2)) {
+ misdatos2 <- misdatos2[genesII]
+ }
+
+
+
+
+ ## Preparing biotype files
+
+ if (agru.biotype) { # If you want to group biotypes
+
+ biogroups <- read.delim(file.agru, header = FALSE, sep = "\t", as.is = TRUE)
+ biogrupos <- unique(biogroups)
+
+ # Creating a list for groupes of biotypes
+ bio.agru <- vector("list", length = length(table(biogrupos[,2])))
+ names(bio.agru) <- names(table(biogrupos[,2]))
+
+ for (i in 1:length(bio.agru)) {
+
+ bio.agru[[i]] <- biogrupos[is.element(biogrupos[,2],
+ names(bio.agru)[i]),1]
+ }
+
+ biotipus <- bio.agru
+
+ bio.agru2 <- NULL
+
+ for (i in 1:length(bio.agru)) {
+ bio.agru2 <- c(bio.agru2, rep(names(bio.agru)[i], length(bio.agru[[i]])))
+ }
+ names(bio.agru2) <- unlist(bio.agru)
+
+ } else { # No grouping
+
+ biotipus <- as.list(names(table(myinfo)))
+ names(biotipus) <- names(table(myinfo))
+
+ bio.agru2 <- names(table(myinfo))
+ names(bio.agru2) <- bio.agru2
+
+ }
+
+
+
+###########################################################################
+###########################################################################
+
+
+#### FEATURES DETECTION per BIOTYPE
+
+ if (agru.biotype) {
+
+ mybioagru <- bio.agru2[myinfo]
+
+ } else { mybioagru <- myinfo }
+
+ detect <- misdatos1 > k
+
+ genome <- 100*table(bio.agru2[myinfo])/sum(table(bio.agru2[myinfo]))
+
+ ordre <- order(genome, decreasing = TRUE)
+
+ perdet1 <- genome*table(mybioagru, detect)[,2]/
+ table(bio.agru2[myinfo])[rownames(table(mybioagru, detect))]
+ perdet2 <- 100*table(mybioagru, detect)[,2]/sum(table(mybioagru, detect)[,2])
+
+ ceros <- rep(0, length(genome))
+
+ biotable <- as.matrix(rbind(genome[ordre], perdet1[ordre],
+ perdet2[ordre], ceros))
+ rownames(biotable) <- c("genome", "detectionVSgenome", "detectionVSsample",
+ "ceros")
+
+ if (is.null(misdatos2)) {
+
+ # Saving data in a txt file
+ mybiotable <- cbind(colnames(biotable), t(biotable[-4,]))
+ colnames(mybiotable)[1] <- "biotype"
+
+ write.table(mybiotable,
+ file.path(opt$dirOut, "DetectionPerGroup.txt"),
+ sep = "\t", quote = FALSE, col.names = TRUE, row.names = FALSE)
+
+ # Plot (1 sample)
+ plot.png("DetectionPerGroup.png", width.factor = 2)
+ par(mar = c(11, 4, 2, 2), bg = "#e6e6e6")
+
+ barplot(biotable[c(1,3),], main = "Detection per group",
+ xlab = "", ylab = "%features", axis.lty = 1, legend = FALSE,
+ beside = TRUE, col = c("grey", 2), las = 2,
+ ylim = c(0, 100), border = c("grey", 2))
+
+ rect(par("usr")[1], par("usr")[3], par("usr")[2], par("usr")[4],
+ col = "white")
+
+ barplot(biotable[c(1,3),], main = "Detection per group",
+ xlab = "", ylab = "%features", axis.lty = 1, legend = FALSE,
+ beside = TRUE, col = c("grey", 2), las = 2, add = TRUE,
+ ylim = c(0, 100), border = c("grey", 2))
+
+ barplot(biotable[c(2,4),], main = "Detection per group",
+ xlab = "", ylab = "%features", axis.lty = 1, legend = FALSE,
+ beside = TRUE, col = c(2, 1), las = 2, density = 30,
+ ylim = c(0, 100), border = 2, add = TRUE)
+
+ legend(x = "top", bty = "n", horiz = TRUE,
+ fill = c("grey", 2, 2), density = c(NA,30,NA),
+ border = c("grey", 2, 2),
+ legend = c("% in genome", "detected", "% in sample"))
+
+ garbage <- dev.off()
+
+ } else {
+
+ detect2 <- misdatos2>k
+
+ perdet3 <- genome*table(mybioagru, detect2)[names(genome),2]/
+ table(bio.agru2[myinfo])[names(genome)]
+ perdet4 <- 100*table(mybioagru, detect2)[,2]/
+ sum(table(mybioagru, detect2)[,2])
+
+ biotable2 <- as.matrix(rbind(genome[ordre], perdet3[ordre],
+ perdet4[ordre], ceros))
+ rownames(biotable2) <- c("genome", "detectionVSgenome", "detectionVSsample",
+ "ceros")
+
+
+ # Saving data in a txt file
+ mybiotable <- cbind(colnames(biotable), t(biotable[-4,]))
+ colnames(mybiotable)[1] <- "biotype"
+ mybiotable2 <- t(biotable2[-c(1,4),])
+ mybiotable2 <- mybiotable2[rownames(mybiotable),]
+
+ mybiotable12 <- cbind(mybiotable, mybiotable2)
+ colnames(mybiotable12)[-c(1,2)] <- apply(cbind(colnames(mybiotable12)[-c(1,2)],
+ rep(1:2, each = 2)), 1, paste, collapse = "_")
+
+ write.table(mybiotable12,
+ file.path(opt$dirOut, "DetectionPerGroup.txt"),
+ sep = "\t", quote = FALSE, col.names = TRUE, row.names = FALSE)
+
+
+ # Plot (2 samples)
+ plot.png("DetectionPerGroup.png", width.factor = 2, height.factor = 2)
+ #png(filename = file.path(opt$dirOut, "DetectionPerGroup.png"),
+ # width = 3*480*2, height = 3*480*2, units = "px", pointsize = 3*12)
+
+ par(mar = c(11, 4, 2, 2), mfrow = c(2,1), bg = "#e6e6e6")
+
+ # Datos1
+ barplot(biotable[c(1,3),],
+ main = paste("Detection per group:", nom1),
+ xlab = "", ylab = "%features", axis.lty = 1, legend = FALSE,
+ beside = TRUE, col = c("grey", 2), las = 2,
+ ylim = c(0, 100), border = c("grey", 2))
+
+ rect(par("usr")[1], par("usr")[3], par("usr")[2], par("usr")[4],
+ col = "white")
+
+ barplot(biotable[c(1,3),],
+ main = paste("Detection per group:", nom1),
+ xlab = "", ylab = "%features", axis.lty = 1, legend = FALSE,
+ beside = TRUE, col = c("grey", 2), las = 2, add = TRUE,
+ ylim = c(0, 100), border = c("grey", 2))
+
+ barplot(biotable[c(2,4),],
+ main = paste("Detection per group:", nom1),
+ xlab = "", ylab = "%features", axis.lty = 1, legend = FALSE,
+ beside = TRUE, col = c(2, 1), las = 2, density = 30,
+ ylim = c(0, 100), border = 2, add = TRUE)
+
+ legend(x = "top", bty = "n", horiz = TRUE,
+ fill = c("grey", 2, 2), density = c(NA,30,NA),
+ border = c("grey", 2, 2),
+ legend = c("% in genome", "detected", "% in sample"))
+
+
+ # Datos2
+ barplot(biotable2[c(1,3),],
+ main = paste("Detection per group:", nom2),
+ xlab = "", ylab = "%features", axis.lty = 1, legend = FALSE,
+ beside = TRUE, col = c("grey", 4), las = 2,
+ ylim = c(0, 100), border = c("grey", 4))
+
+ rect(par("usr")[1], par("usr")[3], par("usr")[2], par("usr")[4],
+ col = "white")
+
+ barplot(biotable2[c(1,3),],
+ main = paste("Detection per group:", nom2),
+ xlab = "", ylab = "%features", axis.lty = 1, legend = FALSE,
+ beside = TRUE, col = c("grey", 4), las = 2, add = TRUE,
+ ylim = c(0, 100), border = c("grey", 4))
+
+ barplot(biotable2[c(2,4),],
+ main = paste("Detection per group:", nom2),
+ xlab = "", ylab = "%features", axis.lty = 1, legend = FALSE,
+ beside = TRUE, col = c(4, 1), las = 2, density = 30,
+ ylim = c(0, 100), border = 4, add = TRUE)
+
+ legend(x = "top", bty = "n", horiz = TRUE,
+ fill = c("grey", 4, 4), density = c(NA,30,NA),
+ border = c("grey", 4, 4),
+ legend = c("% in genome", "detected", "% in sample"))
+
+ garbage <- dev.off()
+
+ }
+
+}
+
+
+
+
+
+###########################################################################
+###########################################################################
+
+
+#### SATURATION GLOBAL PLOT
+
+plot.png("GlobalSaturation.png")
+#png(filename = paste(opt$dirOut, "GlobalSaturation.png", sep=""),
+# width = 3*480, height = 3*480, units = "px", pointsize = 3*12)
+
+par(mar = c(5,6,4,6), bg = "#e6e6e6")
+
+satur.plot2(datos1 = misdatos1, datos2 = misdatos2,
+ myoutput = file.path(opt$dirOut, "GlobalSaturation.txt"),
+ tit = "Global Saturation Plot", k = k,
+ #yleftlim = NULL, yrightlim = NULL,
+ cex.main = cm, cex.lab = cl, cex.axis = ca, cex = cc,
+ legend = c(nom1, nom2))
+
+garbage <- dev.off()
+
+
+
+
+
+
+
+
+############################################################################
+
+
+
+#### SATURATION PLOTS per BIOTYPE
+
+if (!is.null(opt$info)) {
+
+ satbio.mine <- saturbio.dat(datos1 = misdatos1, datos2 = misdatos2, k = k,
+ infobio = myinfo, biotypes = biotipus)
+
+ mytable1 <- satbio.mine$depth1
+ mytable2 <- satbio.mine$depth2
+
+ for (i in 1:length(biotipus)) {
+
+ mytable1 <- cbind(mytable1, satbio.mine$cond1[[i]], satbio.mine$newdet1[[i]])
+ mytable2 <- cbind(mytable2, satbio.mine$cond2[[i]], satbio.mine$newdet2[[i]])
+
+ plot.png(paste0(names(biotipus)[i],".png"))
+ #png(paste(opt$dirOut, names(biotipus)[i],".png", sep = ""),
+ # width = 3*480, height = 3*480, pointsize = 3*12)
+
+ par(mar = c(5,6,4,6), bg = "#e6e6e6")
+
+ titulo <- paste("Number of features with reads >", k)
+
+ saturbio.plot(depth1 = satbio.mine$depth1, depth2 = satbio.mine$depth2,
+ sat1 = satbio.mine$cond1[[i]], sat2 = satbio.mine$cond2[[i]],
+ newdet1 = satbio.mine$newdet1[[i]],
+ newdet2 = satbio.mine$newdet2[[i]],
+ bionum = satbio.mine$bionum[i],
+ main = paste(names(biotipus)[i],
+ " (", satbio.mine$bionum[i], ")", sep = ""),
+ legend = c(nom1, nom2),
+ yleftlim = c(0, satbio.mine$bionum[i]),
+ ylabL = titulo,
+ ylabR = "New detections per million reads",
+ cex = cc, cex.main = cm, cex.lab = cl)
+
+ garbage <- dev.off()
+
+ }
+
+ colnames(mytable1) <- c("depth",
+ apply(cbind(rep(c("detec","newdetec"), length(satbio.mine$cond1)),
+ rep(names(satbio.mine$cond1), each = 2)),
+ 1, paste, collapse = "_"))
+
+ write.table(mytable1, file.path(opt$dirOut, "SaturationPerGroup_1.txt"),
+ sep = "\t", quote = FALSE, col.names = TRUE, row.names = FALSE)
+
+ if(!is.null(mytable2)) {
+
+ colnames(mytable2) <- c("depth",
+ apply(cbind(rep(c("detec","newdetec"), length(satbio.mine$cond2)),
+ rep(names(satbio.mine$cond2), each = 2)),
+ 1, paste, collapse = "_"))
+
+ write.table(mytable2, file.path(opt$dirOut, "SaturationPerGroup_2.txt"),
+ sep = "\t", quote = FALSE, col.names = TRUE, row.names = FALSE)
+
+ }
+
+
+
+
+
+############################################################################
+############################################################################
+
+
+
+#### COUNTS DISTRIBUTION -- per BIOTYPE
+
+ countdist.mine <- countsbio.dat(misdatos1, misdatos2, k = k, nbox = 1,
+ infobio = myinfo, biotypes = biotipus)
+
+ countlist <- countdist.mine$cond1[[1]]
+
+ for (i in 2:length(countdist.mine$cond1)) {
+ countlist <- c(countlist, countdist.mine$cond1[[i]])
+ }
+ names(countlist) <- names(countdist.mine$cond1)
+
+ ysup <- max(sapply(countlist, quantile, probs = 0.75, na.rm = TRUE),
+ na.rm = TRUE)*1.3
+
+ if (is.null(misdatos2)) {
+
+ plot.png("counts_boxplot.png")
+ #png(paste(opt$dirOut, "counts_boxplot.png", sep=""),
+ # width = 3*480, height = 3*480, pointsize = 3*12)
+
+ par(mar = c(11,4,6,2), bg = "#e6e6e6")
+
+ } else {
+
+ countlist2 <- countdist.mine$cond2[[1]]
+
+ for (i in 2:length(countdist.mine$cond2)) {
+ countlist2 <- c(countlist2, countdist.mine$cond2[[i]])
+ }
+ names(countlist2) <- names(countdist.mine$cond2)
+
+ ysup2 <- max(sapply(countlist2, quantile, probs = 0.75, na.rm = TRUE),
+ na.rm = TRUE)*1.3
+
+ ysup <- max(ysup, ysup2, na.rm = TRUE)
+
+ plot.png("counts_boxplot.png", width.factor = 2)
+ #png(paste(opt$dirOut, "counts_boxplot.png", sep=""),
+ # width = 3*480*2, height = 3*480, pointsize = 3*12)
+
+ par(mar = c(11,4,6,2), mfrow = c(1,2), bg = "#e6e6e6")
+
+ }
+
+ boxplot(countlist[ordre], las = 2,
+ main = paste("Counts distribution per group:", nom1),
+ ylim = c(k, ysup), col = 2)
+
+ rect(par("usr")[1], par("usr")[3], par("usr")[2], par("usr")[4], col = "white")
+
+ boxplot(countlist[ordre], las = 2,
+ main = paste("Counts distribution per group:", nom1),
+ ylim = c(k, ysup), col = 2, add = TRUE,
+ ylab = "Read counts of detected features")
+
+ cuantos <- sapply(countlist, length)
+ cuantos1 <- which(cuantos == 1)
+ sumant <- sapply(countlist, sum, na.rm = TRUE)
+ sumant0 <- which(sumant == 0)
+ cuantosNA <- intersect(cuantos1, sumant0)
+ cuantos[cuantosNA] <- 0
+ mtext(cuantos[ordre], 3, at = 1:length(countlist), cex = 1, las = 2)
+
+
+ # txt file
+ write.table(unlist(countlist), file.path(opt$dirOut, "Counts_boxplot_1.txt"),
+ sep = "\t", quote = FALSE, col.names = FALSE, row.names = TRUE)
+
+
+
+ if (!is.null(misdatos2)) {
+
+ write.table(unlist(countlist2), file.path(opt$dirOut, "Counts_boxplot_2.txt"),
+ sep = "\t", quote = FALSE, col.names = FALSE, row.names = TRUE)
+
+ boxplot(countlist2[ordre], las = 2,
+ main = paste("Counts distribution per group:", nom2),
+ ylim = c(k, ysup), col = 4)
+
+ rect(par("usr")[1], par("usr")[3], par("usr")[2], par("usr")[4],
+ col = "white")
+
+ boxplot(countlist2[ordre], las = 2,
+ main = paste("Counts distribution per group:", nom2),
+ ylim = c(k, ysup), col = 4, add = TRUE,
+ ylab = "Read counts of detected features")
+
+ cuantos <- sapply(countlist2, length)
+ cuantos1 <- which(cuantos == 1)
+ sumant <- sapply(countlist2, sum, na.rm = TRUE)
+ sumant0 <- which(sumant == 0)
+ cuantosNA <- intersect(cuantos1, sumant0)
+ cuantos[cuantosNA] <- 0
+ mtext(cuantos[ordre], 3, at = 1:length(countlist2), cex = 1, las = 2)
+
+ }
+
+ garbage <- dev.off()
+
+
+
+
+
+
+############################################################################
+
+
+
+#### COUNTS DISTRIBUTION -- per BIOTYPE + sequencing depth
+
+ countbio.mine <- countsbio.dat(misdatos1, misdatos2, k = k,
+ infobio = myinfo, biotypes = biotipus)
+
+ mytable1 <- c("depth", "--", countbio.mine$depth1)
+ mytable2 <- c("depth", "--", countbio.mine$depth2)
+
+ mystats <- c("lower_whisker", "lower_quartile", "median", "upper_quartile", "upper_whisker")
+
+ for (i in 1:length(biotipus)) {
+
+ mytable1 <- rbind(mytable1,
+ cbind(mystats, names(countbio.mine$cond1)[i],
+ sapply(countbio.mine$cond1[[i]],
+ function(x) { boxplot(x, plot = FALSE)$stats })))
+ mytable1 <- rbind(mytable1, c("number", names(countbio.mine$cond1)[i],
+ sapply(countbio.mine$cond1[[i]],
+ function(x) { boxplot(x, plot = FALSE)$n })))
+
+ mytable2 <- rbind(mytable2,
+ cbind(mystats, names(countbio.mine$cond2)[i],
+ sapply(countbio.mine$cond2[[i]],
+ function(x) { boxplot(x, plot = FALSE)$stats })))
+ mytable2 <- rbind(mytable2, c("number", names(countbio.mine$cond2)[i],
+ sapply(countbio.mine$cond2[[i]],
+ function(x) { boxplot(x, plot = FALSE)$n })))
+
+
+ plot.png( paste0( names(biotipus)[i],"_boxplot.png" ) )
+ #png(paste(opt$dirOut, names(biotipus)[i],"_boxplot.png", sep = ""),
+ # width = 3*480, height = 3*480, pointsize = 3*12)
+
+ countbio.plot(depth1 = countbio.mine$depth1,
+ depth2 = countbio.mine$depth2,
+ sat1 = countbio.mine$cond1[[i]],
+ sat2 = countbio.mine$cond2[[i]],
+ bionum = countbio.mine$bionum[[i]], las = 1, cex = 1.2,
+ legend = c(nom1, nom2),
+ main = names(biotipus)[i],
+ ylab = "Read counts of detected features",
+ xlab = "Sequencing Depth (million reads)")
+
+
+
+ garbage <- dev.off()
+ }
+
+ colnames(mytable1) <- c("stat", "group", paste("depth", 1:length(countbio.mine$depth1), sep = ""))
+
+ write.table(mytable1, file.path(opt$dirOut, "CountsPerGroup_boxplot_1.txt"),
+ sep = "\t", quote = FALSE, col.names = TRUE, row.names = FALSE)
+
+
+ if(!is.null(misdatos2)) {
+
+ colnames(mytable2) <- c("stat", "group", paste("depth", 1:length(countbio.mine$depth2), sep = ""))
+
+ write.table(mytable2, file.path(opt$dirOut, "CountsPerGroup_boxplot_2.txt"),
+ sep = "\t", quote = FALSE, col.names = TRUE, row.names = FALSE)
+
+ }
+
+ }
+
+
+
+
+
+
+############################################################################
+
+
+#### CORRELATION PLOT
+
+
+if (!is.null(misdatos2)) {
+
+ plot.png("correlation_plot.png")
+ #png(paste(opt$dirOut, "correlation_plot.png", sep = ""),
+ # width = 3*480, height = 3*480, pointsize = 3*12)
+
+ cor.plot.2D(misdatos1, misdatos2, noplot = 0.001, log.scale = TRUE,
+ xlab = paste("log2(", nom1, "+1)", sep = ""),
+ ylab = paste("log2(", nom2, "+1)", sep = ""))
+
+ garbage <- dev.off()
+
+ }
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/cli/scripts/utils.r b/cli/scripts/utils.r
new file mode 100644
index 0000000..5a99ae1
--- /dev/null
+++ b/cli/scripts/utils.r
@@ -0,0 +1,226 @@
+#if(!require("Repitools",quietly=T)) { source("http://bioconductor.org/biocLite.R"); biocLite("Repitools") }
+suppressPackageStartupMessages(library(Repitools))
+#if(!require("GenomicFeatures",quietly=T)) { source("http://bioconductor.org/biocLite.R"); biocLite("GenomicFeatures") }
+suppressPackageStartupMessages(require(GenomicFeatures,quietly=T))
+suppressPackageStartupMessages(require(rtracklayer,quietly=T))
+
+buildAnnotation <- function(regions=NULL){
+#TODO: Make it work for different organisms
+#TODO: Allow to pass a file with the annotation previously dowloaded
+#TODO: Think how to construct the annotation for other regions like CpG islands
+
+
+ if(is.null(regions)){
+ stop("ERROR! regions cannot be NULL!")
+ }else{
+ print(paste("STATUS:Reading regions from",regions))
+ annot <- import(regions,asRangedData=F)
+ print(paste("Read",length(annot[,1]),"regions"))
+ }
+
+ annot
+}
+
+txdb2GRanges <- function(txdb){
+ tmp=unfactor(as.list(txdb))
+ # TODO: Potential problem with the chromosome names! Right now it is forcing to the format chr1 but maybe that the bam file has other staff
+ annot=GRanges(seqnames=paste("chr",tmp$transcripts$tx_chrom,sep=""),ranges=IRanges(start=tmp$transcripts$tx_start,end=tmp$transcripts$tx_end),strand=tmp$transcripts$tx_strand,tx_name=tmp$transcripts$tx_name,tx_id=tmp$transcripts$tx_id,gene_id=tmp$genes$gene_id[match(tmp$transcripts$tx_id,tmp$genes$tx_id)])
+ g2tx=values(annot)
+ #Now just keep the longest transcript, that's what we want
+ tmp=width(annot)
+ names(tmp)=values(annot)$tx_name
+ tmp=split(tmp,values(annot)$gene_id)
+ tmp=lapply(tmp,function(u){u[which.max(u)]})
+ tmp=sapply(tmp,names)
+ annot=annot[match(tmp,values(annot)$tx_name)]
+
+ annot
+}
+
+getBamFilesFromDFLine <- function(sample){
+ #print("In getBamFilesFromDFLine")
+ #print(sample)
+ bam.files <- c()
+ for(i in c("medips","input")){
+ #print(paste(i,sample[i]))
+ bam.files <- if(!is.na(sample[i])) c(bam.files, sample[i]) else bam.files
+ }
+ bam.files
+}
+
+getDataFromMatrix <- function(sample, names, with.NA=F){
+ #print("In getDataFromMatrix")
+ ret <- c()
+ for(i in 1:nrow(sample)){
+ for(n in names){
+ ret <- if(with.NA | !is.na(sample[i,n])) c(ret,as.character(sample[i,n])) else ret
+ }
+ }
+ ret
+
+}
+
+getBamFilesFromMatrix <- function(sample){
+ #OBSOLETE: Use getDataFromMatrix(sample1,c("medips","input"))
+ ret -> getDataFromMatrix(sample1,c("medips","input"))
+ ret
+}
+
+#TODO: Allow to pass the design
+#TODO: Parse from the xml the paramenters up,down,freq,s.width
+#TODO: Use the replicates and compose them
+buildFeatureScores <- function(grl.stored=NULL, sample1=NULL, sample2=NULL, design=NULL, annot, up=2000,down=500,freq=100,s.width=300,dist="base"){
+# Attention!!! If grl.stored is used, the variable for the GRangeList has to be called grl
+ if(!is.null(grl.stored)){
+ #print(paste("Loading",grl.stored))
+ load(grl.stored)
+ sample.names <- names(grl)
+ }else{
+ medips.files1 <- getDataFromMatrix(sample1,c("medips"))
+ sample.types <- c(getDataFromMatrix(sample1,c("sample.name")))
+ input.files1 <- getDataFromMatrix(sample1,c("input"))
+ sample.types <- c(sample.types, rep(paste(getDataFromMatrix(sample1,c("sample.name"))[1],"input",sep="-"),length(input.files1)))
+ #medips.files2 <- getDataFromMatrix(sample2,c("medips"))
+ #sample.types <- c(sample.types, getDataFromMatrix(sample2,c("sample.name")))
+ #input.files2 <- getDataFromMatrix(sample2,c("input"))
+ #sample.types <- c(sample.types, rep(paste(getDataFromMatrix(sample2,c("sample.name"))[1],"input",sep="-"),length(input.files1)))
+ #print("sample.types")
+ #print(sample.types)
+
+ #bam.files <- c(medips.files1,input.files1,medips.files2,input.files2)
+
+ bam.files <- c(medips.files1,input.files1)
+
+ #bam.files <- c(getDataFromMatrix(sample1,c("medips","input")),getDataFromMatrix(sample2,c("medips","input")))
+ print("STATUS:Processing BAM files:")
+ #print(bam.files)
+ #bam.names <- c(getDataFromMatrix(sample1,c("replicate.name")),getDataFromMatrix(sample2,c("replicate.name")))
+ bam.names <- c( getDataFromMatrix(sample1,c("replicate.name") ) )
+
+ #print("bam.names")
+ #print(bam.names)
+ granges <- lapply(bam.files,BAM2GRanges)
+ grl <- mergeReplicates(GRangesList(granges),sample.types)
+ names(grl) <- unique(sample.types) # With unique we remove the keep only one name per replicate
+ #sample.names <- c(getDataFromMatrix(sample1,c("sample.name"))[1],getDataFromMatrix(sample2,c("sample.name"))[1])
+ sample.names <- c(getDataFromMatrix(sample1,c("sample.name"))[1])
+ #print("sample.names")
+ #print(sample.names)
+ }
+ print("STATUS:Building feature scores:")
+ #print(paste("Building featureScores for",names(grl),"up =",up,"down =",down,"freq =",freq,"s.width =",s.width))
+
+fs <- featureScores(grl,annot,up=up,down=down,freq=freq,s.width=s.width,verbose=TRUE,dist=dist)
+
+ print("STATUS: Features scores built")
+ if (is.null(design)){
+ #print("TODO! Remove this. Right now it does the default behaviour (substract 1-2 and 3-4)")
+ #l.forScores <- list(tables(fs)[[1]] - tables(fs)[[2]], tables(fs)[[3]] - tables(fs)[[4]])
+ l.forScores <- list(tables(fs)[[1]] - tables(fs)[[2]])
+
+ fs at scores <- l.forScores
+ names(fs) <- sample.names
+ }else{
+ print("TODO! Consider different designs!")
+ }
+ fs
+}
+
+
+heatmapCluster <- function(featureScores=NULL,grl.stored=NULL,design=NULL,ma.file=NULL,
+ expr.threshold=NULL,n.clusters=c(25),dirOut,expName,transcripts=NULL, plot.type='heatmap'){
+
+ if (!is.null(grl.stored)){
+ if (!is.null(transcripts)){
+
+ annot <- buildAnnotation(transcripts=transcripts)
+ }else{
+ stop("TODO! Load the annotation file from the file system. Precompute it!")
+ }
+ fs = buildFeatureScores(grl.stored=grl.stored,annot=annot)
+ }
+ else{
+ fs = featureScores
+ }
+
+ if(is.null(expr.threshold)){
+ expr.threshold <- c(0)
+ }
+
+ for(th in expr.threshold){
+ for(cl in n.clusters){
+ if(!is.null(ma.file)){
+ ma <- read.table(ma.file, header=T,row.names=1)
+ expr <- ma[annot at elementMetadata$tx_name,1]
+ expr[which((expr >= -th & expr <= th))] <- NA
+ }else{
+ expr=NULL
+ }
+
+ if (is.null(design)){
+ #l.forScores <- list(tables(featureScores)[[1]] - tables(featureScores)[[2]], tables(featureScores)[[3]] - tables(featureScores)[[4]])
+ #featureScores at scores <- l.forScores
+ #file.name <- paste(expName,th,cl,sep="-")
+ file.name <- paste(expName,". ",cl," Clusters",sep="") # We do not support the microarray at this moment
+ print(paste("Creating",file.path(dirOut,paste(file.name,".jpg",sep=""))))
+ jpeg(file.path(dirOut,paste(file.name,".jpg",sep="")),quality=100,h=2400,w=800)
+ cp=clusterPlots(fs,n.clusters=cl,expr=expr,plot.type=plot.type,t.name=file.name)
+ dev.off()
+ browser()
+ #cl <- as.data.frame(getClusters(cp))
+ report.path <- file.path(dirOut,paste(file=paste(file.name,".txt",sep="")))
+ cluster.levels = levels(clusters(cp))
+ for ( cluster.level in cluster.levels ) {
+ write(paste("START_CLUSTER=",cluster.level), report.path, append = TRUE )
+ t <- attr(annot[which(clusters(cp) == cluster.level)], "elementMetadata")
+ lapply(t, write, report.path, append=TRUE, ncolumns=1000)
+ write("END_CLUSTER\n", report.path, append = TRUE)
+ }
+ print(report.path)
+ # write.table(cl, report.path)
+ }
+ cl
+ }
+ }
+
+}
+# For getting a matrx (is it?) from the ClusterPlot cp
+getClusters <- function(cp){
+ cl <- clusters(cp)
+ ids <- values(cp at anno)$gene_id
+ an<-cbind(c,ids)
+ #print(head(an))
+ an
+}
+
+printClusters <- function() {
+ write(cl, c)
+}
+
+# From functions.R of the NAR paper
+unfactor=function(var){
+ if (is.factor(var)){
+ tmp=names(var)
+ tmpopt=getOption("warn")
+ options(warn=-1)
+ out=as.numeric(levels(var))[as.integer(var)]
+ options(warn=tmpopt)
+ if(any(is.na(out)) & any(is.na(out)!=is.na(var))){
+ out=as.character(levels(var))[as.integer(var)]
+ }
+ names(out)=tmp
+ }else if(is.data.frame(var)){
+ #Have to use a loop, since calling apply will return a matrix
+ out=var
+ for(i in 1:dim(var)[2]){
+ out[,i]=unfactor(var[,i])
+ }
+ }else if(is.list(var)){
+ #Mmmmm, recursion
+ out=lapply(var,unfactor)
+ }else{
+ #The default option
+ out=var
+ }
+ return(out)
+}
diff --git a/cli/species/human.ens68.txt b/cli/species/human.ens68.txt
new file mode 100644
index 0000000..8165ccf
--- /dev/null
+++ b/cli/species/human.ens68.txt
@@ -0,0 +1,55076 @@
+"biotypes" "length" "gc"
+"ENSG00000111671" "protein_coding" 1004 59.25
+"ENSG00000212040" "miRNA" 78 38.46
+"ENSG00000110514" "protein_coding" 2762 55.25
+"ENSG00000184381" "protein_coding" 988 59.92
+"ENSG00000086015" "protein_coding" 2089 53.33
+"ENSG00000211769" "TR_J_gene" 48 66.67
+"ENSG00000211768" "TR_J_gene" 50 60.00
+"ENSG00000204228" "protein_coding" 961 59.83
+"ENSG00000255071" "processed_transcript" 743 53.03
+"ENSG00000211767" "TR_J_gene" 49 59.18
+"ENSG00000211766" "TR_J_gene" 46 69.57
+"ENSG00000211765" "TR_J_gene" 51 56.86
+"ENSG00000211764" "TR_J_gene" 50 60.00
+"ENSG00000169740" "protein_coding" 874 48.89
+"ENSG00000215869" "processed_transcript" 1225 56.00
+"ENSG00000261609" "lincRNA" 4185 45.84
+"ENSG00000261608" "pseudogene" 778 60.41
+"ENSG00000261607" "pseudogene" 271 50.92
+"ENSG00000261606" "processed_transcript" 4960 58.99
+"ENSG00000215866" "lincRNA" 1096 54.41
+"ENSG00000261604" "antisense" 1384 36.16
+"ENSG00000215860" "pseudogene" 2424 45.81
+"ENSG00000261602" "antisense" 575 38.26
+"ENSG00000261600" "lincRNA" 528 26.52
+"ENSG00000266468" "miRNA" 59 59.32
+"ENSG00000266469" "antisense" 860 46.40
+"ENSG00000168298" "protein_coding" 785 60.38
+"ENSG00000266462" "miRNA" 70 54.29
+"ENSG00000266463" "miRNA" 64 75.00
+"ENSG00000266460" "lincRNA" 597 46.06
+"ENSG00000266461" "miRNA" 84 63.10
+"ENSG00000266466" "antisense" 965 49.33
+"ENSG00000266467" "misc_RNA" 298 55.37
+"ENSG00000266465" "miRNA" 70 54.29
+"ENSG00000262558" "antisense" 913 57.72
+"ENSG00000262559" "protein_coding" 824 47.03
+"ENSG00000212072" "miRNA" 104 34.62
+"ENSG00000185436" "protein_coding" 1825 58.73
+"ENSG00000212070" "miRNA" 107 34.58
+"ENSG00000238413" "misc_RNA" 112 44.64
+"ENSG00000212076" "miRNA" 70 54.29
+"ENSG00000262557" "3prime_overlapping_ncrna" 2929 38.07
+"ENSG00000262554" "pseudogene" 208 51.92
+"ENSG00000212075" "miRNA" 91 35.16
+"ENSG00000225108" "pseudogene" 1456 65.18
+"ENSG00000184384" "protein_coding" 5820 47.46
+"ENSG00000248287" "pseudogene" 247 45.34
+"ENSG00000225100" "pseudogene" 326 58.59
+"ENSG00000225101" "pseudogene" 798 50.80
+"ENSG00000225102" "antisense" 276 38.77
+"ENSG00000225105" "processed_transcript" 302 53.31
+"ENSG00000225106" "antisense" 808 56.19
+"ENSG00000225107" "lincRNA" 833 42.98
+"ENSG00000221489" "miRNA" 80 47.50
+"ENSG00000221488" "miRNA" 94 29.79
+"ENSG00000226455" "antisense" 647 52.70
+"ENSG00000226454" "sense_intronic" 421 49.17
+"ENSG00000226453" "lincRNA" 822 45.62
+"ENSG00000226450" "pseudogene" 1490 63.15
+"ENSG00000221484" "miRNA" 113 43.36
+"ENSG00000221487" "miRNA" 116 33.62
+"ENSG00000226458" "sense_intronic" 941 39.96
+"ENSG00000250334" "lincRNA" 2066 41.75
+"ENSG00000183055" "pseudogene" 704 36.65
+"ENSG00000183054" "protein_coding" 2592 41.54
+"ENSG00000255076" "sense_intronic" 309 45.63
+"ENSG00000181562" "protein_coding" 927 42.39
+"ENSG00000203871" "protein_coding" 1477 46.62
+"ENSG00000250566" "pseudogene" 973 38.23
+"ENSG00000250567" "lincRNA" 555 36.22
+"ENSG00000250564" "lincRNA" 669 42.90
+"ENSG00000250565" "protein_coding" 1318 48.10
+"ENSG00000250562" "pseudogene" 214 40.65
+"ENSG00000250563" "pseudogene" 1378 51.31
+"ENSG00000187961" "protein_coding" 1429 64.36
+"ENSG00000250561" "pseudogene" 952 49.68
+"ENSG00000125409" "protein_coding" 985 49.60
+"ENSG00000187969" "protein_coding" 844 51.66
+"ENSG00000250569" "pseudogene" 940 46.81
+"ENSG00000211448" "protein_coding" 1730 47.00
+"ENSG00000220685" "pseudogene" 798 47.85
+"ENSG00000162843" "protein_coding" 2271 41.54
+"ENSG00000168484" "protein_coding" 705 58.68
+"ENSG00000162849" "protein_coding" 5712 58.10
+"ENSG00000149243" "protein_coding" 1734 60.63
+"ENSG00000221157" "miRNA" 88 44.32
+"ENSG00000221156" "miRNA" 85 25.88
+"ENSG00000221159" "miRNA" 97 50.52
+"ENSG00000184708" "protein_coding" 1756 50.72
+"ENSG00000184709" "protein_coding" 1209 74.69
+"ENSG00000255074" "pseudogene" 512 55.86
+"ENSG00000163462" "protein_coding" 2520 62.26
+"ENSG00000163463" "protein_coding" 955 54.39
+"ENSG00000163464" "protein_coding" 2488 52.41
+"ENSG00000163466" "protein_coding" 904 46.35
+"ENSG00000163467" "protein_coding" 568 49.00
+"ENSG00000163468" "protein_coding" 1124 48.63
+"ENSG00000162599" "protein_coding" 3170 46.32
+"ENSG00000162598" "protein_coding" 1332 45.36
+"ENSG00000162592" "protein_coding" 2213 58.66
+"ENSG00000162591" "protein_coding" 2572 67.44
+"ENSG00000029363" "protein_coding" 2552 38.24
+"ENSG00000162595" "protein_coding" 1801 48.21
+"ENSG00000162594" "protein_coding" 2077 38.94
+"ENSG00000263609" "lincRNA" 830 41.29
+"ENSG00000263608" "misc_RNA" 248 57.26
+"ENSG00000118640" "protein_coding" 747 53.35
+"ENSG00000263600" "miRNA" 97 36.08
+"ENSG00000263603" "lincRNA" 577 54.53
+"ENSG00000168488" "protein_coding" 1859 57.87
+"ENSG00000263604" "pseudogene" 199 60.80
+"ENSG00000263607" "misc_RNA" 300 51.67
+"ENSG00000263606" "pseudogene" 1124 40.13
+"ENSG00000201465" "snoRNA" 132 48.48
+"ENSG00000259168" "antisense" 723 51.66
+"ENSG00000201467" "snoRNA" 132 46.97
+"ENSG00000201466" "misc_RNA" 102 38.24
+"ENSG00000253141" "lincRNA" 602 48.20
+"ENSG00000115073" "protein_coding" 1359 61.31
+"ENSG00000253143" "lincRNA" 736 42.93
+"ENSG00000253142" "sense_intronic" 898 43.88
+"ENSG00000259161" "pseudogene" 726 43.11
+"ENSG00000259160" "pseudogene" 178 59.55
+"ENSG00000259163" "processed_transcript" 861 43.88
+"ENSG00000259162" "pseudogene" 622 53.47
+"ENSG00000201469" "rRNA" 113 54.87
+"ENSG00000253148" "protein_coding" 1794 32.05
+"ENSG00000259167" "pseudogene" 884 44.34
+"ENSG00000259166" "lincRNA" 513 46.98
+"ENSG00000213853" "protein_coding" 2535 49.64
+"ENSG00000213851" "pseudogene" 897 58.64
+"ENSG00000029534" "protein_coding" 3856 57.65
+"ENSG00000213857" "pseudogene" 1060 58.30
+"ENSG00000213856" "pseudogene" 850 48.00
+"ENSG00000213854" "pseudogene" 900 58.56
+"ENSG00000258597" "pseudogene" 721 51.32
+"ENSG00000213859" "protein_coding" 1879 65.63
+"ENSG00000112685" "protein_coding" 1791 47.11
+"ENSG00000225816" "pseudogene" 697 37.88
+"ENSG00000225814" "pseudogene" 670 50.30
+"ENSG00000225815" "lincRNA" 964 45.25
+"ENSG00000225812" "pseudogene" 298 47.32
+"ENSG00000225813" "pseudogene" 717 58.72
+"ENSG00000225810" "processed_transcript" 811 50.43
+"ENSG00000225811" "antisense" 602 40.37
+"ENSG00000225818" "lincRNA" 496 43.27
+"ENSG00000225819" "antisense" 444 38.51
+"ENSG00000229306" "lincRNA" 323 41.49
+"ENSG00000229307" "processed_transcript" 376 43.62
+"ENSG00000229304" "sense_intronic" 544 41.91
+"ENSG00000229305" "pseudogene" 1075 45.67
+"ENSG00000229302" "pseudogene" 515 38.45
+"ENSG00000229303" "pseudogene" 540 50.00
+"ENSG00000238489" "snRNA" 107 43.93
+"ENSG00000229301" "lincRNA" 528 46.59
+"ENSG00000238487" "snRNA" 63 26.98
+"ENSG00000238486" "snoRNA" 104 42.31
+"ENSG00000238485" "snoRNA" 104 39.42
+"ENSG00000238484" "snoRNA" 104 40.38
+"ENSG00000238483" "snoRNA" 104 37.50
+"ENSG00000238482" "snRNA" 107 37.38
+"ENSG00000238481" "snoRNA" 105 39.05
+"ENSG00000229309" "lincRNA" 290 45.17
+"ENSG00000055070" "protein_coding" 1503 55.92
+"ENSG00000264660" "antisense" 1145 49.12
+"ENSG00000227410" "processed_transcript" 822 65.57
+"ENSG00000227411" "pseudogene" 1225 55.76
+"ENSG00000227412" "pseudogene" 1218 42.53
+"ENSG00000227413" "pseudogene" 355 41.97
+"ENSG00000227415" "processed_transcript" 707 37.91
+"ENSG00000227416" "pseudogene" 429 54.08
+"ENSG00000227417" "pseudogene" 646 44.74
+"ENSG00000227418" "processed_transcript" 1590 34.65
+"ENSG00000155714" "protein_coding" 1246 41.22
+"ENSG00000182010" "protein_coding" 3195 36.92
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diff --git a/cli/species/mouse.ens68.txt b/cli/species/mouse.ens68.txt
new file mode 100644
index 0000000..f410b36
--- /dev/null
+++ b/cli/species/mouse.ens68.txt
@@ -0,0 +1,37316 @@
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+"ENSMUSG00000092210" "protein_coding" 1001 48.35
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diff --git a/doc/Makefile b/doc/Makefile
new file mode 100644
index 0000000..943ff5a
--- /dev/null
+++ b/doc/Makefile
@@ -0,0 +1,161 @@
+# Makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS =
+SPHINXBUILD = sphinx-build
+PAPER =
+BUILDDIR = _build
+
+# Internal variables.
+PAPEROPT_a4 = -D latex_paper_size=a4
+PAPEROPT_letter = -D latex_paper_size=letter
+ALLSPHINXOPTS = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
+# the i18n builder cannot share the environment and doctrees with the others
+I18NSPHINXOPTS = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
+
+.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext
+
+help:
+ @echo "Please use \`make <target>' where <target> is one of"
+ @echo " html to make standalone HTML files"
+ @echo " dirhtml to make HTML files named index.html in directories"
+ @echo " singlehtml to make a single large HTML file"
+ @echo " pickle to make pickle files"
+ @echo " json to make JSON files"
+ @echo " htmlhelp to make HTML files and a HTML help project"
+ @echo " qthelp to make HTML files and a qthelp project"
+ @echo " devhelp to make HTML files and a Devhelp project"
+ @echo " epub to make an epub"
+ @echo " latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
+ @echo " latexpdf to make LaTeX files and run them through pdflatex"
+ @echo " text to make text files"
+ @echo " man to make manual pages"
+ @echo " texinfo to make Texinfo files"
+ @echo " info to make Texinfo files and run them through makeinfo"
+ @echo " gettext to make PO message catalogs"
+ @echo " changes to make an overview of all changed/added/deprecated items"
+ @echo " linkcheck to check all external links for integrity"
+ @echo " doctest to run all doctests embedded in the documentation (if enabled)"
+
+clean:
+ -rm -rf $(BUILDDIR)/*
+
+html:
+ $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
+ @echo
+ @echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
+
+html2:
+ $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
+ @echo
+ cp -r plasmodium $(BUILDDIR)/html
+ cp -r plasmodium_RNA-seq $(BUILDDIR)/html
+ cp -r count-data $(BUILDDIR)/html
+ @echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
+
+dirhtml:
+ $(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
+ @echo
+ @echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
+
+singlehtml:
+ $(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
+ @echo
+ @echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
+
+pickle:
+ $(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
+ @echo
+ @echo "Build finished; now you can process the pickle files."
+
+json:
+ $(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
+ @echo
+ @echo "Build finished; now you can process the JSON files."
+
+htmlhelp:
+ $(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp
+ @echo
+ @echo "Build finished; now you can run HTML Help Workshop with the" \
+ ".hhp project file in $(BUILDDIR)/htmlhelp."
+
+qthelp:
+ $(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp
+ @echo
+ @echo "Build finished; now you can run "qcollectiongenerator" with the" \
+ ".qhcp project file in $(BUILDDIR)/qthelp, like this:"
+ @echo "# qcollectiongenerator $(BUILDDIR)/qthelp/Qualimap.qhcp"
+ @echo "To view the help file:"
+ @echo "# assistant -collectionFile $(BUILDDIR)/qthelp/Qualimap.qhc"
+
+devhelp:
+ $(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
+ @echo
+ @echo "Build finished."
+ @echo "To view the help file:"
+ @echo "# mkdir -p $$HOME/.local/share/devhelp/Qualimap"
+ @echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/Qualimap"
+ @echo "# devhelp"
+
+epub:
+ $(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
+ @echo
+ @echo "Build finished. The epub file is in $(BUILDDIR)/epub."
+
+latex:
+ $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+ @echo
+ @echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex."
+ @echo "Run \`make' in that directory to run these through (pdf)latex" \
+ "(use \`make latexpdf' here to do that automatically)."
+
+latexpdf:
+ $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+ @echo "Running LaTeX files through pdflatex..."
+ $(MAKE) -C $(BUILDDIR)/latex all-pdf
+ @echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
+
+text:
+ $(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text
+ @echo
+ @echo "Build finished. The text files are in $(BUILDDIR)/text."
+
+man:
+ $(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man
+ @echo
+ @echo "Build finished. The manual pages are in $(BUILDDIR)/man."
+
+texinfo:
+ $(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
+ @echo
+ @echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo."
+ @echo "Run \`make' in that directory to run these through makeinfo" \
+ "(use \`make info' here to do that automatically)."
+
+info:
+ $(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
+ @echo "Running Texinfo files through makeinfo..."
+ make -C $(BUILDDIR)/texinfo info
+ @echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo."
+
+gettext:
+ $(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale
+ @echo
+ @echo "Build finished. The message catalogs are in $(BUILDDIR)/locale."
+
+changes:
+ $(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
+ @echo
+ @echo "The overview file is in $(BUILDDIR)/changes."
+
+linkcheck:
+ $(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck
+ @echo
+ @echo "Link check complete; look for any errors in the above output " \
+ "or in $(BUILDDIR)/linkcheck/output.txt."
+
+doctest:
+ $(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
+ @echo "Testing of doctests in the sources finished, look at the " \
+ "results in $(BUILDDIR)/doctest/output.txt."
diff --git a/doc/README b/doc/README
new file mode 100644
index 0000000..defc5b2
--- /dev/null
+++ b/doc/README
@@ -0,0 +1,22 @@
+The documentation is written in ReStructuredText and can be generated with Sphinx.
+
+Sphinx can be downloaded from here:
+http://sphinx.pocoo.org/
+
+To generate documentation install Sphinx and use the following commands::
+
+make html
+make pdflatex
+
+
+Note:
+
+To build pdf version on Ubuntu the following packages have to be installed:
+
+ texlive-latex-recommended
+ texlive-latex-extra
+ texlive-fonts-recommended
+
+
+
+
diff --git a/doc/_templates/layout.html b/doc/_templates/layout.html
new file mode 100644
index 0000000..4b0e322
--- /dev/null
+++ b/doc/_templates/layout.html
@@ -0,0 +1,18 @@
+{% extends "!layout.html" %}
+
+{%- block extrahead %}
+{{ super() }}
+<script type="text/javascript">
+
+ var _gaq = _gaq || [];
+ _gaq.push(['_setAccount', 'UA-31924634-1']);
+ _gaq.push(['_trackPageview']);
+
+ (function() {
+ var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
+ ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
+ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
+ })();
+
+</script>
+{% endblock %}
diff --git a/doc/analysis.rst b/doc/analysis.rst
new file mode 100644
index 0000000..067c301
--- /dev/null
+++ b/doc/analysis.rst
@@ -0,0 +1,555 @@
+.. _analysis-types:
+
+Analysis types
+==============
+
+.. _bamqc:
+
+BAM QC
+------
+
+BAM QC reports information for the evaluation of the quality of the provided alignment data (a BAM file). In short, the basic statistics of the alignment (number of reads, coverage, GC-content, etc.) are summarized and a number of useful graphs are produced. This analysis can be performed with any kind of sequencing data, e.g. whole-genome sequencing, exome sequencing, RNA-seq, ChIP-seq, etc.
+
+In addition, it is possible to provide an annotation file so the results are computed for the reads mapping inside (and optionally outside) of the corresponding genomic regions, which can be especially useful for evaluating *target-enrichment* sequencing studies.
+
+To start a new BAM QC analysis activate main menu item :menuselection:`File --> New Analysis --> BAM QC`.
+
+
+Examples
+^^^^^^^^
+
+- `Whole-genome sequencing: HG00096.chrom20.bam <http://kokonech.github.io/qualimap/HG00096.chr20_bamqc/qualimapReport.html>`_. HTML report for sample alignment file from `1000 Genomes project <http://1000genomes.org>`_.
+
+
+- `Whole-genome sequencing: ERRR089819.bam <http://kokonech.github.io/qualimap/ERR089819_report.pdf>`_. PDF report created using the whole-genome sequencing data of *Caenorhabditis elegans* from the following `study <http://www.ebi.ac.uk/ena/data/view/ERP000975>`_.
+
+- See the :ref:`Sample data <samples>` section for more details about the data used in the examples.
+
+
+Input Parameters
+^^^^^^^^^^^^^^^^
+
+:guilabel:`BAM file`
+ Path to the sequence alignment file in **BAM format**. Note, that the BAM file has to be **sorted by chromosomal coordinates**. Sorting can be performed with `samtools sort <http://samtools.sourceforge.net/>`_.
+
+:guilabel:`Analyze regions`
+ Activating this option allows the analysis of the alignment data for the **regions of interest**.
+
+:guilabel:`Regions file(GFF/BED file)`
+ The path to the annotation file that defines the regions of interest. The file must be **tab-separated** and have `GFF <http://genome.ucsc.edu/FAQ/FAQformat.html#format3>`_/`GTF <http://genome.ucsc.edu/FAQ/FAQformat.html#format4>`_ or `BED <http://genome.ucsc.edu/FAQ/FAQformat.html# format1>`_ format.
+
+.. note:: A typical problem when working with human genome annotations is the inconsistency between chromosome names due to "chr" prefix. For example, Ensemble annotations do not include this prefix, while UCSC annotations do. This can become a problem when asscociating regions file with the BAM alignment. Qualimap handles this problem: if the reference sequence of a region has "chr" prefix, it tries to search for sequence name with prefix and without prefix.
+
+:guilabel:`Library strand specificity`
+
+ The sequencing protocol strand specificity: *non-strand-specific*, *forward-stranded* or *reverse-stranded*. This information is required to calculate the number of **correct strand** reads.
+
+:guilabel:`Analyze outside regions`
+ If checked, the information about the **reads** that are **mapped outside** of the regions of interest will be also computed and shown in a separate section.
+
+:guilabel:`Chromosome limits`
+ If selected, vertical dotted lines will be placed at the beginning of each chromosome according to the information found in the header of the BAM file.
+
+.. _input-gc-content:
+
+:guilabel:`Compare GC content distribution with`
+ This allows to **compare** the **GC distribution** of the sample with the selected pre-calculated **genome** GC distribution. Currently two genome distributions are available: human (hg19) and mouse (mm9). More species will be included in future releases.
+
+:guilabel:`Skip duplicates`
+ This option allows to skip duplicated alignments from analysis. If the duplicates are not flagged in BAM file, then they will be detected by Qualimap. Type of skipped duplicates will be shown in report.
+
+:guilabel:`Detect overlapping paired-end reads`
+ In case of small insert size the paired-end read alignmetns might overlap in high proportion. Using this option detection of overlapping pairs can be activated. Additionally, adapted mean coverage is calcualted based on extraction of pair overlap-region.
+
+Advanced parameters
+"""""""""""""""""""
+
+:guilabel:`Number of windows`
+ Number of **windows** used to **split** the reference **genome**. This value is used for computing the graphs that plot information across the reference. Basically, reads falling in the same window are aggregated in the same bin. The higher the number, the bigger the resolution of the plots but also longer time will be used to process the data. By default 400 windows are used.
+
+:guilabel:`Homopolymer size`
+ Only homopolymers of this size or larger will be considered when estimating homopolymer indels count.
+
+:guilabel:`Number of threads`
+ In order to speed up the computation, the BAM QC analysis **computation** can be performed **in parallel** on a multicore system using the given number of threads. More information on the parallelization of qualimap can be found in :ref:`FAQ <faq>`. The default number of threads equals number of available processors.
+
+:guilabel:`Size of the chunk`
+ In order to **reduce the load of I/O**, reads are analyzed in chunks. Each chunk contains the selected number of reads which will be loaded into memory and analyzed by a single thread. Smaller numbers may result in lower performance, but also the memory consumption will be reduced. The default value is 1000 reads.
+
+
+Output
+^^^^^^
+
+:guilabel:`Summary`
+
+ **Basic information** and statistics for the alignment data. The following sections are available:
+
+ *Globals*
+
+ This section contains information about the total number of reads, number of mapped reads, paired-end mapping performance, read length distribution, number of clipped reads and duplication rate (estimated from the start positions of read alignments).
+
+ *ACGT Content*
+
+ Nucleotide content and GC percentage in the mapped reads.
+
+ *Coverage*
+
+ Mean and standard deviation of the coverage depth.
+
+ *Mapping quality*
+
+ Mean mapping quality of the mapped reads.
+
+ *Insert size*
+
+ Mean, standard deviation and percentiles of the insert size distribution if applicable. The features are computed based on the TLEN field of the SAM file.
+
+ *Mismatches and indels*
+
+ The section reports general alignment error rate (computed as a ratio of total collected edit distance to the number of mapped bases), total number of mismatches and total number of indels (computed from the CIGAR values). Additionally fraction of the homopolymer indels among total indels is provided. Note, the error rate and mismatches metrics are based on optional fields of a SAM record (**NM** for edit distance, **MD** for mismatches). The features are not reported if these fields [...]
+
+ *Chromosome stats*
+
+ Number of mapped bases, mean and standard deviation of the coverage depth for each chromosome as defined by the header of the SAM file.
+
+ For region-based analysis the information is given inside of regions, including some additional information like, for example, number of correct strand reads.
+
+:guilabel:`Input`
+
+ Here one can check the **input data** and the **parameters** used for the analysis.
+
+:guilabel:`Coverage Across Reference`
+
+ This plot consists of two figures. The upper figure provides the **coverage distribution** (red line) and coverage deviation across the reference sequence. The coverage is measured in *X* [#X]_. The lower figure shows **GC content** across reference (black line) together with its average value (red dotted line).
+
+:guilabel:`Coverage Histogram`
+
+ Histogram of the number of **genomic locations** having a given **coverage rate**. The bins of the *x*-axis are conveniently scaled by aggregating some coverage values in order to produce a representative histogram also in presence of the usual NGS peaks of coverage.
+
+:guilabel:`Coverage Histogram (0-50X)`
+
+ Histogram of the number of **genomic locations** having a given **coverage rate**. In this graph genome locations with a coverage greater than **50X** are grouped into the last bin. By doing so a higher resolution of the most common values for the coverage rate is obtained.
+
+
+:guilabel:`Genome Fraction Coverage`
+
+ Provides a visual way of knowing how much **reference** has been **sequenced** with **at least** a given **coverage rate**. This graph should be interpreted as in this example:
+
+ If one aims a coverage rate of **at least 25X** (*x*-axis), how much of reference (*y*-axis) will be considered? The answer to this question in the case of the whole-genome sequencing `provided example <http://qualimap.bioinfo.cipf.es/samples/ERR089819_result/qualimapReport.html#genome_coverage_quotes.png>`_ is **~83%**.
+
+:guilabel:`Duplication Rate Histogram`
+
+ This plot shows the **distribution** of **duplicated** read **starts**. Due to several factors (e.g. amount of starting material, sample preparation, etc) it is possible that the same **fragments** are **sequenced several times**. For some experiments where enrichment is used (e.g. ChIP-seq ) this is expected at some *low* rate. If most of the reads share the exact same genomic positions there is very likely an associated bias.
+
+
+:guilabel:`Mapped Reads Nucleotide Content`
+
+ This plot shows the **nucleotide content per position** of the **mapped reads**.
+
+:guilabel:`Mapped Reads GC Content Distribution`
+
+ This graph shows the distribution of **GC content** per **mapped read**. If compared with a precomputed :ref:`genome distribution <input-gc-content>`, this plot allows to check if there is a shift in the GC content.
+
+:guilabel:`Mapped Reads Clipping Profile`
+
+ Represents the percentage of clipped bases across the reads. The clipping is detected via SAM format CIGAR codes ‘H’ (hard clipping) and ‘S’ (soft clipping). In addition, the total number of clipped reads can be found in the report Summary. The plot is not shown if there are no clipped-reads are found. Total number of clipped reads can be found in :guilabel:`Summary`. `Example <http://qualimap.bioinfo.cipf.es/samples/HG00096.chrom20_result/qualimapReport.html#genome_reads_clipping_prof [...]
+
+
+:guilabel:`Homopolymer Indels`
+
+ This bar plot shows separately the number of indels that are within a **homopolymer** of A's, C's, G's or T's together with the number of **indels** that are not within a homopolymer. Large numbers of homopolymer indels may indicate a problem in a sequencing process. An indel is considered homopolymeric if it is found within a homopolymer (defined as at least 5 equal consecutive bases). Owing to the fact that Qualimap works directly from BAM files (and not from reference genomes), we m [...]
+ Indel statistics cam be found in a dedicated section of the Summary report.
+
+ This chart is not shown if the sample doesn't contain any indels.
+
+
+:guilabel:`Mapping Quality Across Reference`
+
+ This plot provides the **mapping quality** distribution **across the reference**. To construct the plot mean mapping quality is computed for each window.
+
+:guilabel:`Mapping Quality Histogram`
+
+ Histogram of the number of **genomic locations** having a given **mapping quality**. To construct the histogram mean mapping quality is computed at each genome position with non-zero coverage and collected. According to Specification of the `SAM format <http://samtools.sourceforge.net/SAM1.pdf>`_ the range for the mapping quality is [0-255].
+
+
+:guilabel:`Insert Size Across Reference`
+
+ This plot provides the **insert size** distribution **across the reference**. Insert size is collected from the SAM alignment field TLEN. Only positive values are taken into account. To construct the plot mean insert size is computed for each window.
+
+:guilabel:`Insert Size Histogram`
+
+ Histogram of **insert size** distribution. To construct the histogram all collected insert size values are applied.
+
+
+.. _rnaseqqc:
+
+RNA-seq QC
+----------
+
+RNA-seq QC reports quality control metrics and bias estimations which are specific for whole transcriptome sequencing, including reads genomic origin, junction analysis, transcript coverage and 5'-3' bias computation. This analysis could be applied as a complementary tool together with :ref:`BAM QC<bamqc>` and additionally to produce gene counts for further analysis with :ref:`Counts QC <countsqc>`.
+
+To start a new RNA-seq QC analysis activate main menu item :menuselection:`File --> New Analysis --> RNA-seq QC`.
+
+Examples
+^^^^^^^^
+
+- `RNA-seq QC report <http://kokonech.github.io/qualimap/kidney_rnaseqqc/qualimapReport.html>`_. This report was produced using the RNA-seq alignment of *Homo sapiens* kidney sample [Marioni]_ and Ensembl v.64 GTF file.
+- These data can be downloaded from :ref:`here <bam-samples>`.
+
+Input parameters
+^^^^^^^^^^^^^^^^
+
+
+:guilabel:`BAM file`
+ Path to the sequence alignment file in **BAM** format, produced by a splicing-aware aligner similar to `Tophat <http://tophat.cbcb.umd.edu>`_.
+
+:guilabel:`GTF file`
+ Genomic annotations in Ensembl **GTF** format. The corresponding annotations can be downloaded from the `Ensembl website <www.ensembl.org/downloads.html>`_.
+
+.. note:: Only annotations in GTF format are supported for this analysis mode. GTF annotations allow to reconstruct the exon structure of transcripts to compute the coverage. For simple region-based analysis please use BAM QC.
+
+:guilabel:`Library protocol`
+ The strand-specficity of the sequencing library. By default non-strand specific library is assumed.
+
+
+:guilabel:`Paired-end analysis`
+ This option activates counting of pair fragments instead of counting of single reads. Only valid for paired-end sequencing experiments.
+
+:guilabel:`Alignment sorted by name`
+ The paired-end analysis requires the BAM file to be sorted by name. If the BAM file is already sorted by name, then this option should be check, otherwise temporary BAM sorted by name will be created.
+
+:guilabel:`Output counts`
+ If checked, the gene counts will be saved to a specified file.
+
+:guilabel:`Path to counts`
+ Path to the output file with the computed counts.
+
+
+Advanced parameters
+"""""""""""""""""""
+
+:guilabel:`Multi-mapped reads`
+ Select method to count reads that are mapped to several genome locations. By default only **uniquely-mapped-reads** are used to compute counts. However, it is possible to include multimapped reads by activating **proprtional** method. More details :ref:`here <multimapped-reads-count>`.
+
+
+Output
+^^^^^^
+
+:guilabel:`Summary`
+
+ The summary contains the following sections:
+
+ *Reads alignment*
+
+ The assignment of read counts per-category:
+ - total number of mapped reads
+ - total number of alignments
+ - number of secondary alignments (duplicates are marked as SAM flag)
+ - number of non-unique alignments (SAM format "NH" tag of a read is more than one)
+ - number of reads aligned to genes, also without any feature (intronic and intergenic)
+ - number of ambiguous alignments
+ - number of unmapped reads.
+
+ *Transcript coverage profile*
+
+ The profile provides ratios between mean coverage at the 5' region, the 3' region and the whole transcript. The 5' bias is the ratio between mean coverage at the 5' region and the whole transcript, while the 3' bias is the ratio between mean coverage at the 3' region and the whole transcript. 5'-3' bias is the ratio between both biases.
+
+ To compute these values for each transcript mean coverage along with mean coverage in first 100 bp (5' region) and last 100 bp (3'region) are calculated and collected. Afterwards, the collected values are sorted and median is selected from each array to compute the ratios.
+
+ *Reads genomic origin*
+
+ Shows how many alignments fall into exonic, intronic and intergenic regions along with number of intronic/intergenic alignments overlapping exons. Exonic region includes 5'UTR,protein coding region and 3'UTR region.
+
+ *Junction analysis*
+
+ Total number of reads with splice junctions and 10 most frequent junction rates.
+
+:guilabel:`Input`
+
+ Here one can check the **input data** and the **parameters** used for the analysis.
+
+
+:guilabel:`Reads Genomic Origin`
+
+ Pie chart showing how many of read alignments fall into exonic, intronic and intergenic regions.
+
+:guilabel:`Coverage Profile (Total)`
+
+ The plot shows mean coverage profile of the transcripts. All transcripts with non-zero coverage are used to calculate this plot.
+
+:guilabel:`Coverage Profile (Low)`
+
+ The plot shows mean coverage profile of 500 lowest-expressed genes.
+
+:guilabel:`Coverage Profile (Total)`
+
+ The plot shows mean coverage profile of 500 highest-expressed genes.
+
+:guilabel:`Coverage Histogram (0-50x)`
+
+ Coverage of transcripts from 0 to 50X. If certain genes have higher coverage level they are added to the last column (50X).
+
+:guilabel:`Junction Analysis`
+
+ This pie chart shows analysis of junction positions in spliced alignments. **Known** category represents percentage of alignments where both junction sides are known. **Partly known** represents alignments where only one junction side is known. All other alignments with junctions are marked as **Novel**.
+
+
+.. _countsqc:
+
+Counts QC
+---------
+
+In **RNA-seq** experiments, the reads are usually **first mapped** to a reference genome. It is assumed that if the **number of reads** mapping to a certain biological feature of interest (gene, transcript, exon, ...) is sufficient, it can be used as an **estimation** of the **abundance** of that feature in the sample and interpreted as the quantification of the **expression level** of the corresponding region.
+
+These **count data** can be utilized for example to assess differential expression between two or more experimental conditions. Before assessing differential expression analysis, researchers should be aware of some potential **limitations** of RNA-seq data, as for example: Has the **saturation** been reached or more features could be detected by increasing the sequencing depth? Which **type of features** are being detected in the experiment? How good is the **quantification** of expressi [...]
+
+
+Starting from **version 2.0** Counts QC module has been redisigned to work with **multiple samples** under different conditions. The new functionality is based on `NOISeq package <http://www.bioconductor.org/packages/release/bioc/html/NOISeq.html>`_, therefore to use Counts QC it is required to have **R** language along with **NOISeq** and **optparse** packages installed.
+
+To run this analysis activate from the main menu :menuselection:`File --> New Analysis --> Counts QC`.
+
+.. note::
+
+ If count data need to be generated, one can use the provided tool :ref:`compute-counts`.
+
+Example
+^^^^^^^
+
+- RNA-seq counts analysis from 2 experiments can be found :ref:`here <counts-example-output>`
+
+
+- Sample counts data can be downloaded from :ref:`here <counts-samples>`.
+
+Input Parameters
+^^^^^^^^^^^^^^^^
+
+:guilabel:`Samples`
+
+ The input samples can be added using button :guilabel:`Add`.
+
+ For each input sample it is required to provide the following information:
+
+ * **Sample name**. Name of the analyzed sample as it will be used as a legend in the plots.
+
+ * **Path** to the input file containing the counts data for the sample. This must be a **tab-delimited** file with at least **two columns**. First column of the file must contain feature IDs, while other columns should contain counts for features. Rows starting with # symbol and empty lines are ignored.
+
+ * **Data column index**. By default it is assumed that the counts are contained in the second column of the input file. However if the input file contains counts for multiple samples it is possible to define the column corresponding for the sample.
+
+ * **Condition index**. If comparison of conditions is activated, this index defines under which condition was the input sample.
+
+ Each added sample will be shown in **Samples** table. One can edit samples using button :guilabel:`Edit` and remove them using button :guilabel:`Remove`.
+
+
+:guilabel:`Counts threshold`
+
+ In order to **remove** the influence of **spurious reads**, a feature is considered as detected if its corresponding number of counts is **greater than this threshold**. By default, the threshold value is set to 5 counts, meaning that features having less than 5 counts will not be taken into account.
+
+
+:guilabel:`Compare conditions`
+
+ This option allows to compare groups of samples under different conditions. The name of a specific condition can be given using field :guilabel:`Condition name`.
+
+.. note::
+
+ Currently Qualimap allows to compare samples under two conditions. More conditions will be supported in future versions.
+
+:guilabel:`Include feature classification`
+
+ **Optional**. This option enables analysis of distribution of counts among feature groups defined by the biotype. In addition GC-content and length bias will be estimated.
+
+:guilabel:`Species`
+
+ For convinience, Qualimap provides the `Ensembl <http://www.ensembl.org/>`_ annotations for certain species (currently *Human* and *Mouse*). In order to use these annotations, **Ensembl Gene IDs** should be used as the feature IDs on the **count files** (e.g. ENSG00000251282). If this is true, mark the box to enable this option and select the corresponding species. More annotations and species will be made available in future releases.
+
+
+:guilabel:`Info File`
+
+ File containing annotations of the features of the count files. It must be a **four-column** **tab-delimited** text file, with the features names or IDs in the first column, the group (e.g. the biotype from Ensembl database) in the second column, feature length in the third column and feature GC-content in the last column (see `human.ens68.txt <http://kokonech.github.io/qualimap/samples/human.ens68.txt>`_ for an example). Please, make sure that the **features IDs** on this file are t [...]
+
+.. note::
+ To generate info file based on an arbitrary GTF annotations and genome FASTA file, one can use the following `Python script <https://bitbucket.org/kokonech/qualimap/src/master/util/createQualimapInfoFile.py?at=master>`_ available from Qualimap repo.
+
+
+Output
+^^^^^^
+
+Many of plots in Counts QC mode are created using `NOISeq package <http://www.bioconductor.org/packages/release/bioc/html/NOISeq.html>`_. The `NOISeq vignette <http://www.bioconductor.org/packages/release/bioc/vignettes/NOISeq/inst/doc/NOISeq.pdf>`_ contains a lot of useful information about the plots and how to interpret them. Here we provide short explanation of the plots.
+
+Global Plots
+""""""""""""
+
+Plots from this report present a global overview of the counts data and include all samples.
+
+:guilabel:`Counts Density`
+
+ This plot shows density of counts computed from the histogram of log-transformed counts. In order to avoid infinite values in case of zero counts the transformation *log2(expr + 0.5)* is applied, where *expr* is a number of read counts for a given feature. Only log-transformed counts having value greater than 1 are plotted.
+
+
+:guilabel:`Scatterplot Matrix`
+
+ The panel shows a scatterplot along with smoothed line (lower panel) and Pearson correlation coefficients (upper panel) for each pair of samples. Plots are generated using log-transformed counts.
+
+:guilabel:`Saturation`
+
+ This plot provides information about the level of saturation in the samples, so it helps the user to decide if more sequencing is needed and more features could be detected when increasing the number of reads. These are some tips for the interpretation of the plot:
+
+ * The increasing sequencing depth of the sample is represented at the *x*-axis. The maximum value is the real sequencing depth of the sample(s). Smaller sequencing depths correspond to samples randomly generated from the original sample(s).
+ * The curves are associated to the left *y*-axis. They represent the number of detected features at each of the sequencing depths in the *x*-axis. By "detected features" we refer to features with more than *k* counts, where *k* is the *Count threshold* selected by the user.
+ * The bars are associated to the right *y*-axis. They represent the number of newly detected features when increasing the sequencing depth in one million reads at each sequencing depth value.
+
+.. An example for this plot can be seen `here <http://qualimap.bioinfo.cipf.es/samples/counts_result/qualimapReport.html#GlobalSaturation.png>`_.
+
+
+.. TODO: fix this
+
+.. :guilabel:`Samples Correlation`
+
+.. When two samples are provided, this plot determines the **correlation level** between both samples. Due to the often wide range of expression data (counts), a log2-transformation is applied in order to improve the graphical representation. Features not detected in any of the two samples are removed for this analysis. To avoid infinite values in the case of genes with 0 counts in one of the samples, log2(expression + 1) is used. Thus, sample 1 is depicted in X-axis and sample 2 in Y-axis.
+ The colors of the plot should be interpreted as a map. The blue color is the level of the sea and the white color the top of the mountain. Hence, the higher you are over the sea level, the more genes you have in that range of X-Y values.
+ In addition, the title of the plot includes the **Pearson's correlation coefficient**, which indicates if both samples present a linear relationship.
+
+
+:guilabel:`Counts Distribution`
+
+ This box plot shows the global distribution of counts in each sample.
+
+:guilabel:`Features With Low Counts`
+
+ This plot shows the proportion of features with low counts in the samples. Such features are usually less reliable and could be filtered out. In this plot, the bars show the percentage of features within each sample having more than 0 counts per million (CPM), or more than 1, 2, 5 and 10 CPM.
+
+
+Individual Sample Plots
+"""""""""""""""""""""""
+
+Apart from global overview there are plots generated individually for each sample.
+
+:guilabel:`Saturation`
+
+ For each sample, a saturation plot is generated like the one described in :guilabel:`Global Saturation`.
+
+When a **Info File** is provided by the user or annotations are chosen from those supplied by Qualimap, additional series of plots are generated:
+
+:guilabel:`Bio Detection`
+
+ This barplot allows the user to know which kind of features are being detected his sample(s). The *x*-axis shows all the groups included in the annotations file. The gray bars are the percentage of features of each group within the reference genome (or transcriptome, etc.). The striped color bars are the percentages of features of each group detected in the sample with regard to the genome. The solid color bars are the percentages that each group represents in the total detected featur [...]
+
+:guilabel:`Counts Per Biotype`
+
+ A boxplot per each group describes the counts distribution in the given biotype.
+
+:guilabel:`Length Bias`
+
+ The plot describes the relationship between the length of the features and the expression values. The length is divided into bins. Mean expression of features falling into a particular length interval is computed and plotted. A cubic spline regression model is fitted to explain the relation between length and expression. `Coefficient of determination R^2 <http://en.wikipedia.org/wiki/Coefficient_of_determination>`_ and p-value are shown together with regression curve.
+
+:guilabel:`GC Bias`
+
+ The plot describes the relantionship between the GC-content of the features and the expression values. The data for the plot is generated similar to :guilabel:`Length Bias` plot. The GC content divided into beans and then mean expression of features corresponding to given GC interval are computed. The relation between GC-content and expression is investigated using cubic spline regression model.
+
+
+Comparison Plots
+""""""""""""""""
+
+When **Compare conditions** option is selected, additional plots comparing data in groups of samples having the same biological condition or treatment are available.
+
+:guilabel:`Counts Distribution`
+
+ The plot is similar to the one in :guilabel:`Global` report. It compares distributions of **mean** counts across conditions.
+
+:guilabel:`Features With Low Counts`
+
+ The plot is similar to the one in :guilabel:`Global` report. It compares proportions of features with low counts using **mean** counts across conditions.
+
+:guilabel:`Bio Detection`
+
+ The plot is similar to the one in :guilabel:`Indvidual Sample Plots` report. It compares distribution of the detected features for the given biotype for **mean** counts across conditions.
+
+:guilabel:`Length Bias`
+
+ The plot is similar to the one in :guilabel:`Individual Sample Plots` report. It analyzes relation between feature length and expression across conditions.
+
+:guilabel:`GC Bias`
+
+ The plot is similar to the one in :guilabel:`Individual Sample Plots` report. It analyzes realtion between GC-content and expression across conditions.
+
+
+.. _multibamqc:
+
+Multi-sample BAM QC
+-------------------
+
+Very often in genomics one has to work with multiple samples, which could represent sequencing results from either biological replicates or different conditions. For example, to reliably detect significant mutations from sequencing data in cancer it is required to analyze tens or even hundreds of samples from matched normal-tumor data. When performing such large scale experiments it is always important to know if all samples pass the quality controls. To detect possible outliers one can [...]
+
+QualiMap provides an automated solution for this task. Basically, the QC metrics computed in *BAM QC analysis* are combined together for all samples. Additionally **Principal Component Analysis** is performed to analyze variability and detect outliers.
+
+One can apply multi-sample analysis for precomputed results of QualiMap BAM QC or directly for raw BAM files. In latter case firstly BAM QC analysis will be performed for each input file and then multi-sample analysis will be executed.
+
+To start a new multi-sample BAM QC analysis activate main menu item :menuselection:`File --> New Analysis --> Multisample BAM QC`.
+
+Examples
+^^^^^^^^
+
+- `gH2AX Chip-seq data: 4 conditions, 3 replicates per condition <http://kokonech.github.io/qualimap/gh2ax_multibamqc/multisampleBamQcReport.html>`_. Example report for a ChIP-seq experiment having 12 samples.
+
+- See the :ref:`Sample data <samples>` section for more details about the data used in the example.
+
+Input Parameters
+^^^^^^^^^^^^^^^^
+
+There are 2 types of input data that are accepted by *Multi-sample BAM QC*:
+
+1. By default directory with the summary statistics and plot data produced by BAM QC analysis is expected as input data for multi-sample comparison.
+
+2. If a special **"raw data" mode** is activated, then BAM files can be provided as input. In this case Qualimap will first run the :ref:`BAM QC analysis<bamqc>` on each indvidual BAM file, and then multi-sample report will be computed.
+
+The input samples can be added using button :guilabel:`Add`. For each sample one has to provide the following information:
+
+1. **Name** of the sample as it will be used in legend.
+
+2. **Path** to the folder with which contains results of BAM QC analysis performed on the sample. The folder must include file **genome_results.txt** and subfolder **raw_data_qualimapReport** containing data of BAM QC plots. If **"Raw data" mode** is activated then the path to the BAM file should be provided.
+
+.. note::
+
+ In QualiMap version <= 2.0 directory with raw data of BAM QC analysis was called **raw_data**. This name is also supported.
+
+Each added sample will be shown in **Samples** table. One can edit samples using button :guilabel:`Edit` and remove them using button :guilabel:`Remove`.
+
+
+:guilabel:`"Raw data" mode: run BAM QC on input samples`
+
+
+ Activate this checkbox to analyze BAM files directly. A selected set of options is available to customize *BAM QC* process. One can read detailed explantion of these options in a :ref:`corresponding section<bamqc>` of the manual.
+
+
+To start the analysis click button :guilabel:`Run analysis`.
+
+
+Output
+^^^^^^
+
+:guilabel:`Summary`
+
+ The summary table contains comparison of selected critical alignment metrics for all samples. The metrics include mean and standard deviation of coverage, mean GC content, mean insert size and mean mapping qualities.
+
+:guilabel:`Input`
+
+ Here one can check the **input data** and the **parameters** used for the analysis.
+
+:guilabel:`PCA`
+
+ The alignment features presented in the *Summary* section undergo `Principal Component Analysis <http://en.wikipedia.org/wiki/Principal_component_analysis>`_. Afterwards the `biplot <http://en.wikipedia.org/wiki/Biplot>`_ presenting first and second principal component is constructed. The plot shows how much variability demonstarte the analyzed samples. It allows to detect if any samples group together and if there are any outliers among analyzed samples.
+
+:guilabel:`Coverage Across Reference`, :guilabel:`Coverage Histogram (0-50X)` , :guilabel:`Genome Fraction Coverage`, :guilabel:`Duplication Rate Histogram`, :guilabel:`Mapped Reads GC Content`, :guilabel:`Mapped Reads GC Content Distribution`, :guilabel:`Mapped Reads Clipping Profile`, :guilabel:`Mapping Quality Across Reference`, :guilabel:`Mapping Quality Histogram`, :guilabel:`Insert Size Across Reference`, :guilabel:`Insert Size Histogram`
+
+ The following plots demonstrate the comparison of samples using data from corresponding plots computed during BAM QC analysis. Each curve on a plot represents a single sample.
+
+ Please refer to documentation of :ref:`BAM QC<bamqc>` for detailed information about the plots.
+
+
+\*\*\*
+
+
+.. [#X] Example for the meaning of *X*: If one genomic region has a coverage of 10X, it means that, on average, 10 different reads are mapped to each nucleotide of the region.
+
+.. [#biomart] Downloaded from `Biomart v.61 <http://feb2011.archive.ensembl.org/biomart/martview>`_.
+
+.. [Marioni] Marioni JC et al, "RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays". Genome Res. 2008. 18: 1509-1517.
diff --git a/doc/command_line.rst b/doc/command_line.rst
new file mode 100644
index 0000000..25cae7b
--- /dev/null
+++ b/doc/command_line.rst
@@ -0,0 +1,310 @@
+.. _command-line:
+
+Command Line Interface
+======================
+
+General Description
+-------------------
+
+Each analysis type presented in QualiMap GUI is also available as command line tool. The common pattern to launch the tool is the following::
+
+ qualimap <tool_name> <tool_options>
+
+:guilabel:`<tool_name>` is the name of the desired analysis. This could be: :ref:`bamqc<cmdline-bamqc>`, :ref:`rnaseq<cmdline-rnaseqqc>`, :ref:`multi-bamqc <cmdline-multibamqc>`, :ref:`counts<cmdline-countsqc>`, :ref:`clustering<cmdline-clustering>` or :ref:`comp-counts<cmdline-counts>`.
+
+:guilabel:`<tool_options>` are specific to each type analysis. If not option is provided for the specific tool a full list of available options will be shown
+
+.. note:: If you are using Qualimap on Unix server without X11 system, make sure that the DISPLAY environment variable is unset. Otherwise this might result in problems when running Qualimap. :ref:`Here<x11problem>` is an instruction how to solve this issue.
+
+To show available tools use command::
+
+ qualimap --help
+
+There are certain options that are common to most of the command line tools::
+
+ -outdir <arg> Output folder for HTML report and raw
+ data.
+ -outfile <arg> Output file for PDF report (default value
+ is report.pdf).
+ -outformat <arg> Format of the ouput report (PDF or HTML,
+ default is HTML).
+
+
+These options allow to confugre output of Qualimap.
+*-outdir* option sets the output folder for HTML report and raw data::
+
+ qualimap bamqc -bam file.bam -outdir qualimap_results
+
+| If the *-outfile* option is given then the output will be produced in PDF format. In this case *-outdir* option controls only the path to raw data.
+Example::
+
+ qualimap bamqc -bam file.bam -outfile result.pdf
+
+| It is also possible to explictily set output format by using option *-outformat*. In this case report will be saved in the output dir under default name.
+Example::
+
+ qualimap bamqc -bam file.bam -outdir qualimap_results -outformat pdf
+
+| Additionally each tool has its own defaults for output directory name. Check tools' description for details.
+
+
+.. _cmdline-bamqc:
+
+BAM QC
+------
+
+
+The following command allows to perform BAM QC analysis::
+
+ usage: qualimap bamqc -bam <arg> [-c] [-gd <arg>] [-gff <arg>] [-hm <arg>] [-nr
+ <arg>] [-nt <arg>] [-nw <arg>] [-oc <arg>] [-os] [-outdir <arg>]
+ [-outfile <arg>] [-outformat <arg>] [-p <arg>]
+ -bam <arg> Input mapping file in BAM format
+ -c,--paint-chromosome-limits Paint chromosome limits inside charts
+ -gd,--genome-gc-distr <arg> Species to compare with genome GC
+ distribution. Possible values: HUMAN or
+ MOUSE.
+ -gff,--feature-file <arg> Feature file with regions of interest in
+ GFF/GTF or BED format
+ -hm <arg> Minimum size for a homopolymer to be
+ considered in indel analysis (default is
+ 3)
+ -ip,--collect-overlap-pairs Activate this option to collect statistics
+ of overlapping paired-end reads
+ -nr <arg> Number of reads analyzed in a chunk
+ (default is 1000)
+ -nt <arg> Number of threads (default is 8)
+ -nw <arg> Number of windows (default is 400)
+ -oc,--output-genome-coverage <arg> File to save per base non-zero coverage.
+ Warning: large files are expected for large
+ genomes
+ -os,--outside-stats Report information for the regions outside
+ those defined by feature-file (ignored
+ when -gff option is not set)
+ -outdir <arg> Output folder for HTML report and raw
+ data.
+ -outfile <arg> Output file for PDF report (default value
+ is report.pdf).
+ -outformat <arg> Format of the ouput report (PDF or HTML,
+ default is HTML).
+ -p,--sequencing-protocol <arg> Sequencing library protocol:
+ strand-specific-forward,
+ strand-specific-reverse or
+ non-strand-specific (default)
+ -sd,--skip-duplicated Activate this option to skip duplicated
+ alignments from analysis. If the
+ duplicates are not flagged in BAM file,
+ then they will be detected by Qualimap.
+
+
+
+| The only required parameter is :guilabel:`bam` -- the input mapping file.
+| If :guilabel:`outdir` is not provided, it will be created automatically in the same folder where BAM file is located.
+|
+| Detailed explanation of available options can be found :ref:`here<bamqc>`.
+
+Example (data available :ref:`here<bam-samples>`)::
+
+ qualimap bamqc -bam ERR089819.bam -c
+
+
+
+.. _cmdline-rnaseqqc:
+
+RNA-seq QC
+----------
+
+To perform RNA-seq QC analysis use the following command::
+
+ usage: qualimap rnaseq [-a <arg>] -bam <arg> -gtf <arg> [-oc <arg>] [-outdir
+ <arg>] [-outfile <arg>] [-outformat <arg>] [-p <arg>]
+ -a,--algorithm <arg> Counting algorithm:
+ uniquely-mapped-reads(default) or
+ proportional.
+ -bam <arg> Input mapping file in BAM format.
+ -gtf <arg> Annotations file in Ensembl GTF format.
+ -oc <arg> Path to output computed counts.
+ -outdir <arg> Output folder for HTML report and raw data.
+ -outfile <arg> Output file for PDF report (default value is
+ report.pdf).
+ -outformat <arg> Format of the ouput report (PDF or HTML,
+ default is HTML).
+ -p,--sequencing-protocol <arg> Sequencing library protocol:
+ strand-specific-forward,
+ strand-specific-reverse or non-strand-specific
+ (default)
+
+
+| The required parameteres for this type of analysis are the spliced-alignment file in BAM format and annotations in GTF format.
+
+| Detailed explanation of available options can be found :ref:`here<rnaseqqc>`.
+
+Example (data available :ref:`here<annotation-files>`)::
+
+ qualimap rnaseq -bam kidney.bam -gtf human.64.gtf -outdir rnaseq_qc_results
+
+
+
+.. _cmdline-multibamqc:
+
+Multi-sample BAM QC
+-------------------
+
+To perform multi-sample BAM QC use the following command::
+
+ usage: qualimap multi-bamqc [-c] -d <arg> [-gff <arg>] [-hm <arg>] [-nr <arg>]
+ [-nw <arg>] [-outdir <arg>] [-outfile <arg>] [-outformat <arg>] [-r]
+ -c,--paint-chromosome-limits Only for -r mode. Paint chromosome limits inside
+ charts
+ -d,--data <arg> File describing the input data. Format of the
+ file is a 2-column tab-delimited table.
+ Column 1: sample name
+ Column 2: either path to the BAM QC result or
+ path to BAM file (-r mode)
+ -gff,--feature-file <arg> Only for -r mode. Feature file with regions of
+ interest in GFF/GTF or BED format
+ -hm <arg> Only for -r mode. Minimum size for a homopolymer
+ to be considered in indel analysis (default is
+ 3)
+ -nr <arg> Only for -r mode. Number of reads analyzed in a
+ chunk (default is 1000)
+ -nw <arg> Only for -r mode. Number of windows (default is
+ 400)
+ -outdir <arg> Output folder for HTML report and raw data.
+ -outfile <arg> Output file for PDF report (default value is
+ report.pdf).
+ -outformat <arg> Format of the ouput report (PDF or HTML, default
+ is HTML).
+ -r,--run-bamqc Raw BAM files are provided as input. If this
+ option is activated BAM QC process first will be
+ run for each sample, then multi-sample analysis
+ will be performed.
+
+
+| The main argument for this command is the configuration file describing input data (-d). This has to be a 2-column tab-delimted file. The first column should contain the sample name and the second column should contain either path to the results of BAM QC analysis or path to the BAM file (if -r mode is activated). The path for the data could be absolute or relative to the location of the configuration file.
+
+| Detailed explanation of the analysis can be found here :ref:`here<multibamqc>`.
+
+Example (data available :ref:`here<multibamqc-samples>`)::
+
+ unzip gh2ax_chip_seq.zip
+ cd gh2ax_chip_seq.txt
+ qualimap multi-bamqc -i gh2ax_chip_seq.txt -outdir gh2ax_multibamqc
+
+
+
+.. _cmdline-countsqc:
+
+Counts QC
+---------
+
+To perform counts QC analysis use the following command::
+
+ usage: qualimap counts [-c] -d <arg> [-i <arg>] [-k <arg>] [-outdir <arg>]
+ [-outfile <arg>] [-outformat <arg>] [-R <arg>] [-s <arg>]
+ -c,--compare Perform comparison of conditions. Currently 2 maximum
+ is possible.
+ -d,--data <arg> File describing the input data. Format of the file is
+ a 4 column tab-delimited table.
+ Column 1: sample name
+ Column 2: condition of the sample
+ Column 3: path to the counts data for the sample
+ Column 4: index of the column with counts
+ -i,--info <arg> Path to info file containing genes GC-content, length
+ and type.
+ -k,--threshold <arg> Threshold for the number of counts
+ -outdir <arg> Output folder for HTML report and raw data.
+ -outfile <arg> Output file for PDF report (default value is
+ report.pdf).
+ -outformat <arg> Format of the ouput report (PDF or HTML, default is
+ HTML).
+ -R,--rscriptpath <arg> Path to Rscript executable (by default it is assumed
+ to be available from system $PATH)
+ -s,--species <arg> Use built-in info file for the given species: HUMAN or
+ MOUSE.
+
+| The main argument for this command is the configuration file describing the input samples (-d). This has to be a 4-column tab-delimited file. The first column should contain the name of the sample, the second - name of the biological condition (e.g treated or untreated), the third - path to the file containing counts data for the sample and the fourth - the index of the column in the data file which contains counts. This is useful when counts for all samples are contained in the one fi [...]
+
+| Detailed explanation of the analysis can be found :ref:`here<countsqc>`.
+
+Example. Note: requires counts file `mouse_counts_ensembl.txt <http://kokonech.github.io/qualimap/samples/mouse_counts_ensembl.txt>`_ (data available :ref:`here<counts-samples>`)::
+
+ qualimap counts -d GlcN_countsqc_input.txt -c -s mouse -outdir glcn_mice_counts
+
+
+.. _cmdline-clustering:
+
+Clustering
+----------
+
+To perform clustering of epigenomic signals use the following command::
+
+ usage: qualimap clustering [-b <arg>] [-c <arg>] -control <arg> [-expr <arg>]
+ [-f <arg>] [-l <arg>] [-name <arg>] [-outdir <arg>] [-outformat <arg>]
+ [-r <arg>] -regions <arg> -sample <arg> [-viz <arg>]
+ -b,--bin-size <arg> size of the bin (default is 100)
+ -c,--clusters <arg> comma-separated list of cluster sizes
+ -control <arg> comma-separated list of control BAM files
+ -expr <arg> name of the experiment
+ -f,--fragment-length <arg> smoothing length of a fragment
+ -l <arg> upstream offset (default is 2000)
+ -name <arg> comma-separated names of the replicates
+ -outdir <arg> output folder
+ -outformat <arg> output report format (PDF or HTML, default is
+ HTML)
+ -r <arg> downstream offset (default is 500)
+ -regions <arg> path to regions file
+ -sample <arg> comma-separated list of sample BAM files
+ -viz <arg> visualization type: heatmap or line
+
+
+| Detailed explanation of available options can be found :ref:`here<clustering>`.
+
+Example (data available :ref:`here<clustering-samples>`)::
+
+ qualimap clustering -sample clustering/hmeDIP.bam -control clustering/input.bam -regions annotations/transcripts.human.64.bed -outdir clustering_result
+
+
+.. _cmdline-counts:
+
+Compute counts
+--------------
+
+To compute counts from mapping data use the following command::
+
+ usage: qualimap comp-counts [-a <arg>] -bam <arg> -gtf <arg> [-id <arg>] [-out
+ <arg>] [-p <arg>] [-pe] [-s <arg>] [-type <arg>]
+ -a,--algorithm <arg> Counting algorithm:
+ uniquely-mapped-reads(default) or proportional
+ -bam <arg> Mapping file in BAM format
+ -gtf <arg> Region file in GTF, GFF or BED format. If GTF
+ format is provided, counting is based on
+ attributes, otherwise based on feature name
+ -id <arg> GTF-specific. Attribute of the GTF to be used
+ as feature ID. Regions with the same ID will
+ be aggregated as part of the same feature.
+ Default: gene_id.
+ -out <arg> Path to output file
+ -p,--sequencing-protocol <arg> Sequencing library protocol:
+ strand-specific-forward,
+ strand-specific-reverse or non-strand-specific
+ (default)
+ -pe,--paired Setting this flag for paired-end experiments
+ will result in counting fragments instead of
+ reads
+ -s,--sorted <arg> This flag indicates that the input file is
+ already sorted by name. If not set, additional
+ sorting by name will be performed. Only
+ required for paired-end analysis.
+ -type <arg> GTF-specific. Value of the third column of the
+ GTF considered for counting. Other types will
+ be ignored. Default: exon
+
+| Detailed explanation of available options can be found :ref:`here<compute-counts>`.
+
+Example (data available :ref:`here<counts-samples>`)::
+
+ qualimap comp-counts -bam kidney.bam -gtf ../annotations/human.64.gtf -out kidney.counts
+
+
+
diff --git a/doc/conf.py b/doc/conf.py
new file mode 100644
index 0000000..cda5215
--- /dev/null
+++ b/doc/conf.py
@@ -0,0 +1,253 @@
+# -*- coding: utf-8 -*-
+#
+# Qualimap documentation build configuration file, created by
+# sphinx-quickstart on Mon Mar 12 11:54:43 2012.
+#
+# This file is execfile()d with the current directory set to its containing dir.
+#
+# Note that not all possible configuration values are present in this
+# autogenerated file.
+#
+# All configuration values have a default; values that are commented out
+# serve to show the default.
+
+import sys, os
+
+
+def getVersion():
+ pom = open("../pom.xml")
+ for line in pom:
+ if "<version>" in line:
+ v = line.split(">")[1].split("<")[0]
+ print v
+ return v
+
+ return "unknown"
+
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#sys.path.insert(0, os.path.abspath('.'))
+
+# -- General configuration -----------------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+#needs_sphinx = '1.0'
+
+# Add any Sphinx extension module names here, as strings. They can be extensions
+# coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
+extensions = []
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# The suffix of source filenames.
+source_suffix = '.rst'
+
+# The encoding of source files.
+#source_encoding = 'utf-8-sig'
+
+# The master toctree document.
+master_doc = 'index'
+
+# General information about the project.
+project = u'Qualimap'
+copyright = u'2012, Max Planck Institute For Infection Biology, Berlin'
+
+# The version info for the project you're documenting, acts as replacement for
+# |version| and |release|, also used in various other places throughout the
+# built documents.
+#
+# The short X.Y version.
+version = '1'
+# The full version, including alpha/beta/rc tags.
+release = getVersion()
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#language = None
+
+# There are two options for replacing |today|: either, you set today to some
+# non-false value, then it is used:
+#today = ''
+# Else, today_fmt is used as the format for a strftime call.
+#today_fmt = '%B %d, %Y'
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+exclude_patterns = ['_build']
+
+# The reST default role (used for this markup: `text`) to use for all documents.
+#default_role = None
+
+# If true, '()' will be appended to :func: etc. cross-reference text.
+#add_function_parentheses = True
+
+# If true, the current module name will be prepended to all description
+# unit titles (such as .. function::).
+#add_module_names = True
+
+# If true, sectionauthor and moduleauthor directives will be shown in the
+# output. They are ignored by default.
+#show_authors = False
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+
+# A list of ignored prefixes for module index sorting.
+#modindex_common_prefix = []
+
+
+# -- Options for HTML output ---------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages. See the documentation for
+# a list of builtin themes.
+html_theme = 'agogo'
+
+# Theme options are theme-specific and customize the look and feel of a theme
+# further. For a list of options available for each theme, see the
+# documentation.
+#html_theme_options = {}
+
+# Add any paths that contain custom themes here, relative to this directory.
+#html_theme_path = []
+
+# The name for this set of Sphinx documents. If None, it defaults to
+# "<project> v<release> documentation".
+#html_title = None
+
+# A shorter title for the navigation bar. Default is the same as html_title.
+#html_short_title = None
+
+# The name of an image file (relative to this directory) to place at the top
+# of the sidebar.
+html_logo = 'images/qualimap_logo_small.png'
+
+# The name of an image file (within the static path) to use as favicon of the
+# docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32
+# pixels large.
+#html_favicon = None
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']
+
+# If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
+# using the given strftime format.
+#html_last_updated_fmt = '%b %d, %Y'
+
+# If true, SmartyPants will be used to convert quotes and dashes to
+# typographically correct entities.
+#html_use_smartypants = True
+
+# Custom sidebar templates, maps document names to template names.
+#html_sidebars = {}
+
+# Additional templates that should be rendered to pages, maps page names to
+# template names.
+#html_additional_pages = {}
+
+# If false, no module index is generated.
+#html_domain_indices = True
+
+# If false, no index is generated.
+html_use_index = False
+
+# If true, the index is split into individual pages for each letter.
+#html_split_index = False
+
+# If true, links to the reST sources are added to the pages.
+html_show_sourcelink = False
+
+# If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
+html_show_sphinx = False
+
+# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
+html_show_copyright = False
+
+# If true, an OpenSearch description file will be output, and all pages will
+# contain a <link> tag referring to it. The value of this option must be the
+# base URL from which the finished HTML is served.
+#html_use_opensearch = ''
+
+# This is the file name suffix for HTML files (e.g. ".xhtml").
+#html_file_suffix = None
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'Qualimapdoc'
+
+
+# -- Options for LaTeX output --------------------------------------------------
+
+latex_elements = {
+# The paper size ('letterpaper' or 'a4paper').
+'papersize': 'a4paper',
+
+# The font size ('10pt', '11pt' or '12pt').
+#'pointsize': '10pt',
+
+# Additional stuff for the LaTeX preamble.
+#preamble': 'Qua qua qua!'
+}
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title, author, documentclass [howto/manual]).
+latex_documents = [
+ ('index', 'QualimapManual.tex', u'Qualimap Documentation',
+ u'F. Garcia-Alcalde, K. Okonechnikov, et al', 'manual', 'True'),
+]
+
+# The name of an image file (relative to this directory) to place at the top of
+# the title page.
+#latex_logo = None
+
+# For "manual" documents, if this is true, then toplevel headings are parts,
+# not chapters.
+#latex_use_parts = False
+
+# If true, show page references after internal links.
+#latex_show_pagerefs = False
+
+# If true, show URL addresses after external links.
+#latex_show_urls = False
+
+# Documents to append as an appendix to all manuals.
+#latex_appendices = []
+
+# If false, no module index is generated.
+#latex_domain_indices = True
+
+# -- Options for manual page output --------------------------------------------
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [
+ ('index', 'qualimap', u'Qualimap Documentation',
+ [u'MPIIB'], 1)
+]
+
+# If true, show URL addresses after external links.
+#man_show_urls = False
+
+
+# -- Options for Texinfo output ------------------------------------------------
+
+# Grouping the document tree into Texinfo files. List of tuples
+# (source start file, target name, title, author,
+# dir menu entry, description, category)
+texinfo_documents = [
+ ('index', 'Qualimap', u'Qualimap Documentation',
+ u'fgarcia, kokonech', 'Qualimap', 'One line description of project.',
+ 'Miscellaneous'),
+]
+
+# Documents to append as an appendix to all manuals.
+#texinfo_appendices = []
+
+# If false, no module index is generated.
+#texinfo_domain_indices = True
+
+# How to display URL addresses: 'footnote', 'no', or 'inline'.
+#texinfo_show_urls = 'footnote'
diff --git a/doc/count-data/DetectionPerGroup.png b/doc/count-data/DetectionPerGroup.png
new file mode 100644
index 0000000..cbb90a8
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new file mode 100644
index 0000000..3e96e34
--- /dev/null
+++ b/doc/count-data/_static/agogo.css
@@ -0,0 +1,471 @@
+/*
+ * agogo.css_t
+ * ~~~~~~~~~~~
+ *
+ * Sphinx stylesheet -- agogo theme.
+ *
+ * :copyright: Copyright 2007-2011 by the Sphinx team, see AUTHORS.
+ * :license: BSD, see LICENSE for details.
+ *
+ */
+
+* {
+ margin: 0px;
+ padding: 0px;
+}
+
+body {
+ font-family: "Verdana", Arial, sans-serif;
+ line-height: 1.4em;
+ color: black;
+ background-color: #eeeeec;
+}
+
+
+/* Page layout */
+
+div.header, div.content, div.footer {
+ width: 70em;
+ margin-left: auto;
+ margin-right: auto;
+}
+
+div.header-wrapper {
+ background: url(bgtop.png) top left repeat-x;
+ border-bottom: 3px solid #2e3436;
+}
+
+
+/* Default body styles */
+a {
+ color: #ce5c00;
+}
+
+div.bodywrapper a, div.footer a {
+ text-decoration: underline;
+}
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+ clear: both;
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+ float: left;
+}
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+ float: right;
+}
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+ margin-top: 1em;
+ margin-bottom: 1em;
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+ margin-bottom: 0;
+ margin-left: 1.5em;
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+ font-weight: normal;
+ color: #3465a4;
+ margin-bottom: .8em;
+}
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+ color: #204a87;
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+ border-bottom: 1px solid #3465a4;
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+ color: #dddddd;
+ padding-left: .3em;
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+ margin-bottom: 10px;
+ padding: 2px 7px 1px 7px;
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+ margin: 0px 10px 5px 0px;
+ font-weight: bold;
+}
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+dt:target, .highlighted {
+ background-color: #fbe54e;
+}
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+/* Header */
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+ font-size: 180%;
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+}
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+ float: right;
+}
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+ border: 0;
+}
+
+
+/* Content */
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+ padding-top: 20px;
+ padding-bottom: 20px;
+}
+
+div.document {
+ width: 50em;
+ float: left;
+}
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+ text-align: justify;
+}
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+}
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+ margin: 1.5em;
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+ margin-top: .4em;
+ margin-bottom: 1em;
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+}
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+ padding: 3px;
+ background-color: #eeeeec;
+ border-top: 2px solid #dddddd;
+ border-bottom: 2px solid #dddddd;
+ margin-top: .8em;
+ margin-bottom: .8em;
+}
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+}
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+ padding: 0px;
+}
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+ margin: 1em;
+}
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+}
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+ float: right;
+ font-size: .9em;
+}
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+}
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+ text-transform: uppercase;
+ font-size: 130%;
+ letter-spacing: .1em;
+}
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+div.sidebar ul {
+ list-style-type: none;
+}
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+div.sidebar li.toctree-l1 a {
+ display: block;
+ padding: 1px;
+ border: 1px solid #dddddd;
+ background-color: #eeeeec;
+ margin-bottom: .4em;
+ padding-left: 3px;
+ color: #2e3436;
+}
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+div.sidebar li.toctree-l2 a {
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+ border: none;
+ margin-left: 1em;
+ border-bottom: 1px solid #dddddd;
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+ background-color: transparent;
+ border: none;
+ margin-left: 2em;
+ border-bottom: 1px solid #dddddd;
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+}
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+}
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+ border-right: none;
+}
+
+div.sidebar input[type="text"] {
+ width: 170px;
+}
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+div.sidebar input[type="submit"] {
+ width: 30px;
+}
+
+
+/* Footer */
+
+div.footer-wrapper {
+ background: url(bgfooter.png) top left repeat-x;
+ border-top: 4px solid #babdb6;
+ padding-top: 10px;
+ padding-bottom: 10px;
+ min-height: 80px;
+}
+
+div.footer, div.footer a {
+ color: #888a85;
+}
+
+div.footer .right {
+ text-align: right;
+}
+
+div.footer .left {
+ text-transform: uppercase;
+}
+
+
+/* Styles copied from basic theme */
+
+img.align-left, .figure.align-left, object.align-left {
+ clear: left;
+ float: left;
+ margin-right: 1em;
+}
+
+img.align-right, .figure.align-right, object.align-right {
+ clear: right;
+ float: right;
+ margin-left: 1em;
+}
+
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+ display: block;
+ margin-left: auto;
+ margin-right: auto;
+}
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+img.align-center-qualimap {
+ display: block;
+ margin-left: auto;
+ margin-right: auto;
+ width: 100%
+}
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+.align-left {
+ text-align: left;
+}
+
+.align-center {
+ text-align: center;
+}
+
+.align-right {
+ text-align: right;
+}
+
+/* -- search page ----------------------------------------------------------- */
+
+ul.search {
+ margin: 10px 0 0 20px;
+ padding: 0;
+}
+
+ul.search li {
+ padding: 5px 0 5px 20px;
+ background-image: url(file.png);
+ background-repeat: no-repeat;
+ background-position: 0 7px;
+}
+
+ul.search li a {
+ font-weight: bold;
+}
+
+ul.search li div.context {
+ color: #888;
+ margin: 2px 0 0 30px;
+ text-align: left;
+}
+
+ul.keywordmatches li.goodmatch a {
+ font-weight: bold;
+}
+
+/* -- index page ------------------------------------------------------------ */
+
+table.contentstable {
+ width: 90%;
+}
+
+table.contentstable p.biglink {
+ line-height: 150%;
+}
+
+a.biglink {
+ font-size: 1.3em;
+}
+
+span.linkdescr {
+ font-style: italic;
+ padding-top: 5px;
+ font-size: 90%;
+}
+
+/* -- general index --------------------------------------------------------- */
+
+table.indextable td {
+ text-align: left;
+ vertical-align: top;
+}
+
+table.indextable dl, table.indextable dd {
+ margin-top: 0;
+ margin-bottom: 0;
+}
+
+table.indextable tr.pcap {
+ height: 10px;
+}
+
+table.indextable tr.cap {
+ margin-top: 10px;
+ background-color: #f2f2f2;
+}
+
+img.toggler {
+ margin-right: 3px;
+ margin-top: 3px;
+ cursor: pointer;
+}
+
+/* -- viewcode extension ---------------------------------------------------- */
+
+.viewcode-link {
+ float: right;
+}
+
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+ float: right;
+ font-family:: "Verdana", Arial, sans-serif;
+}
+
+div.viewcode-block:target {
+ margin: -1px -3px;
+ padding: 0 3px;
+ background-color: #f4debf;
+ border-top: 1px solid #ac9;
+ border-bottom: 1px solid #ac9;
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diff --git a/doc/count-data/_static/basic.css b/doc/count-data/_static/basic.css
new file mode 100644
index 0000000..1e02c5d
--- /dev/null
+++ b/doc/count-data/_static/basic.css
@@ -0,0 +1,540 @@
+/*
+ * basic.css
+ * ~~~~~~~~~
+ *
+ * Sphinx stylesheet -- basic theme.
+ *
+ * :copyright: Copyright 2007-2011 by the Sphinx team, see AUTHORS.
+ * :license: BSD, see LICENSE for details.
+ *
+ */
+
+/* -- main layout ----------------------------------------------------------- */
+
+div.clearer {
+ clear: both;
+}
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+/* -- relbar ---------------------------------------------------------------- */
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+div.related {
+ width: 100%;
+ font-size: 90%;
+}
+
+div.related h3 {
+ display: none;
+}
+
+div.related ul {
+ margin: 0;
+ padding: 0 0 0 10px;
+ list-style: none;
+}
+
+div.related li {
+ display: inline;
+}
+
+div.related li.right {
+ float: right;
+ margin-right: 5px;
+}
+
+/* -- sidebar --------------------------------------------------------------- */
+
+div.sphinxsidebarwrapper {
+ padding: 10px 5px 0 10px;
+}
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+div.sphinxsidebar {
+ float: left;
+ width: 0px;
+ margin-left: -100%;
+ font-size: 90%;
+}
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+div.sphinxsidebar ul {
+ list-style: none;
+}
+
+div.sphinxsidebar ul ul,
+div.sphinxsidebar ul.want-points {
+ margin-left: 20px;
+ list-style: square;
+}
+
+div.sphinxsidebar ul ul {
+ margin-top: 0;
+ margin-bottom: 0;
+}
+
+div.sphinxsidebar form {
+ margin-top: 10px;
+}
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+div.sphinxsidebar input {
+ border: 1px solid #98dbcc;
+ font-family: sans-serif;
+ font-size: 1em;
+}
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+div.sphinxsidebar #searchbox input[type="text"] {
+ width: 170px;
+}
+
+div.sphinxsidebar #searchbox input[type="submit"] {
+ width: 30px;
+}
+
+img {
+ border: 0;
+}
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+
+ul.search {
+ margin: 10px 0 0 20px;
+ padding: 0;
+}
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+ul.search li {
+ padding: 5px 0 5px 20px;
+ background-image: url(file.png);
+ background-repeat: no-repeat;
+ background-position: 0 7px;
+}
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+ul.search li a {
+ font-weight: bold;
+}
+
+ul.search li div.context {
+ color: #888;
+ margin: 2px 0 0 30px;
+ text-align: left;
+}
+
+ul.keywordmatches li.goodmatch a {
+ font-weight: bold;
+}
+
+/* -- index page ------------------------------------------------------------ */
+
+table.contentstable {
+ width: 90%;
+}
+
+table.contentstable p.biglink {
+ line-height: 150%;
+}
+
+a.biglink {
+ font-size: 1.3em;
+}
+
+span.linkdescr {
+ font-style: italic;
+ padding-top: 5px;
+ font-size: 90%;
+}
+
+/* -- general index --------------------------------------------------------- */
+
+table.indextable {
+ width: 100%;
+}
+
+table.indextable td {
+ text-align: left;
+ vertical-align: top;
+}
+
+table.indextable dl, table.indextable dd {
+ margin-top: 0;
+ margin-bottom: 0;
+}
+
+table.indextable tr.pcap {
+ height: 10px;
+}
+
+table.indextable tr.cap {
+ margin-top: 10px;
+ background-color: #f2f2f2;
+}
+
+img.toggler {
+ margin-right: 3px;
+ margin-top: 3px;
+ cursor: pointer;
+}
+
+div.modindex-jumpbox {
+ border-top: 1px solid #ddd;
+ border-bottom: 1px solid #ddd;
+ margin: 1em 0 1em 0;
+ padding: 0.4em;
+}
+
+div.genindex-jumpbox {
+ border-top: 1px solid #ddd;
+ border-bottom: 1px solid #ddd;
+ margin: 1em 0 1em 0;
+ padding: 0.4em;
+}
+
+/* -- general body styles --------------------------------------------------- */
+
+a.headerlink {
+ visibility: hidden;
+}
+
+h1:hover > a.headerlink,
+h2:hover > a.headerlink,
+h3:hover > a.headerlink,
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+h5:hover > a.headerlink,
+h6:hover > a.headerlink,
+dt:hover > a.headerlink {
+ visibility: visible;
+}
+
+div.body p.caption {
+ text-align: inherit;
+}
+
+div.body td {
+ text-align: left;
+}
+
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+ padding-left: 1em;
+}
+
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+ margin-top: 0 !important;
+}
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+p.rubric {
+ margin-top: 30px;
+ font-weight: bold;
+}
+
+img.align-left, .figure.align-left, object.align-left {
+ clear: left;
+ float: left;
+ margin-right: 1em;
+}
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+ clear: right;
+ float: right;
+ margin-left: 1em;
+}
+
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+ display: block;
+ margin-left: auto;
+ margin-right: auto;
+}
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+ text-align: left;
+}
+
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+ text-align: center;
+}
+
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+ text-align: right;
+}
+
+/* -- sidebars -------------------------------------------------------------- */
+
+div.sidebar {
+ margin: 0 0 0.5em 1em;
+ border: 1px solid #ddb;
+ padding: 7px 7px 0 7px;
+ background-color: #ffe;
+ width: 40%;
+ float: right;
+}
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+p.sidebar-title {
+ font-weight: bold;
+}
+
+/* -- topics ---------------------------------------------------------------- */
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+div.topic {
+ border: 1px solid #ccc;
+ padding: 7px 7px 0 7px;
+ margin: 10px 0 10px 0;
+}
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+p.topic-title {
+ font-size: 1.1em;
+ font-weight: bold;
+ margin-top: 10px;
+}
+
+/* -- admonitions ----------------------------------------------------------- */
+
+div.admonition {
+ margin-top: 10px;
+ margin-bottom: 10px;
+ padding: 7px;
+}
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+div.admonition dt {
+ font-weight: bold;
+}
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+div.admonition dl {
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+ font-weight: bold;
+}
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+div.body p.centered {
+ text-align: center;
+ margin-top: 25px;
+}
+
+/* -- tables ---------------------------------------------------------------- */
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+ border-collapse: collapse;
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+ margin-left: 1px;
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+/* -- other body styles ----------------------------------------------------- */
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+}
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+dd p {
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+}
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+ padding: 5px;
+ border: 3px solid red;
+}
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+}
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+ margin-top: 1em;
+ margin-bottom: 1em;
+}
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+ font-family: sans-serif;
+}
+
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+}
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+}
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+ border-bottom: dotted 1px;
+ cursor: help;
+}
+
+/* -- code displays --------------------------------------------------------- */
+
+pre {
+ overflow: auto;
+ overflow-y: hidden; /* fixes display issues on Chrome browsers */
+}
+
+td.linenos pre {
+ padding: 5px 0px;
+ border: 0;
+ background-color: transparent;
+ color: #aaa;
+}
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+table.highlighttable {
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+}
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+}
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+ font-weight: bold;
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+ font-family: sans-serif;
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+}
+
+/* -- math display ---------------------------------------------------------- */
+
+img.math {
+ vertical-align: middle;
+}
+
+div.body div.math p {
+ text-align: center;
+}
+
+span.eqno {
+ float: right;
+}
+
+/* -- printout stylesheet --------------------------------------------------- */
+
+ at media print {
+ div.document,
+ div.documentwrapper,
+ div.bodywrapper {
+ margin: 0 !important;
+ width: 100%;
+ }
+
+ div.sphinxsidebar,
+ div.related,
+ div.footer,
+ #top-link {
+ display: none;
+ }
+}
\ No newline at end of file
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index 0000000..09b54be
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diff --git a/doc/count-data/_static/comment.png b/doc/count-data/_static/comment.png
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diff --git a/doc/count-data/_static/doctools.js b/doc/count-data/_static/doctools.js
new file mode 100644
index 0000000..d4619fd
--- /dev/null
+++ b/doc/count-data/_static/doctools.js
@@ -0,0 +1,247 @@
+/*
+ * doctools.js
+ * ~~~~~~~~~~~
+ *
+ * Sphinx JavaScript utilities for all documentation.
+ *
+ * :copyright: Copyright 2007-2011 by the Sphinx team, see AUTHORS.
+ * :license: BSD, see LICENSE for details.
+ *
+ */
+
+/**
+ * select a different prefix for underscore
+ */
+$u = _.noConflict();
+
+/**
+ * make the code below compatible with browsers without
+ * an installed firebug like debugger
+if (!window.console || !console.firebug) {
+ var names = ["log", "debug", "info", "warn", "error", "assert", "dir",
+ "dirxml", "group", "groupEnd", "time", "timeEnd", "count", "trace",
+ "profile", "profileEnd"];
+ window.console = {};
+ for (var i = 0; i < names.length; ++i)
+ window.console[names[i]] = function() {};
+}
+ */
+
+/**
+ * small helper function to urldecode strings
+ */
+jQuery.urldecode = function(x) {
+ return decodeURIComponent(x).replace(/\+/g, ' ');
+}
+
+/**
+ * small helper function to urlencode strings
+ */
+jQuery.urlencode = encodeURIComponent;
+
+/**
+ * This function returns the parsed url parameters of the
+ * current request. Multiple values per key are supported,
+ * it will always return arrays of strings for the value parts.
+ */
+jQuery.getQueryParameters = function(s) {
+ if (typeof s == 'undefined')
+ s = document.location.search;
+ var parts = s.substr(s.indexOf('?') + 1).split('&');
+ var result = {};
+ for (var i = 0; i < parts.length; i++) {
+ var tmp = parts[i].split('=', 2);
+ var key = jQuery.urldecode(tmp[0]);
+ var value = jQuery.urldecode(tmp[1]);
+ if (key in result)
+ result[key].push(value);
+ else
+ result[key] = [value];
+ }
+ return result;
+};
+
+/**
+ * small function to check if an array contains
+ * a given item.
+ */
+jQuery.contains = function(arr, item) {
+ for (var i = 0; i < arr.length; i++) {
+ if (arr[i] == item)
+ return true;
+ }
+ return false;
+};
+
+/**
+ * highlight a given string on a jquery object by wrapping it in
+ * span elements with the given class name.
+ */
+jQuery.fn.highlightText = function(text, className) {
+ function highlight(node) {
+ if (node.nodeType == 3) {
+ var val = node.nodeValue;
+ var pos = val.toLowerCase().indexOf(text);
+ if (pos >= 0 && !jQuery(node.parentNode).hasClass(className)) {
+ var span = document.createElement("span");
+ span.className = className;
+ span.appendChild(document.createTextNode(val.substr(pos, text.length)));
+ node.parentNode.insertBefore(span, node.parentNode.insertBefore(
+ document.createTextNode(val.substr(pos + text.length)),
+ node.nextSibling));
+ node.nodeValue = val.substr(0, pos);
+ }
+ }
+ else if (!jQuery(node).is("button, select, textarea")) {
+ jQuery.each(node.childNodes, function() {
+ highlight(this);
+ });
+ }
+ }
+ return this.each(function() {
+ highlight(this);
+ });
+};
+
+/**
+ * Small JavaScript module for the documentation.
+ */
+var Documentation = {
+
+ init : function() {
+ this.fixFirefoxAnchorBug();
+ this.highlightSearchWords();
+ this.initIndexTable();
+ },
+
+ /**
+ * i18n support
+ */
+ TRANSLATIONS : {},
+ PLURAL_EXPR : function(n) { return n == 1 ? 0 : 1; },
+ LOCALE : 'unknown',
+
+ // gettext and ngettext don't access this so that the functions
+ // can safely bound to a different name (_ = Documentation.gettext)
+ gettext : function(string) {
+ var translated = Documentation.TRANSLATIONS[string];
+ if (typeof translated == 'undefined')
+ return string;
+ return (typeof translated == 'string') ? translated : translated[0];
+ },
+
+ ngettext : function(singular, plural, n) {
+ var translated = Documentation.TRANSLATIONS[singular];
+ if (typeof translated == 'undefined')
+ return (n == 1) ? singular : plural;
+ return translated[Documentation.PLURALEXPR(n)];
+ },
+
+ addTranslations : function(catalog) {
+ for (var key in catalog.messages)
+ this.TRANSLATIONS[key] = catalog.messages[key];
+ this.PLURAL_EXPR = new Function('n', 'return +(' + catalog.plural_expr + ')');
+ this.LOCALE = catalog.locale;
+ },
+
+ /**
+ * add context elements like header anchor links
+ */
+ addContextElements : function() {
+ $('div[id] > :header:first').each(function() {
+ $('<a class="headerlink">\u00B6</a>').
+ attr('href', '#' + this.id).
+ attr('title', _('Permalink to this headline')).
+ appendTo(this);
+ });
+ $('dt[id]').each(function() {
+ $('<a class="headerlink">\u00B6</a>').
+ attr('href', '#' + this.id).
+ attr('title', _('Permalink to this definition')).
+ appendTo(this);
+ });
+ },
+
+ /**
+ * workaround a firefox stupidity
+ */
+ fixFirefoxAnchorBug : function() {
+ if (document.location.hash && $.browser.mozilla)
+ window.setTimeout(function() {
+ document.location.href += '';
+ }, 10);
+ },
+
+ /**
+ * highlight the search words provided in the url in the text
+ */
+ highlightSearchWords : function() {
+ var params = $.getQueryParameters();
+ var terms = (params.highlight) ? params.highlight[0].split(/\s+/) : [];
+ if (terms.length) {
+ var body = $('div.body');
+ window.setTimeout(function() {
+ $.each(terms, function() {
+ body.highlightText(this.toLowerCase(), 'highlighted');
+ });
+ }, 10);
+ $('<p class="highlight-link"><a href="javascript:Documentation.' +
+ 'hideSearchWords()">' + _('Hide Search Matches') + '</a></p>')
+ .appendTo($('#searchbox'));
+ }
+ },
+
+ /**
+ * init the domain index toggle buttons
+ */
+ initIndexTable : function() {
+ var togglers = $('img.toggler').click(function() {
+ var src = $(this).attr('src');
+ var idnum = $(this).attr('id').substr(7);
+ $('tr.cg-' + idnum).toggle();
+ if (src.substr(-9) == 'minus.png')
+ $(this).attr('src', src.substr(0, src.length-9) + 'plus.png');
+ else
+ $(this).attr('src', src.substr(0, src.length-8) + 'minus.png');
+ }).css('display', '');
+ if (DOCUMENTATION_OPTIONS.COLLAPSE_INDEX) {
+ togglers.click();
+ }
+ },
+
+ /**
+ * helper function to hide the search marks again
+ */
+ hideSearchWords : function() {
+ $('#searchbox .highlight-link').fadeOut(300);
+ $('span.highlighted').removeClass('highlighted');
+ },
+
+ /**
+ * make the url absolute
+ */
+ makeURL : function(relativeURL) {
+ return DOCUMENTATION_OPTIONS.URL_ROOT + '/' + relativeURL;
+ },
+
+ /**
+ * get the current relative url
+ */
+ getCurrentURL : function() {
+ var path = document.location.pathname;
+ var parts = path.split(/\//);
+ $.each(DOCUMENTATION_OPTIONS.URL_ROOT.split(/\//), function() {
+ if (this == '..')
+ parts.pop();
+ });
+ var url = parts.join('/');
+ return path.substring(url.lastIndexOf('/') + 1, path.length - 1);
+ }
+};
+
+// quick alias for translations
+_ = Documentation.gettext;
+
+$(document).ready(function() {
+ Documentation.init();
+});
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diff --git a/doc/count-data/_static/jquery.js b/doc/count-data/_static/jquery.js
new file mode 100644
index 0000000..7c24308
--- /dev/null
+++ b/doc/count-data/_static/jquery.js
@@ -0,0 +1,154 @@
+/*!
+ * jQuery JavaScript Library v1.4.2
+ * http://jquery.com/
+ *
+ * Copyright 2010, John Resig
+ * Dual licensed under the MIT or GPL Version 2 licenses.
+ * http://jquery.org/license
+ *
+ * Includes Sizzle.js
+ * http://sizzlejs.com/
+ * Copyright 2010, The Dojo Foundation
+ * Released under the MIT, BSD, and GPL Licenses.
+ *
+ * Date: Sat Feb 13 22:33:48 2010 -0500
+ */
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+this.end;this.pos=this.state=1;this.update();this.options.curAnim[this.prop]=true;for(var f in this.options.curAnim)if(this.options.curAnim[f]!==true)d=false;if(d){if(this.options.display!=null){this.elem.style.overflow=this.options.overflow;a=c.data(this.elem,"olddisplay");this.elem.style.display=a?a:this.options.display;if(c.css(this.elem,"display")==="none")this.elem.style.display="block"}this.options.hide&&c(this.elem).hide();if(this.options.hide||this.options.show)for(var e in this. [...]
+e,this.options.orig[e]);this.options.complete.call(this.elem)}return false}else{e=b-this.startTime;this.state=e/this.options.duration;a=this.options.easing||(c.easing.swing?"swing":"linear");this.pos=c.easing[this.options.specialEasing&&this.options.specialEasing[this.prop]||a](this.state,e,0,1,this.options.duration);this.now=this.start+(this.end-this.start)*this.pos;this.update()}return true}};c.extend(c.fx,{tick:function(){for(var a=c.timers,b=0;b<a.length;b++)a[b]()||a.splice(b--,1);a [...]
+c.fx.stop()},stop:function(){clearInterval(W);W=null},speeds:{slow:600,fast:200,_default:400},step:{opacity:function(a){c.style(a.elem,"opacity",a.now)},_default:function(a){if(a.elem.style&&a.elem.style[a.prop]!=null)a.elem.style[a.prop]=(a.prop==="width"||a.prop==="height"?Math.max(0,a.now):a.now)+a.unit;else a.elem[a.prop]=a.now}}});if(c.expr&&c.expr.filters)c.expr.filters.animated=function(a){return c.grep(c.timers,function(b){return a===b.elem}).length};c.fn.offset="getBoundingClien [...]
+function(a){var b=this[0];if(a)return this.each(function(e){c.offset.setOffset(this,a,e)});if(!b||!b.ownerDocument)return null;if(b===b.ownerDocument.body)return c.offset.bodyOffset(b);var d=b.getBoundingClientRect(),f=b.ownerDocument;b=f.body;f=f.documentElement;return{top:d.top+(self.pageYOffset||c.support.boxModel&&f.scrollTop||b.scrollTop)-(f.clientTop||b.clientTop||0),left:d.left+(self.pageXOffset||c.support.boxModel&&f.scrollLeft||b.scrollLeft)-(f.clientLeft||b.clientLeft||0)}}:fun [...]
+this[0];if(a)return this.each(function(r){c.offset.setOffset(this,a,r)});if(!b||!b.ownerDocument)return null;if(b===b.ownerDocument.body)return c.offset.bodyOffset(b);c.offset.initialize();var d=b.offsetParent,f=b,e=b.ownerDocument,j,i=e.documentElement,o=e.body;f=(e=e.defaultView)?e.getComputedStyle(b,null):b.currentStyle;for(var k=b.offsetTop,n=b.offsetLeft;(b=b.parentNode)&&b!==o&&b!==i;){if(c.offset.supportsFixedPosition&&f.position==="fixed")break;j=e?e.getComputedStyle(b,null):b.cu [...]
+k-=b.scrollTop;n-=b.scrollLeft;if(b===d){k+=b.offsetTop;n+=b.offsetLeft;if(c.offset.doesNotAddBorder&&!(c.offset.doesAddBorderForTableAndCells&&/^t(able|d|h)$/i.test(b.nodeName))){k+=parseFloat(j.borderTopWidth)||0;n+=parseFloat(j.borderLeftWidth)||0}f=d;d=b.offsetParent}if(c.offset.subtractsBorderForOverflowNotVisible&&j.overflow!=="visible"){k+=parseFloat(j.borderTopWidth)||0;n+=parseFloat(j.borderLeftWidth)||0}f=j}if(f.position==="relative"||f.position==="static"){k+=o.offsetTop;n+=o. [...]
+f.position==="fixed"){k+=Math.max(i.scrollTop,o.scrollTop);n+=Math.max(i.scrollLeft,o.scrollLeft)}return{top:k,left:n}};c.offset={initialize:function(){var a=s.body,b=s.createElement("div"),d,f,e,j=parseFloat(c.curCSS(a,"marginTop",true))||0;c.extend(b.style,{position:"absolute",top:0,left:0,margin:0,border:0,width:"1px",height:"1px",visibility:"hidden"});b.innerHTML="<div style='position:absolute;top:0;left:0;margin:0;border:5px solid #000;padding:0;width:1px;height:1px;'><div></div></d [...]
+a.insertBefore(b,a.firstChild);d=b.firstChild;f=d.firstChild;e=d.nextSibling.firstChild.firstChild;this.doesNotAddBorder=f.offsetTop!==5;this.doesAddBorderForTableAndCells=e.offsetTop===5;f.style.position="fixed";f.style.top="20px";this.supportsFixedPosition=f.offsetTop===20||f.offsetTop===15;f.style.position=f.style.top="";d.style.overflow="hidden";d.style.position="relative";this.subtractsBorderForOverflowNotVisible=f.offsetTop===-5;this.doesNotIncludeMarginInBodyOffset=a.offsetTop!==j [...]
+c.offset.initialize=c.noop},bodyOffset:function(a){var b=a.offsetTop,d=a.offsetLeft;c.offset.initialize();if(c.offset.doesNotIncludeMarginInBodyOffset){b+=parseFloat(c.curCSS(a,"marginTop",true))||0;d+=parseFloat(c.curCSS(a,"marginLeft",true))||0}return{top:b,left:d}},setOffset:function(a,b,d){if(/static/.test(c.curCSS(a,"position")))a.style.position="relative";var f=c(a),e=f.offset(),j=parseInt(c.curCSS(a,"top",true),10)||0,i=parseInt(c.curCSS(a,"left",true),10)||0;if(c.isFunction(b))b= [...]
+d,e);d={top:b.top-e.top+j,left:b.left-e.left+i};"using"in b?b.using.call(a,d):f.css(d)}};c.fn.extend({position:function(){if(!this[0])return null;var a=this[0],b=this.offsetParent(),d=this.offset(),f=/^body|html$/i.test(b[0].nodeName)?{top:0,left:0}:b.offset();d.top-=parseFloat(c.curCSS(a,"marginTop",true))||0;d.left-=parseFloat(c.curCSS(a,"marginLeft",true))||0;f.top+=parseFloat(c.curCSS(b[0],"borderTopWidth",true))||0;f.left+=parseFloat(c.curCSS(b[0],"borderLeftWidth",true))||0;return{ [...]
+f.top,left:d.left-f.left}},offsetParent:function(){return this.map(function(){for(var a=this.offsetParent||s.body;a&&!/^body|html$/i.test(a.nodeName)&&c.css(a,"position")==="static";)a=a.offsetParent;return a})}});c.each(["Left","Top"],function(a,b){var d="scroll"+b;c.fn[d]=function(f){var e=this[0],j;if(!e)return null;if(f!==w)return this.each(function(){if(j=wa(this))j.scrollTo(!a?f:c(j).scrollLeft(),a?f:c(j).scrollTop());else this[d]=f});else return(j=wa(e))?"pageXOffset"in j?j[a?"pag [...]
+"pageXOffset"]:c.support.boxModel&&j.document.documentElement[d]||j.document.body[d]:e[d]}});c.each(["Height","Width"],function(a,b){var d=b.toLowerCase();c.fn["inner"+b]=function(){return this[0]?c.css(this[0],d,false,"padding"):null};c.fn["outer"+b]=function(f){return this[0]?c.css(this[0],d,false,f?"margin":"border"):null};c.fn[d]=function(f){var e=this[0];if(!e)return f==null?null:this;if(c.isFunction(f))return this.each(function(j){var i=c(this);i[d](f.call(this,j,i[d]()))});return" [...]
+e&&e.document?e.document.compatMode==="CSS1Compat"&&e.document.documentElement["client"+b]||e.document.body["client"+b]:e.nodeType===9?Math.max(e.documentElement["client"+b],e.body["scroll"+b],e.documentElement["scroll"+b],e.body["offset"+b],e.documentElement["offset"+b]):f===w?c.css(e,d):this.css(d,typeof f==="string"?f:f+"px")}});A.jQuery=A.$=c})(window);
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diff --git a/doc/count-data/_static/pygments.css b/doc/count-data/_static/pygments.css
new file mode 100644
index 0000000..1a14f2a
--- /dev/null
+++ b/doc/count-data/_static/pygments.css
@@ -0,0 +1,62 @@
+.highlight .hll { background-color: #ffffcc }
+.highlight { background: #eeffcc; }
+.highlight .c { color: #408090; font-style: italic } /* Comment */
+.highlight .err { border: 1px solid #FF0000 } /* Error */
+.highlight .k { color: #007020; font-weight: bold } /* Keyword */
+.highlight .o { color: #666666 } /* Operator */
+.highlight .cm { color: #408090; font-style: italic } /* Comment.Multiline */
+.highlight .cp { color: #007020 } /* Comment.Preproc */
+.highlight .c1 { color: #408090; font-style: italic } /* Comment.Single */
+.highlight .cs { color: #408090; background-color: #fff0f0 } /* Comment.Special */
+.highlight .gd { color: #A00000 } /* Generic.Deleted */
+.highlight .ge { font-style: italic } /* Generic.Emph */
+.highlight .gr { color: #FF0000 } /* Generic.Error */
+.highlight .gh { color: #000080; font-weight: bold } /* Generic.Heading */
+.highlight .gi { color: #00A000 } /* Generic.Inserted */
+.highlight .go { color: #303030 } /* Generic.Output */
+.highlight .gp { color: #c65d09; font-weight: bold } /* Generic.Prompt */
+.highlight .gs { font-weight: bold } /* Generic.Strong */
+.highlight .gu { color: #800080; font-weight: bold } /* Generic.Subheading */
+.highlight .gt { color: #0040D0 } /* Generic.Traceback */
+.highlight .kc { color: #007020; font-weight: bold } /* Keyword.Constant */
+.highlight .kd { color: #007020; font-weight: bold } /* Keyword.Declaration */
+.highlight .kn { color: #007020; font-weight: bold } /* Keyword.Namespace */
+.highlight .kp { color: #007020 } /* Keyword.Pseudo */
+.highlight .kr { color: #007020; font-weight: bold } /* Keyword.Reserved */
+.highlight .kt { color: #902000 } /* Keyword.Type */
+.highlight .m { color: #208050 } /* Literal.Number */
+.highlight .s { color: #4070a0 } /* Literal.String */
+.highlight .na { color: #4070a0 } /* Name.Attribute */
+.highlight .nb { color: #007020 } /* Name.Builtin */
+.highlight .nc { color: #0e84b5; font-weight: bold } /* Name.Class */
+.highlight .no { color: #60add5 } /* Name.Constant */
+.highlight .nd { color: #555555; font-weight: bold } /* Name.Decorator */
+.highlight .ni { color: #d55537; font-weight: bold } /* Name.Entity */
+.highlight .ne { color: #007020 } /* Name.Exception */
+.highlight .nf { color: #06287e } /* Name.Function */
+.highlight .nl { color: #002070; font-weight: bold } /* Name.Label */
+.highlight .nn { color: #0e84b5; font-weight: bold } /* Name.Namespace */
+.highlight .nt { color: #062873; font-weight: bold } /* Name.Tag */
+.highlight .nv { color: #bb60d5 } /* Name.Variable */
+.highlight .ow { color: #007020; font-weight: bold } /* Operator.Word */
+.highlight .w { color: #bbbbbb } /* Text.Whitespace */
+.highlight .mf { color: #208050 } /* Literal.Number.Float */
+.highlight .mh { color: #208050 } /* Literal.Number.Hex */
+.highlight .mi { color: #208050 } /* Literal.Number.Integer */
+.highlight .mo { color: #208050 } /* Literal.Number.Oct */
+.highlight .sb { color: #4070a0 } /* Literal.String.Backtick */
+.highlight .sc { color: #4070a0 } /* Literal.String.Char */
+.highlight .sd { color: #4070a0; font-style: italic } /* Literal.String.Doc */
+.highlight .s2 { color: #4070a0 } /* Literal.String.Double */
+.highlight .se { color: #4070a0; font-weight: bold } /* Literal.String.Escape */
+.highlight .sh { color: #4070a0 } /* Literal.String.Heredoc */
+.highlight .si { color: #70a0d0; font-style: italic } /* Literal.String.Interpol */
+.highlight .sx { color: #c65d09 } /* Literal.String.Other */
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+.highlight .ss { color: #517918 } /* Literal.String.Symbol */
+.highlight .bp { color: #007020 } /* Name.Builtin.Pseudo */
+.highlight .vc { color: #bb60d5 } /* Name.Variable.Class */
+.highlight .vg { color: #bb60d5 } /* Name.Variable.Global */
+.highlight .vi { color: #bb60d5 } /* Name.Variable.Instance */
+.highlight .il { color: #208050 } /* Literal.Number.Integer.Long */
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diff --git a/doc/count-data/_static/report.css b/doc/count-data/_static/report.css
new file mode 100644
index 0000000..19ae268
--- /dev/null
+++ b/doc/count-data/_static/report.css
@@ -0,0 +1,50 @@
+div.summary{
+
+}
+
+table.summary{
+
+ border: 0px;
+ width: 100%;
+ vertical-align: top;
+
+}
+
+div.table-summary{
+ margin-left:auto;
+ margin-right:auto;
+ padding-bottom: 20px;
+}
+
+td.column1{
+ width: 60%;
+}
+
+table.hovertable {
+
+ font-size:14px;
+
+ border-width: 1px;
+ border-color: #999999;
+ border-collapse: collapse;
+}
+table.hovertable th {
+ background-color:#FFFFFF;
+ border-width: 1px;
+ padding: 8px;
+ border-style: solid;
+ border-color: #a9c6c9;
+}
+table.hovertable tr {
+ background-color:#FFFFFF;
+}
+table.hovertable td {
+ border-width: 1px;
+ padding: 8px;
+ border-style: solid;
+ border-color: #a9c6c9;
+}
+
+
+
+
diff --git a/doc/count-data/_static/searchtools.js b/doc/count-data/_static/searchtools.js
new file mode 100644
index 0000000..663be4c
--- /dev/null
+++ b/doc/count-data/_static/searchtools.js
@@ -0,0 +1,560 @@
+/*
+ * searchtools.js_t
+ * ~~~~~~~~~~~~~~~~
+ *
+ * Sphinx JavaScript utilties for the full-text search.
+ *
+ * :copyright: Copyright 2007-2011 by the Sphinx team, see AUTHORS.
+ * :license: BSD, see LICENSE for details.
+ *
+ */
+
+/**
+ * helper function to return a node containing the
+ * search summary for a given text. keywords is a list
+ * of stemmed words, hlwords is the list of normal, unstemmed
+ * words. the first one is used to find the occurance, the
+ * latter for highlighting it.
+ */
+
+jQuery.makeSearchSummary = function(text, keywords, hlwords) {
+ var textLower = text.toLowerCase();
+ var start = 0;
+ $.each(keywords, function() {
+ var i = textLower.indexOf(this.toLowerCase());
+ if (i > -1)
+ start = i;
+ });
+ start = Math.max(start - 120, 0);
+ var excerpt = ((start > 0) ? '...' : '') +
+ $.trim(text.substr(start, 240)) +
+ ((start + 240 - text.length) ? '...' : '');
+ var rv = $('<div class="context"></div>').text(excerpt);
+ $.each(hlwords, function() {
+ rv = rv.highlightText(this, 'highlighted');
+ });
+ return rv;
+}
+
+
+/**
+ * Porter Stemmer
+ */
+var Stemmer = function() {
+
+ var step2list = {
+ ational: 'ate',
+ tional: 'tion',
+ enci: 'ence',
+ anci: 'ance',
+ izer: 'ize',
+ bli: 'ble',
+ alli: 'al',
+ entli: 'ent',
+ eli: 'e',
+ ousli: 'ous',
+ ization: 'ize',
+ ation: 'ate',
+ ator: 'ate',
+ alism: 'al',
+ iveness: 'ive',
+ fulness: 'ful',
+ ousness: 'ous',
+ aliti: 'al',
+ iviti: 'ive',
+ biliti: 'ble',
+ logi: 'log'
+ };
+
+ var step3list = {
+ icate: 'ic',
+ ative: '',
+ alize: 'al',
+ iciti: 'ic',
+ ical: 'ic',
+ ful: '',
+ ness: ''
+ };
+
+ var c = "[^aeiou]"; // consonant
+ var v = "[aeiouy]"; // vowel
+ var C = c + "[^aeiouy]*"; // consonant sequence
+ var V = v + "[aeiou]*"; // vowel sequence
+
+ var mgr0 = "^(" + C + ")?" + V + C; // [C]VC... is m>0
+ var meq1 = "^(" + C + ")?" + V + C + "(" + V + ")?$"; // [C]VC[V] is m=1
+ var mgr1 = "^(" + C + ")?" + V + C + V + C; // [C]VCVC... is m>1
+ var s_v = "^(" + C + ")?" + v; // vowel in stem
+
+ this.stemWord = function (w) {
+ var stem;
+ var suffix;
+ var firstch;
+ var origword = w;
+
+ if (w.length < 3)
+ return w;
+
+ var re;
+ var re2;
+ var re3;
+ var re4;
+
+ firstch = w.substr(0,1);
+ if (firstch == "y")
+ w = firstch.toUpperCase() + w.substr(1);
+
+ // Step 1a
+ re = /^(.+?)(ss|i)es$/;
+ re2 = /^(.+?)([^s])s$/;
+
+ if (re.test(w))
+ w = w.replace(re,"$1$2");
+ else if (re2.test(w))
+ w = w.replace(re2,"$1$2");
+
+ // Step 1b
+ re = /^(.+?)eed$/;
+ re2 = /^(.+?)(ed|ing)$/;
+ if (re.test(w)) {
+ var fp = re.exec(w);
+ re = new RegExp(mgr0);
+ if (re.test(fp[1])) {
+ re = /.$/;
+ w = w.replace(re,"");
+ }
+ }
+ else if (re2.test(w)) {
+ var fp = re2.exec(w);
+ stem = fp[1];
+ re2 = new RegExp(s_v);
+ if (re2.test(stem)) {
+ w = stem;
+ re2 = /(at|bl|iz)$/;
+ re3 = new RegExp("([^aeiouylsz])\\1$");
+ re4 = new RegExp("^" + C + v + "[^aeiouwxy]$");
+ if (re2.test(w))
+ w = w + "e";
+ else if (re3.test(w)) {
+ re = /.$/;
+ w = w.replace(re,"");
+ }
+ else if (re4.test(w))
+ w = w + "e";
+ }
+ }
+
+ // Step 1c
+ re = /^(.+?)y$/;
+ if (re.test(w)) {
+ var fp = re.exec(w);
+ stem = fp[1];
+ re = new RegExp(s_v);
+ if (re.test(stem))
+ w = stem + "i";
+ }
+
+ // Step 2
+ re = /^(.+?)(ational|tional|enci|anci|izer|bli|alli|entli|eli|ousli|ization|ation|ator|alism|iveness|fulness|ousness|aliti|iviti|biliti|logi)$/;
+ if (re.test(w)) {
+ var fp = re.exec(w);
+ stem = fp[1];
+ suffix = fp[2];
+ re = new RegExp(mgr0);
+ if (re.test(stem))
+ w = stem + step2list[suffix];
+ }
+
+ // Step 3
+ re = /^(.+?)(icate|ative|alize|iciti|ical|ful|ness)$/;
+ if (re.test(w)) {
+ var fp = re.exec(w);
+ stem = fp[1];
+ suffix = fp[2];
+ re = new RegExp(mgr0);
+ if (re.test(stem))
+ w = stem + step3list[suffix];
+ }
+
+ // Step 4
+ re = /^(.+?)(al|ance|ence|er|ic|able|ible|ant|ement|ment|ent|ou|ism|ate|iti|ous|ive|ize)$/;
+ re2 = /^(.+?)(s|t)(ion)$/;
+ if (re.test(w)) {
+ var fp = re.exec(w);
+ stem = fp[1];
+ re = new RegExp(mgr1);
+ if (re.test(stem))
+ w = stem;
+ }
+ else if (re2.test(w)) {
+ var fp = re2.exec(w);
+ stem = fp[1] + fp[2];
+ re2 = new RegExp(mgr1);
+ if (re2.test(stem))
+ w = stem;
+ }
+
+ // Step 5
+ re = /^(.+?)e$/;
+ if (re.test(w)) {
+ var fp = re.exec(w);
+ stem = fp[1];
+ re = new RegExp(mgr1);
+ re2 = new RegExp(meq1);
+ re3 = new RegExp("^" + C + v + "[^aeiouwxy]$");
+ if (re.test(stem) || (re2.test(stem) && !(re3.test(stem))))
+ w = stem;
+ }
+ re = /ll$/;
+ re2 = new RegExp(mgr1);
+ if (re.test(w) && re2.test(w)) {
+ re = /.$/;
+ w = w.replace(re,"");
+ }
+
+ // and turn initial Y back to y
+ if (firstch == "y")
+ w = firstch.toLowerCase() + w.substr(1);
+ return w;
+ }
+}
+
+
+/**
+ * Search Module
+ */
+var Search = {
+
+ _index : null,
+ _queued_query : null,
+ _pulse_status : -1,
+
+ init : function() {
+ var params = $.getQueryParameters();
+ if (params.q) {
+ var query = params.q[0];
+ $('input[name="q"]')[0].value = query;
+ this.performSearch(query);
+ }
+ },
+
+ loadIndex : function(url) {
+ $.ajax({type: "GET", url: url, data: null, success: null,
+ dataType: "script", cache: true});
+ },
+
+ setIndex : function(index) {
+ var q;
+ this._index = index;
+ if ((q = this._queued_query) !== null) {
+ this._queued_query = null;
+ Search.query(q);
+ }
+ },
+
+ hasIndex : function() {
+ return this._index !== null;
+ },
+
+ deferQuery : function(query) {
+ this._queued_query = query;
+ },
+
+ stopPulse : function() {
+ this._pulse_status = 0;
+ },
+
+ startPulse : function() {
+ if (this._pulse_status >= 0)
+ return;
+ function pulse() {
+ Search._pulse_status = (Search._pulse_status + 1) % 4;
+ var dotString = '';
+ for (var i = 0; i < Search._pulse_status; i++)
+ dotString += '.';
+ Search.dots.text(dotString);
+ if (Search._pulse_status > -1)
+ window.setTimeout(pulse, 500);
+ };
+ pulse();
+ },
+
+ /**
+ * perform a search for something
+ */
+ performSearch : function(query) {
+ // create the required interface elements
+ this.out = $('#search-results');
+ this.title = $('<h2>' + _('Searching') + '</h2>').appendTo(this.out);
+ this.dots = $('<span></span>').appendTo(this.title);
+ this.status = $('<p style="display: none"></p>').appendTo(this.out);
+ this.output = $('<ul class="search"/>').appendTo(this.out);
+
+ $('#search-progress').text(_('Preparing search...'));
+ this.startPulse();
+
+ // index already loaded, the browser was quick!
+ if (this.hasIndex())
+ this.query(query);
+ else
+ this.deferQuery(query);
+ },
+
+ query : function(query) {
+ var stopwords = ["and","then","into","it","as","are","in","if","for","no","there","their","was","is","be","to","that","but","they","not","such","with","by","a","on","these","of","will","this","near","the","or","at"];
+
+ // Stem the searchterms and add them to the correct list
+ var stemmer = new Stemmer();
+ var searchterms = [];
+ var excluded = [];
+ var hlterms = [];
+ var tmp = query.split(/\s+/);
+ var objectterms = [];
+ for (var i = 0; i < tmp.length; i++) {
+ if (tmp[i] != "") {
+ objectterms.push(tmp[i].toLowerCase());
+ }
+
+ if ($u.indexOf(stopwords, tmp[i]) != -1 || tmp[i].match(/^\d+$/) ||
+ tmp[i] == "") {
+ // skip this "word"
+ continue;
+ }
+ // stem the word
+ var word = stemmer.stemWord(tmp[i]).toLowerCase();
+ // select the correct list
+ if (word[0] == '-') {
+ var toAppend = excluded;
+ word = word.substr(1);
+ }
+ else {
+ var toAppend = searchterms;
+ hlterms.push(tmp[i].toLowerCase());
+ }
+ // only add if not already in the list
+ if (!$.contains(toAppend, word))
+ toAppend.push(word);
+ };
+ var highlightstring = '?highlight=' + $.urlencode(hlterms.join(" "));
+
+ // console.debug('SEARCH: searching for:');
+ // console.info('required: ', searchterms);
+ // console.info('excluded: ', excluded);
+
+ // prepare search
+ var filenames = this._index.filenames;
+ var titles = this._index.titles;
+ var terms = this._index.terms;
+ var fileMap = {};
+ var files = null;
+ // different result priorities
+ var importantResults = [];
+ var objectResults = [];
+ var regularResults = [];
+ var unimportantResults = [];
+ $('#search-progress').empty();
+
+ // lookup as object
+ for (var i = 0; i < objectterms.length; i++) {
+ var others = [].concat(objectterms.slice(0,i),
+ objectterms.slice(i+1, objectterms.length))
+ var results = this.performObjectSearch(objectterms[i], others);
+ // Assume first word is most likely to be the object,
+ // other words more likely to be in description.
+ // Therefore put matches for earlier words first.
+ // (Results are eventually used in reverse order).
+ objectResults = results[0].concat(objectResults);
+ importantResults = results[1].concat(importantResults);
+ unimportantResults = results[2].concat(unimportantResults);
+ }
+
+ // perform the search on the required terms
+ for (var i = 0; i < searchterms.length; i++) {
+ var word = searchterms[i];
+ // no match but word was a required one
+ if ((files = terms[word]) == null)
+ break;
+ if (files.length == undefined) {
+ files = [files];
+ }
+ // create the mapping
+ for (var j = 0; j < files.length; j++) {
+ var file = files[j];
+ if (file in fileMap)
+ fileMap[file].push(word);
+ else
+ fileMap[file] = [word];
+ }
+ }
+
+ // now check if the files don't contain excluded terms
+ for (var file in fileMap) {
+ var valid = true;
+
+ // check if all requirements are matched
+ if (fileMap[file].length != searchterms.length)
+ continue;
+
+ // ensure that none of the excluded terms is in the
+ // search result.
+ for (var i = 0; i < excluded.length; i++) {
+ if (terms[excluded[i]] == file ||
+ $.contains(terms[excluded[i]] || [], file)) {
+ valid = false;
+ break;
+ }
+ }
+
+ // if we have still a valid result we can add it
+ // to the result list
+ if (valid)
+ regularResults.push([filenames[file], titles[file], '', null]);
+ }
+
+ // delete unused variables in order to not waste
+ // memory until list is retrieved completely
+ delete filenames, titles, terms;
+
+ // now sort the regular results descending by title
+ regularResults.sort(function(a, b) {
+ var left = a[1].toLowerCase();
+ var right = b[1].toLowerCase();
+ return (left > right) ? -1 : ((left < right) ? 1 : 0);
+ });
+
+ // combine all results
+ var results = unimportantResults.concat(regularResults)
+ .concat(objectResults).concat(importantResults);
+
+ // print the results
+ var resultCount = results.length;
+ function displayNextItem() {
+ // results left, load the summary and display it
+ if (results.length) {
+ var item = results.pop();
+ var listItem = $('<li style="display:none"></li>');
+ if (DOCUMENTATION_OPTIONS.FILE_SUFFIX == '') {
+ // dirhtml builder
+ var dirname = item[0] + '/';
+ if (dirname.match(/\/index\/$/)) {
+ dirname = dirname.substring(0, dirname.length-6);
+ } else if (dirname == 'index/') {
+ dirname = '';
+ }
+ listItem.append($('<a/>').attr('href',
+ DOCUMENTATION_OPTIONS.URL_ROOT + dirname +
+ highlightstring + item[2]).html(item[1]));
+ } else {
+ // normal html builders
+ listItem.append($('<a/>').attr('href',
+ item[0] + DOCUMENTATION_OPTIONS.FILE_SUFFIX +
+ highlightstring + item[2]).html(item[1]));
+ }
+ if (item[3]) {
+ listItem.append($('<span> (' + item[3] + ')</span>'));
+ Search.output.append(listItem);
+ listItem.slideDown(5, function() {
+ displayNextItem();
+ });
+ } else if (DOCUMENTATION_OPTIONS.HAS_SOURCE) {
+ $.get(DOCUMENTATION_OPTIONS.URL_ROOT + '_sources/' +
+ item[0] + '.txt', function(data) {
+ if (data != '') {
+ listItem.append($.makeSearchSummary(data, searchterms, hlterms));
+ Search.output.append(listItem);
+ }
+ listItem.slideDown(5, function() {
+ displayNextItem();
+ });
+ }, "text");
+ } else {
+ // no source available, just display title
+ Search.output.append(listItem);
+ listItem.slideDown(5, function() {
+ displayNextItem();
+ });
+ }
+ }
+ // search finished, update title and status message
+ else {
+ Search.stopPulse();
+ Search.title.text(_('Search Results'));
+ if (!resultCount)
+ Search.status.text(_('Your search did not match any documents. Please make sure that all words are spelled correctly and that you\'ve selected enough categories.'));
+ else
+ Search.status.text(_('Search finished, found %s page(s) matching the search query.').replace('%s', resultCount));
+ Search.status.fadeIn(500);
+ }
+ }
+ displayNextItem();
+ },
+
+ performObjectSearch : function(object, otherterms) {
+ var filenames = this._index.filenames;
+ var objects = this._index.objects;
+ var objnames = this._index.objnames;
+ var titles = this._index.titles;
+
+ var importantResults = [];
+ var objectResults = [];
+ var unimportantResults = [];
+
+ for (var prefix in objects) {
+ for (var name in objects[prefix]) {
+ var fullname = (prefix ? prefix + '.' : '') + name;
+ if (fullname.toLowerCase().indexOf(object) > -1) {
+ var match = objects[prefix][name];
+ var objname = objnames[match[1]][2];
+ var title = titles[match[0]];
+ // If more than one term searched for, we require other words to be
+ // found in the name/title/description
+ if (otherterms.length > 0) {
+ var haystack = (prefix + ' ' + name + ' ' +
+ objname + ' ' + title).toLowerCase();
+ var allfound = true;
+ for (var i = 0; i < otherterms.length; i++) {
+ if (haystack.indexOf(otherterms[i]) == -1) {
+ allfound = false;
+ break;
+ }
+ }
+ if (!allfound) {
+ continue;
+ }
+ }
+ var descr = objname + _(', in ') + title;
+ anchor = match[3];
+ if (anchor == '')
+ anchor = fullname;
+ else if (anchor == '-')
+ anchor = objnames[match[1]][1] + '-' + fullname;
+ result = [filenames[match[0]], fullname, '#'+anchor, descr];
+ switch (match[2]) {
+ case 1: objectResults.push(result); break;
+ case 0: importantResults.push(result); break;
+ case 2: unimportantResults.push(result); break;
+ }
+ }
+ }
+ }
+
+ // sort results descending
+ objectResults.sort(function(a, b) {
+ return (a[1] > b[1]) ? -1 : ((a[1] < b[1]) ? 1 : 0);
+ });
+
+ importantResults.sort(function(a, b) {
+ return (a[1] > b[1]) ? -1 : ((a[1] < b[1]) ? 1 : 0);
+ });
+
+ unimportantResults.sort(function(a, b) {
+ return (a[1] > b[1]) ? -1 : ((a[1] < b[1]) ? 1 : 0);
+ });
+
+ return [importantResults, objectResults, unimportantResults]
+ }
+}
+
+$(document).ready(function() {
+ Search.init();
+});
\ No newline at end of file
diff --git a/doc/count-data/_static/underscore.js b/doc/count-data/_static/underscore.js
new file mode 100644
index 0000000..5d89914
--- /dev/null
+++ b/doc/count-data/_static/underscore.js
@@ -0,0 +1,23 @@
+// Underscore.js 0.5.5
+// (c) 2009 Jeremy Ashkenas, DocumentCloud Inc.
+// Underscore is freely distributable under the terms of the MIT license.
+// Portions of Underscore are inspired by or borrowed from Prototype.js,
+// Oliver Steele's Functional, and John Resig's Micro-Templating.
+// For all details and documentation:
+// http://documentcloud.github.com/underscore/
+(function(){var j=this,n=j._,i=function(a){this._wrapped=a},m=typeof StopIteration!=="undefined"?StopIteration:"__break__",b=j._=function(a){return new i(a)};if(typeof exports!=="undefined")exports._=b;var k=Array.prototype.slice,o=Array.prototype.unshift,p=Object.prototype.toString,q=Object.prototype.hasOwnProperty,r=Object.prototype.propertyIsEnumerable;b.VERSION="0.5.5";b.each=function(a,c,d){try{if(a.forEach)a.forEach(c,d);else if(b.isArray(a)||b.isArguments(a))for(var e=0,f=a.length [...]
+a[e],e,a);else{var g=b.keys(a);f=g.length;for(e=0;e<f;e++)c.call(d,a[g[e]],g[e],a)}}catch(h){if(h!=m)throw h;}return a};b.map=function(a,c,d){if(a&&b.isFunction(a.map))return a.map(c,d);var e=[];b.each(a,function(f,g,h){e.push(c.call(d,f,g,h))});return e};b.reduce=function(a,c,d,e){if(a&&b.isFunction(a.reduce))return a.reduce(b.bind(d,e),c);b.each(a,function(f,g,h){c=d.call(e,c,f,g,h)});return c};b.reduceRight=function(a,c,d,e){if(a&&b.isFunction(a.reduceRight))return a.reduceRight(b.bin [...]
+var f=b.clone(b.toArray(a)).reverse();b.each(f,function(g,h){c=d.call(e,c,g,h,a)});return c};b.detect=function(a,c,d){var e;b.each(a,function(f,g,h){if(c.call(d,f,g,h)){e=f;b.breakLoop()}});return e};b.select=function(a,c,d){if(a&&b.isFunction(a.filter))return a.filter(c,d);var e=[];b.each(a,function(f,g,h){c.call(d,f,g,h)&&e.push(f)});return e};b.reject=function(a,c,d){var e=[];b.each(a,function(f,g,h){!c.call(d,f,g,h)&&e.push(f)});return e};b.all=function(a,c,d){c=c||b.identity;if(a&&b [...]
+d);var e=true;b.each(a,function(f,g,h){(e=e&&c.call(d,f,g,h))||b.breakLoop()});return e};b.any=function(a,c,d){c=c||b.identity;if(a&&b.isFunction(a.some))return a.some(c,d);var e=false;b.each(a,function(f,g,h){if(e=c.call(d,f,g,h))b.breakLoop()});return e};b.include=function(a,c){if(b.isArray(a))return b.indexOf(a,c)!=-1;var d=false;b.each(a,function(e){if(d=e===c)b.breakLoop()});return d};b.invoke=function(a,c){var d=b.rest(arguments,2);return b.map(a,function(e){return(c?e[c]:e).apply( [...]
+function(a,c){return b.map(a,function(d){return d[c]})};b.max=function(a,c,d){if(!c&&b.isArray(a))return Math.max.apply(Math,a);var e={computed:-Infinity};b.each(a,function(f,g,h){g=c?c.call(d,f,g,h):f;g>=e.computed&&(e={value:f,computed:g})});return e.value};b.min=function(a,c,d){if(!c&&b.isArray(a))return Math.min.apply(Math,a);var e={computed:Infinity};b.each(a,function(f,g,h){g=c?c.call(d,f,g,h):f;g<e.computed&&(e={value:f,computed:g})});return e.value};b.sortBy=function(a,c,d){retur [...]
+function(e,f,g){return{value:e,criteria:c.call(d,e,f,g)}}).sort(function(e,f){e=e.criteria;f=f.criteria;return e<f?-1:e>f?1:0}),"value")};b.sortedIndex=function(a,c,d){d=d||b.identity;for(var e=0,f=a.length;e<f;){var g=e+f>>1;d(a[g])<d(c)?(e=g+1):(f=g)}return e};b.toArray=function(a){if(!a)return[];if(a.toArray)return a.toArray();if(b.isArray(a))return a;if(b.isArguments(a))return k.call(a);return b.values(a)};b.size=function(a){return b.toArray(a).length};b.first=function(a,c,d){return [...]
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+return a};b.delay=function(a,c){var d=b.rest(arguments,2);return setTimeout(function(){return a.apply(a,d)},c)};b.defer=function(a){return b.delay.apply(b,[a,1].concat(b.rest(arguments)))};b.wrap=function(a,c){return function(){var d=[a].concat(b.toArray(arguments));return c.apply(c,d)}};b.compose=function(){var a=b.toArray(arguments);return function(){for(var c=b.toArray(arguments),d=a.length-1;d>=0;d--)c=[a[d].apply(this,c)];return c[0]}};b.keys=function(a){if(b.isArray(a))return b.ran [...]
+var c=[];for(var d in a)q.call(a,d)&&c.push(d);return c};b.values=function(a){return b.map(a,b.identity)};b.functions=function(a){return b.select(b.keys(a),function(c){return b.isFunction(a[c])}).sort()};b.extend=function(a,c){for(var d in c)a[d]=c[d];return a};b.clone=function(a){if(b.isArray(a))return a.slice(0);return b.extend({},a)};b.tap=function(a,c){c(a);return a};b.isEqual=function(a,c){if(a===c)return true;var d=typeof a;if(d!=typeof c)return false;if(a==c)return true;if(!a&&c|| [...]
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diff --git a/doc/count-data/_static/up-pressed.png b/doc/count-data/_static/up-pressed.png
new file mode 100644
index 0000000..8bd587a
Binary files /dev/null and b/doc/count-data/_static/up-pressed.png differ
diff --git a/doc/count-data/_static/up.png b/doc/count-data/_static/up.png
new file mode 100644
index 0000000..b946256
Binary files /dev/null and b/doc/count-data/_static/up.png differ
diff --git a/doc/count-data/_static/websupport.js b/doc/count-data/_static/websupport.js
new file mode 100644
index 0000000..e9bd1b8
--- /dev/null
+++ b/doc/count-data/_static/websupport.js
@@ -0,0 +1,808 @@
+/*
+ * websupport.js
+ * ~~~~~~~~~~~~~
+ *
+ * sphinx.websupport utilties for all documentation.
+ *
+ * :copyright: Copyright 2007-2011 by the Sphinx team, see AUTHORS.
+ * :license: BSD, see LICENSE for details.
+ *
+ */
+
+(function($) {
+ $.fn.autogrow = function() {
+ return this.each(function() {
+ var textarea = this;
+
+ $.fn.autogrow.resize(textarea);
+
+ $(textarea)
+ .focus(function() {
+ textarea.interval = setInterval(function() {
+ $.fn.autogrow.resize(textarea);
+ }, 500);
+ })
+ .blur(function() {
+ clearInterval(textarea.interval);
+ });
+ });
+ };
+
+ $.fn.autogrow.resize = function(textarea) {
+ var lineHeight = parseInt($(textarea).css('line-height'), 10);
+ var lines = textarea.value.split('\n');
+ var columns = textarea.cols;
+ var lineCount = 0;
+ $.each(lines, function() {
+ lineCount += Math.ceil(this.length / columns) || 1;
+ });
+ var height = lineHeight * (lineCount + 1);
+ $(textarea).css('height', height);
+ };
+})(jQuery);
+
+(function($) {
+ var comp, by;
+
+ function init() {
+ initEvents();
+ initComparator();
+ }
+
+ function initEvents() {
+ $('a.comment-close').live("click", function(event) {
+ event.preventDefault();
+ hide($(this).attr('id').substring(2));
+ });
+ $('a.vote').live("click", function(event) {
+ event.preventDefault();
+ handleVote($(this));
+ });
+ $('a.reply').live("click", function(event) {
+ event.preventDefault();
+ openReply($(this).attr('id').substring(2));
+ });
+ $('a.close-reply').live("click", function(event) {
+ event.preventDefault();
+ closeReply($(this).attr('id').substring(2));
+ });
+ $('a.sort-option').live("click", function(event) {
+ event.preventDefault();
+ handleReSort($(this));
+ });
+ $('a.show-proposal').live("click", function(event) {
+ event.preventDefault();
+ showProposal($(this).attr('id').substring(2));
+ });
+ $('a.hide-proposal').live("click", function(event) {
+ event.preventDefault();
+ hideProposal($(this).attr('id').substring(2));
+ });
+ $('a.show-propose-change').live("click", function(event) {
+ event.preventDefault();
+ showProposeChange($(this).attr('id').substring(2));
+ });
+ $('a.hide-propose-change').live("click", function(event) {
+ event.preventDefault();
+ hideProposeChange($(this).attr('id').substring(2));
+ });
+ $('a.accept-comment').live("click", function(event) {
+ event.preventDefault();
+ acceptComment($(this).attr('id').substring(2));
+ });
+ $('a.delete-comment').live("click", function(event) {
+ event.preventDefault();
+ deleteComment($(this).attr('id').substring(2));
+ });
+ $('a.comment-markup').live("click", function(event) {
+ event.preventDefault();
+ toggleCommentMarkupBox($(this).attr('id').substring(2));
+ });
+ }
+
+ /**
+ * Set comp, which is a comparator function used for sorting and
+ * inserting comments into the list.
+ */
+ function setComparator() {
+ // If the first three letters are "asc", sort in ascending order
+ // and remove the prefix.
+ if (by.substring(0,3) == 'asc') {
+ var i = by.substring(3);
+ comp = function(a, b) { return a[i] - b[i]; };
+ } else {
+ // Otherwise sort in descending order.
+ comp = function(a, b) { return b[by] - a[by]; };
+ }
+
+ // Reset link styles and format the selected sort option.
+ $('a.sel').attr('href', '#').removeClass('sel');
+ $('a.by' + by).removeAttr('href').addClass('sel');
+ }
+
+ /**
+ * Create a comp function. If the user has preferences stored in
+ * the sortBy cookie, use those, otherwise use the default.
+ */
+ function initComparator() {
+ by = 'rating'; // Default to sort by rating.
+ // If the sortBy cookie is set, use that instead.
+ if (document.cookie.length > 0) {
+ var start = document.cookie.indexOf('sortBy=');
+ if (start != -1) {
+ start = start + 7;
+ var end = document.cookie.indexOf(";", start);
+ if (end == -1) {
+ end = document.cookie.length;
+ by = unescape(document.cookie.substring(start, end));
+ }
+ }
+ }
+ setComparator();
+ }
+
+ /**
+ * Show a comment div.
+ */
+ function show(id) {
+ $('#ao' + id).hide();
+ $('#ah' + id).show();
+ var context = $.extend({id: id}, opts);
+ var popup = $(renderTemplate(popupTemplate, context)).hide();
+ popup.find('textarea[name="proposal"]').hide();
+ popup.find('a.by' + by).addClass('sel');
+ var form = popup.find('#cf' + id);
+ form.submit(function(event) {
+ event.preventDefault();
+ addComment(form);
+ });
+ $('#s' + id).after(popup);
+ popup.slideDown('fast', function() {
+ getComments(id);
+ });
+ }
+
+ /**
+ * Hide a comment div.
+ */
+ function hide(id) {
+ $('#ah' + id).hide();
+ $('#ao' + id).show();
+ var div = $('#sc' + id);
+ div.slideUp('fast', function() {
+ div.remove();
+ });
+ }
+
+ /**
+ * Perform an ajax request to get comments for a node
+ * and insert the comments into the comments tree.
+ */
+ function getComments(id) {
+ $.ajax({
+ type: 'GET',
+ url: opts.getCommentsURL,
+ data: {node: id},
+ success: function(data, textStatus, request) {
+ var ul = $('#cl' + id);
+ var speed = 100;
+ $('#cf' + id)
+ .find('textarea[name="proposal"]')
+ .data('source', data.source);
+
+ if (data.comments.length === 0) {
+ ul.html('<li>No comments yet.</li>');
+ ul.data('empty', true);
+ } else {
+ // If there are comments, sort them and put them in the list.
+ var comments = sortComments(data.comments);
+ speed = data.comments.length * 100;
+ appendComments(comments, ul);
+ ul.data('empty', false);
+ }
+ $('#cn' + id).slideUp(speed + 200);
+ ul.slideDown(speed);
+ },
+ error: function(request, textStatus, error) {
+ showError('Oops, there was a problem retrieving the comments.');
+ },
+ dataType: 'json'
+ });
+ }
+
+ /**
+ * Add a comment via ajax and insert the comment into the comment tree.
+ */
+ function addComment(form) {
+ var node_id = form.find('input[name="node"]').val();
+ var parent_id = form.find('input[name="parent"]').val();
+ var text = form.find('textarea[name="comment"]').val();
+ var proposal = form.find('textarea[name="proposal"]').val();
+
+ if (text == '') {
+ showError('Please enter a comment.');
+ return;
+ }
+
+ // Disable the form that is being submitted.
+ form.find('textarea,input').attr('disabled', 'disabled');
+
+ // Send the comment to the server.
+ $.ajax({
+ type: "POST",
+ url: opts.addCommentURL,
+ dataType: 'json',
+ data: {
+ node: node_id,
+ parent: parent_id,
+ text: text,
+ proposal: proposal
+ },
+ success: function(data, textStatus, error) {
+ // Reset the form.
+ if (node_id) {
+ hideProposeChange(node_id);
+ }
+ form.find('textarea')
+ .val('')
+ .add(form.find('input'))
+ .removeAttr('disabled');
+ var ul = $('#cl' + (node_id || parent_id));
+ if (ul.data('empty')) {
+ $(ul).empty();
+ ul.data('empty', false);
+ }
+ insertComment(data.comment);
+ var ao = $('#ao' + node_id);
+ ao.find('img').attr({'src': opts.commentBrightImage});
+ if (node_id) {
+ // if this was a "root" comment, remove the commenting box
+ // (the user can get it back by reopening the comment popup)
+ $('#ca' + node_id).slideUp();
+ }
+ },
+ error: function(request, textStatus, error) {
+ form.find('textarea,input').removeAttr('disabled');
+ showError('Oops, there was a problem adding the comment.');
+ }
+ });
+ }
+
+ /**
+ * Recursively append comments to the main comment list and children
+ * lists, creating the comment tree.
+ */
+ function appendComments(comments, ul) {
+ $.each(comments, function() {
+ var div = createCommentDiv(this);
+ ul.append($(document.createElement('li')).html(div));
+ appendComments(this.children, div.find('ul.comment-children'));
+ // To avoid stagnating data, don't store the comments children in data.
+ this.children = null;
+ div.data('comment', this);
+ });
+ }
+
+ /**
+ * After adding a new comment, it must be inserted in the correct
+ * location in the comment tree.
+ */
+ function insertComment(comment) {
+ var div = createCommentDiv(comment);
+
+ // To avoid stagnating data, don't store the comments children in data.
+ comment.children = null;
+ div.data('comment', comment);
+
+ var ul = $('#cl' + (comment.node || comment.parent));
+ var siblings = getChildren(ul);
+
+ var li = $(document.createElement('li'));
+ li.hide();
+
+ // Determine where in the parents children list to insert this comment.
+ for(i=0; i < siblings.length; i++) {
+ if (comp(comment, siblings[i]) <= 0) {
+ $('#cd' + siblings[i].id)
+ .parent()
+ .before(li.html(div));
+ li.slideDown('fast');
+ return;
+ }
+ }
+
+ // If we get here, this comment rates lower than all the others,
+ // or it is the only comment in the list.
+ ul.append(li.html(div));
+ li.slideDown('fast');
+ }
+
+ function acceptComment(id) {
+ $.ajax({
+ type: 'POST',
+ url: opts.acceptCommentURL,
+ data: {id: id},
+ success: function(data, textStatus, request) {
+ $('#cm' + id).fadeOut('fast');
+ $('#cd' + id).removeClass('moderate');
+ },
+ error: function(request, textStatus, error) {
+ showError('Oops, there was a problem accepting the comment.');
+ }
+ });
+ }
+
+ function deleteComment(id) {
+ $.ajax({
+ type: 'POST',
+ url: opts.deleteCommentURL,
+ data: {id: id},
+ success: function(data, textStatus, request) {
+ var div = $('#cd' + id);
+ if (data == 'delete') {
+ // Moderator mode: remove the comment and all children immediately
+ div.slideUp('fast', function() {
+ div.remove();
+ });
+ return;
+ }
+ // User mode: only mark the comment as deleted
+ div
+ .find('span.user-id:first')
+ .text('[deleted]').end()
+ .find('div.comment-text:first')
+ .text('[deleted]').end()
+ .find('#cm' + id + ', #dc' + id + ', #ac' + id + ', #rc' + id +
+ ', #sp' + id + ', #hp' + id + ', #cr' + id + ', #rl' + id)
+ .remove();
+ var comment = div.data('comment');
+ comment.username = '[deleted]';
+ comment.text = '[deleted]';
+ div.data('comment', comment);
+ },
+ error: function(request, textStatus, error) {
+ showError('Oops, there was a problem deleting the comment.');
+ }
+ });
+ }
+
+ function showProposal(id) {
+ $('#sp' + id).hide();
+ $('#hp' + id).show();
+ $('#pr' + id).slideDown('fast');
+ }
+
+ function hideProposal(id) {
+ $('#hp' + id).hide();
+ $('#sp' + id).show();
+ $('#pr' + id).slideUp('fast');
+ }
+
+ function showProposeChange(id) {
+ $('#pc' + id).hide();
+ $('#hc' + id).show();
+ var textarea = $('#pt' + id);
+ textarea.val(textarea.data('source'));
+ $.fn.autogrow.resize(textarea[0]);
+ textarea.slideDown('fast');
+ }
+
+ function hideProposeChange(id) {
+ $('#hc' + id).hide();
+ $('#pc' + id).show();
+ var textarea = $('#pt' + id);
+ textarea.val('').removeAttr('disabled');
+ textarea.slideUp('fast');
+ }
+
+ function toggleCommentMarkupBox(id) {
+ $('#mb' + id).toggle();
+ }
+
+ /** Handle when the user clicks on a sort by link. */
+ function handleReSort(link) {
+ var classes = link.attr('class').split(/\s+/);
+ for (var i=0; i<classes.length; i++) {
+ if (classes[i] != 'sort-option') {
+ by = classes[i].substring(2);
+ }
+ }
+ setComparator();
+ // Save/update the sortBy cookie.
+ var expiration = new Date();
+ expiration.setDate(expiration.getDate() + 365);
+ document.cookie= 'sortBy=' + escape(by) +
+ ';expires=' + expiration.toUTCString();
+ $('ul.comment-ul').each(function(index, ul) {
+ var comments = getChildren($(ul), true);
+ comments = sortComments(comments);
+ appendComments(comments, $(ul).empty());
+ });
+ }
+
+ /**
+ * Function to process a vote when a user clicks an arrow.
+ */
+ function handleVote(link) {
+ if (!opts.voting) {
+ showError("You'll need to login to vote.");
+ return;
+ }
+
+ var id = link.attr('id');
+ if (!id) {
+ // Didn't click on one of the voting arrows.
+ return;
+ }
+ // If it is an unvote, the new vote value is 0,
+ // Otherwise it's 1 for an upvote, or -1 for a downvote.
+ var value = 0;
+ if (id.charAt(1) != 'u') {
+ value = id.charAt(0) == 'u' ? 1 : -1;
+ }
+ // The data to be sent to the server.
+ var d = {
+ comment_id: id.substring(2),
+ value: value
+ };
+
+ // Swap the vote and unvote links.
+ link.hide();
+ $('#' + id.charAt(0) + (id.charAt(1) == 'u' ? 'v' : 'u') + d.comment_id)
+ .show();
+
+ // The div the comment is displayed in.
+ var div = $('div#cd' + d.comment_id);
+ var data = div.data('comment');
+
+ // If this is not an unvote, and the other vote arrow has
+ // already been pressed, unpress it.
+ if ((d.value !== 0) && (data.vote === d.value * -1)) {
+ $('#' + (d.value == 1 ? 'd' : 'u') + 'u' + d.comment_id).hide();
+ $('#' + (d.value == 1 ? 'd' : 'u') + 'v' + d.comment_id).show();
+ }
+
+ // Update the comments rating in the local data.
+ data.rating += (data.vote === 0) ? d.value : (d.value - data.vote);
+ data.vote = d.value;
+ div.data('comment', data);
+
+ // Change the rating text.
+ div.find('.rating:first')
+ .text(data.rating + ' point' + (data.rating == 1 ? '' : 's'));
+
+ // Send the vote information to the server.
+ $.ajax({
+ type: "POST",
+ url: opts.processVoteURL,
+ data: d,
+ error: function(request, textStatus, error) {
+ showError('Oops, there was a problem casting that vote.');
+ }
+ });
+ }
+
+ /**
+ * Open a reply form used to reply to an existing comment.
+ */
+ function openReply(id) {
+ // Swap out the reply link for the hide link
+ $('#rl' + id).hide();
+ $('#cr' + id).show();
+
+ // Add the reply li to the children ul.
+ var div = $(renderTemplate(replyTemplate, {id: id})).hide();
+ $('#cl' + id)
+ .prepend(div)
+ // Setup the submit handler for the reply form.
+ .find('#rf' + id)
+ .submit(function(event) {
+ event.preventDefault();
+ addComment($('#rf' + id));
+ closeReply(id);
+ })
+ .find('input[type=button]')
+ .click(function() {
+ closeReply(id);
+ });
+ div.slideDown('fast', function() {
+ $('#rf' + id).find('textarea').focus();
+ });
+ }
+
+ /**
+ * Close the reply form opened with openReply.
+ */
+ function closeReply(id) {
+ // Remove the reply div from the DOM.
+ $('#rd' + id).slideUp('fast', function() {
+ $(this).remove();
+ });
+
+ // Swap out the hide link for the reply link
+ $('#cr' + id).hide();
+ $('#rl' + id).show();
+ }
+
+ /**
+ * Recursively sort a tree of comments using the comp comparator.
+ */
+ function sortComments(comments) {
+ comments.sort(comp);
+ $.each(comments, function() {
+ this.children = sortComments(this.children);
+ });
+ return comments;
+ }
+
+ /**
+ * Get the children comments from a ul. If recursive is true,
+ * recursively include childrens' children.
+ */
+ function getChildren(ul, recursive) {
+ var children = [];
+ ul.children().children("[id^='cd']")
+ .each(function() {
+ var comment = $(this).data('comment');
+ if (recursive)
+ comment.children = getChildren($(this).find('#cl' + comment.id), true);
+ children.push(comment);
+ });
+ return children;
+ }
+
+ /** Create a div to display a comment in. */
+ function createCommentDiv(comment) {
+ if (!comment.displayed && !opts.moderator) {
+ return $('<div class="moderate">Thank you! Your comment will show up '
+ + 'once it is has been approved by a moderator.</div>');
+ }
+ // Prettify the comment rating.
+ comment.pretty_rating = comment.rating + ' point' +
+ (comment.rating == 1 ? '' : 's');
+ // Make a class (for displaying not yet moderated comments differently)
+ comment.css_class = comment.displayed ? '' : ' moderate';
+ // Create a div for this comment.
+ var context = $.extend({}, opts, comment);
+ var div = $(renderTemplate(commentTemplate, context));
+
+ // If the user has voted on this comment, highlight the correct arrow.
+ if (comment.vote) {
+ var direction = (comment.vote == 1) ? 'u' : 'd';
+ div.find('#' + direction + 'v' + comment.id).hide();
+ div.find('#' + direction + 'u' + comment.id).show();
+ }
+
+ if (opts.moderator || comment.text != '[deleted]') {
+ div.find('a.reply').show();
+ if (comment.proposal_diff)
+ div.find('#sp' + comment.id).show();
+ if (opts.moderator && !comment.displayed)
+ div.find('#cm' + comment.id).show();
+ if (opts.moderator || (opts.username == comment.username))
+ div.find('#dc' + comment.id).show();
+ }
+ return div;
+ }
+
+ /**
+ * A simple template renderer. Placeholders such as <%id%> are replaced
+ * by context['id'] with items being escaped. Placeholders such as <#id#>
+ * are not escaped.
+ */
+ function renderTemplate(template, context) {
+ var esc = $(document.createElement('div'));
+
+ function handle(ph, escape) {
+ var cur = context;
+ $.each(ph.split('.'), function() {
+ cur = cur[this];
+ });
+ return escape ? esc.text(cur || "").html() : cur;
+ }
+
+ return template.replace(/<([%#])([\w\.]*)\1>/g, function() {
+ return handle(arguments[2], arguments[1] == '%' ? true : false);
+ });
+ }
+
+ /** Flash an error message briefly. */
+ function showError(message) {
+ $(document.createElement('div')).attr({'class': 'popup-error'})
+ .append($(document.createElement('div'))
+ .attr({'class': 'error-message'}).text(message))
+ .appendTo('body')
+ .fadeIn("slow")
+ .delay(2000)
+ .fadeOut("slow");
+ }
+
+ /** Add a link the user uses to open the comments popup. */
+ $.fn.comment = function() {
+ return this.each(function() {
+ var id = $(this).attr('id').substring(1);
+ var count = COMMENT_METADATA[id];
+ var title = count + ' comment' + (count == 1 ? '' : 's');
+ var image = count > 0 ? opts.commentBrightImage : opts.commentImage;
+ var addcls = count == 0 ? ' nocomment' : '';
+ $(this)
+ .append(
+ $(document.createElement('a')).attr({
+ href: '#',
+ 'class': 'sphinx-comment-open' + addcls,
+ id: 'ao' + id
+ })
+ .append($(document.createElement('img')).attr({
+ src: image,
+ alt: 'comment',
+ title: title
+ }))
+ .click(function(event) {
+ event.preventDefault();
+ show($(this).attr('id').substring(2));
+ })
+ )
+ .append(
+ $(document.createElement('a')).attr({
+ href: '#',
+ 'class': 'sphinx-comment-close hidden',
+ id: 'ah' + id
+ })
+ .append($(document.createElement('img')).attr({
+ src: opts.closeCommentImage,
+ alt: 'close',
+ title: 'close'
+ }))
+ .click(function(event) {
+ event.preventDefault();
+ hide($(this).attr('id').substring(2));
+ })
+ );
+ });
+ };
+
+ var opts = {
+ processVoteURL: '/_process_vote',
+ addCommentURL: '/_add_comment',
+ getCommentsURL: '/_get_comments',
+ acceptCommentURL: '/_accept_comment',
+ deleteCommentURL: '/_delete_comment',
+ commentImage: '/static/_static/comment.png',
+ closeCommentImage: '/static/_static/comment-close.png',
+ loadingImage: '/static/_static/ajax-loader.gif',
+ commentBrightImage: '/static/_static/comment-bright.png',
+ upArrow: '/static/_static/up.png',
+ downArrow: '/static/_static/down.png',
+ upArrowPressed: '/static/_static/up-pressed.png',
+ downArrowPressed: '/static/_static/down-pressed.png',
+ voting: false,
+ moderator: false
+ };
+
+ if (typeof COMMENT_OPTIONS != "undefined") {
+ opts = jQuery.extend(opts, COMMENT_OPTIONS);
+ }
+
+ var popupTemplate = '\
+ <div class="sphinx-comments" id="sc<%id%>">\
+ <p class="sort-options">\
+ Sort by:\
+ <a href="#" class="sort-option byrating">best rated</a>\
+ <a href="#" class="sort-option byascage">newest</a>\
+ <a href="#" class="sort-option byage">oldest</a>\
+ </p>\
+ <div class="comment-header">Comments</div>\
+ <div class="comment-loading" id="cn<%id%>">\
+ loading comments... <img src="<%loadingImage%>" alt="" /></div>\
+ <ul id="cl<%id%>" class="comment-ul"></ul>\
+ <div id="ca<%id%>">\
+ <p class="add-a-comment">Add a comment\
+ (<a href="#" class="comment-markup" id="ab<%id%>">markup</a>):</p>\
+ <div class="comment-markup-box" id="mb<%id%>">\
+ reStructured text markup: <i>*emph*</i>, <b>**strong**</b>, \
+ <tt>``code``</tt>, \
+ code blocks: <tt>::</tt> and an indented block after blank line</div>\
+ <form method="post" id="cf<%id%>" class="comment-form" action="">\
+ <textarea name="comment" cols="80"></textarea>\
+ <p class="propose-button">\
+ <a href="#" id="pc<%id%>" class="show-propose-change">\
+ Propose a change ▹\
+ </a>\
+ <a href="#" id="hc<%id%>" class="hide-propose-change">\
+ Propose a change ▿\
+ </a>\
+ </p>\
+ <textarea name="proposal" id="pt<%id%>" cols="80"\
+ spellcheck="false"></textarea>\
+ <input type="submit" value="Add comment" />\
+ <input type="hidden" name="node" value="<%id%>" />\
+ <input type="hidden" name="parent" value="" />\
+ </form>\
+ </div>\
+ </div>';
+
+ var commentTemplate = '\
+ <div id="cd<%id%>" class="sphinx-comment<%css_class%>">\
+ <div class="vote">\
+ <div class="arrow">\
+ <a href="#" id="uv<%id%>" class="vote" title="vote up">\
+ <img src="<%upArrow%>" />\
+ </a>\
+ <a href="#" id="uu<%id%>" class="un vote" title="vote up">\
+ <img src="<%upArrowPressed%>" />\
+ </a>\
+ </div>\
+ <div class="arrow">\
+ <a href="#" id="dv<%id%>" class="vote" title="vote down">\
+ <img src="<%downArrow%>" id="da<%id%>" />\
+ </a>\
+ <a href="#" id="du<%id%>" class="un vote" title="vote down">\
+ <img src="<%downArrowPressed%>" />\
+ </a>\
+ </div>\
+ </div>\
+ <div class="comment-content">\
+ <p class="tagline comment">\
+ <span class="user-id"><%username%></span>\
+ <span class="rating"><%pretty_rating%></span>\
+ <span class="delta"><%time.delta%></span>\
+ </p>\
+ <div class="comment-text comment"><#text#></div>\
+ <p class="comment-opts comment">\
+ <a href="#" class="reply hidden" id="rl<%id%>">reply ▹</a>\
+ <a href="#" class="close-reply" id="cr<%id%>">reply ▿</a>\
+ <a href="#" id="sp<%id%>" class="show-proposal">proposal ▹</a>\
+ <a href="#" id="hp<%id%>" class="hide-proposal">proposal ▿</a>\
+ <a href="#" id="dc<%id%>" class="delete-comment hidden">delete</a>\
+ <span id="cm<%id%>" class="moderation hidden">\
+ <a href="#" id="ac<%id%>" class="accept-comment">accept</a>\
+ </span>\
+ </p>\
+ <pre class="proposal" id="pr<%id%>">\
+<#proposal_diff#>\
+ </pre>\
+ <ul class="comment-children" id="cl<%id%>"></ul>\
+ </div>\
+ <div class="clearleft"></div>\
+ </div>\
+ </div>';
+
+ var replyTemplate = '\
+ <li>\
+ <div class="reply-div" id="rd<%id%>">\
+ <form id="rf<%id%>">\
+ <textarea name="comment" cols="80"></textarea>\
+ <input type="submit" value="Add reply" />\
+ <input type="button" value="Cancel" />\
+ <input type="hidden" name="parent" value="<%id%>" />\
+ <input type="hidden" name="node" value="" />\
+ </form>\
+ </div>\
+ </li>';
+
+ $(document).ready(function() {
+ init();
+ });
+})(jQuery);
+
+$(document).ready(function() {
+ // add comment anchors for all paragraphs that are commentable
+ $('.sphinx-has-comment').comment();
+
+ // highlight search words in search results
+ $("div.context").each(function() {
+ var params = $.getQueryParameters();
+ var terms = (params.q) ? params.q[0].split(/\s+/) : [];
+ var result = $(this);
+ $.each(terms, function() {
+ result.highlightText(this.toLowerCase(), 'highlighted');
+ });
+ });
+
+ // directly open comment window if requested
+ var anchor = document.location.hash;
+ if (anchor.substring(0, 9) == '#comment-') {
+ $('#ao' + anchor.substring(9)).click();
+ document.location.hash = '#s' + anchor.substring(9);
+ }
+});
diff --git a/doc/count-data/counts_boxplot.png b/doc/count-data/counts_boxplot.png
new file mode 100644
index 0000000..927e764
Binary files /dev/null and b/doc/count-data/counts_boxplot.png differ
diff --git a/doc/count-data/kidney.counts b/doc/count-data/kidney.counts
new file mode 100644
index 0000000..f176f78
--- /dev/null
+++ b/doc/count-data/kidney.counts
@@ -0,0 +1,51797 @@
+ENSG00000126773 206
+ENSG00000183878 56
+ENSG00000126775 80
+ENSG00000126777 1171
+ENSG00000126778 1
+ENSG00000183888 18
+ENSG00000126785 35
+ENSG00000183889 0
+ENSG00000126787 0
+ENSG00000077616 2
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+++ b/doc/count-data/qualimapReport.html
@@ -0,0 +1,436 @@
+<!DOCTYPE HTML>
+<html>
+ <head>
+ <link rel="stylesheet" href="_static/agogo.css" type="text/css" />
+ <link rel="stylesheet" href="_static/report.css" type="text/css" />
+ <title>Qualimap report: Genomic analysis</title>
+
+ </head>
+<body>
+ <div class="header-wrapper">
+ <div class="header">
+ <p class="logo"><a href="http://qualimap.bioinfo.cipf.es/">
+ <img class="logo" src="_static/qualimap_logo_small.png" alt="Logo"/>
+ </a></p>
+<div class="headertitle"><a href="">Qualimap Report</a></div>
+ </div>
+</div>
+
+<div class="content-wrapper">
+<div class="content">
+<div class="document">
+<div class="documentwrapper">
+<div class="bodywrapper">
+<div class="body">
+<div class=section>
+<h2>Input data and parameters<a class="headerlink" name="input" title="Permalink to this headline"> </a></h2>
+<div class=summary>
+
+
+<div class=table-summary>
+<h3>Liver</h3>
+<table class="summary hovertable">
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Path: </td>
+<td class=column2>/home/fgarcia/qualimapLatestBuild/dataRelease/count-data/liver.counts</td>
+</tr>
+</table>
+</div>
+
+
+<div class=table-summary>
+<h3>Kidney</h3>
+<table class="summary hovertable">
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Path: </td>
+<td class=column2>/home/fgarcia/qualimapLatestBuild/dataRelease/count-data/kidney.counts</td>
+</tr>
+</table>
+</div>
+
+
+<div class=table-summary>
+<h3>Options</h3>
+<table class="summary hovertable">
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Threshold: </td>
+<td class=column2>5</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Species info: </td>
+<td class=column2>/home/fgarcia/qualimapLatestBuild/qualimap-build-24-04-12/./species/human.61.genes.biotypes.txt</td>
+</tr>
+</table>
+</div>
+
+</div>
+</div> <!-- summary section -->
+
+
+
+<div class=section>
+
+<h2>Global Saturation<a class="headerlink" name="GlobalSaturation.png" title="Permalink to this headline"> </a></h2>
+
+<div><img width=100% src="GlobalSaturation.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>Detection Per Class<a class="headerlink" name="DetectionPerGroup.png" title="Permalink to this headline"> </a></h2>
+
+<div><img width=100% src="DetectionPerGroup.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>Counts Per Class<a class="headerlink" name="counts_boxplot.png" title="Permalink to this headline"> </a></h2>
+
+<div><img width=100% src="counts_boxplot.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>snRNA<a class="headerlink" name="snRNA.png" title="Permalink to this headline"> </a></h2>
+
+<div><img width=100% src="snRNA.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>snRNA (boxplot)<a class="headerlink" name="snRNA_boxplot.png" title="Permalink to this headline"> </a></h2>
+
+<div><img width=100% src="snRNA_boxplot.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>miRNA<a class="headerlink" name="miRNA.png" title="Permalink to this headline"> </a></h2>
+
+<div><img width=100% src="miRNA.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>miRNA (boxplot)<a class="headerlink" name="miRNA_boxplot.png" title="Permalink to this headline"> </a></h2>
+
+<div><img width=100% src="miRNA_boxplot.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>snoRNA<a class="headerlink" name="snoRNA.png" title="Permalink to this headline"> </a></h2>
+
+<div><img width=100% src="snoRNA.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>snoRNA (boxplot)<a class="headerlink" name="snoRNA_boxplot.png" title="Permalink to this headline"> </a></h2>
+
+<div><img width=100% src="snoRNA_boxplot.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>lincRNA<a class="headerlink" name="lincRNA.png" title="Permalink to this headline"> </a></h2>
+
+<div><img width=100% src="lincRNA.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>lincRNA (boxplot)<a class="headerlink" name="lincRNA_boxplot.png" title="Permalink to this headline"> </a></h2>
+
+<div><img width=100% src="lincRNA_boxplot.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>TR<a class="headerlink" name="TR.png" title="Permalink to this headline"> </a></h2>
+
+<div><img width=100% src="TR.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>TR (boxplot)<a class="headerlink" name="TR_boxplot.png" title="Permalink to this headline"> </a></h2>
+
+<div><img width=100% src="TR_boxplot.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>protein_coding<a class="headerlink" name="protein_coding.png" title="Permalink to this headline"> </a></h2>
+
+<div><img width=100% src="protein_coding.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>protein_coding (boxplot)<a class="headerlink" name="protein_coding_boxplot.png" title="Permalink to this headline"> </a></h2>
+
+<div><img width=100% src="protein_coding_boxplot.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>misc_RNA<a class="headerlink" name="misc_RNA.png" title="Permalink to this headline"> </a></h2>
+
+<div><img width=100% src="misc_RNA.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>misc_RNA (boxplot)<a class="headerlink" name="misc_RNA_boxplot.png" title="Permalink to this headline"> </a></h2>
+
+<div><img width=100% src="misc_RNA_boxplot.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>rRNA<a class="headerlink" name="rRNA.png" title="Permalink to this headline"> </a></h2>
+
+<div><img width=100% src="rRNA.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>rRNA (boxplot)<a class="headerlink" name="rRNA_boxplot.png" title="Permalink to this headline"> </a></h2>
+
+<div><img width=100% src="rRNA_boxplot.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>scRNA_pseudogene<a class="headerlink" name="scRNA_pseudogene.png" title="Permalink to this headline"> </a></h2>
+
+<div><img width=100% src="scRNA_pseudogene.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>scRNA_pseudogene (boxplot)<a class="headerlink" name="scRNA_pseudogene_boxplot.png" title="Permalink to this headline"> </a></h2>
+
+<div><img width=100% src="scRNA_pseudogene_boxplot.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>processed_transcript<a class="headerlink" name="processed_transcript.png" title="Permalink to this headline"> </a></h2>
+
+<div><img width=100% src="processed_transcript.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>processed_transcript (boxplot)<a class="headerlink" name="processed_transcript_boxplot.png" title="Permalink to this headline"> </a></h2>
+
+<div><img width=100% src="processed_transcript_boxplot.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>tRNA_pseudogene<a class="headerlink" name="tRNA_pseudogene.png" title="Permalink to this headline"> </a></h2>
+
+<div><img width=100% src="tRNA_pseudogene.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>tRNA_pseudogene (boxplot)<a class="headerlink" name="tRNA_pseudogene_boxplot.png" title="Permalink to this headline"> </a></h2>
+
+<div><img width=100% src="tRNA_pseudogene_boxplot.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>IG<a class="headerlink" name="IG.png" title="Permalink to this headline"> </a></h2>
+
+<div><img width=100% src="IG.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>IG (boxplot)<a class="headerlink" name="IG_boxplot.png" title="Permalink to this headline"> </a></h2>
+
+<div><img width=100% src="IG_boxplot.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>pseudogene<a class="headerlink" name="pseudogene.png" title="Permalink to this headline"> </a></h2>
+
+<div><img width=100% src="pseudogene.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>pseudogene (boxplot)<a class="headerlink" name="pseudogene_boxplot.png" title="Permalink to this headline"> </a></h2>
+
+<div><img width=100% src="pseudogene_boxplot.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>mitocondrial<a class="headerlink" name="mitocondrial.png" title="Permalink to this headline"> </a></h2>
+
+<div><img width=100% src="mitocondrial.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>mitocondrial (boxplot)<a class="headerlink" name="mitocondrial_boxplot.png" title="Permalink to this headline"> </a></h2>
+
+<div><img width=100% src="mitocondrial_boxplot.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>Unknown<a class="headerlink" name="unknown.png" title="Permalink to this headline"> </a></h2>
+
+<div><img width=100% src="unknown.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>Unknown (boxplot)<a class="headerlink" name="unknown_boxplot.png" title="Permalink to this headline"> </a></h2>
+
+<div><img width=100% src="unknown_boxplot.png"></div>
+
+</div><!-- graph section -->
+
+
+</div>
+
+</div>
+
+</div>
+
+</div>
+
+
+<div class="sidebar">
+<h3>Contents</h3>
+<li class="toctree-l1"><a class="reference internal" href="#input">Input data & parameters</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#GlobalSaturation.png">Global Saturation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#DetectionPerGroup.png">Detection Per Class</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#counts_boxplot.png">Counts Per Class</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#snRNA.png">snRNA</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#snRNA_boxplot.png">snRNA (boxplot)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#miRNA.png">miRNA</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#miRNA_boxplot.png">miRNA (boxplot)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#snoRNA.png">snoRNA</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#snoRNA_boxplot.png">snoRNA (boxplot)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#lincRNA.png">lincRNA</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#lincRNA_boxplot.png">lincRNA (boxplot)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#TR.png">TR</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#TR_boxplot.png">TR (boxplot)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#protein_coding.png">protein_coding</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#protein_coding_boxplot.png">protein_coding (boxplot)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#misc_RNA.png">misc_RNA</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#misc_RNA_boxplot.png">misc_RNA (boxplot)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#rRNA.png">rRNA</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#rRNA_boxplot.png">rRNA (boxplot)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#scRNA_pseudogene.png">scRNA_pseudogene</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#scRNA_pseudogene_boxplot.png">scRNA_pseudogene (boxplot)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#processed_transcript.png">processed_transcript</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#processed_transcript_boxplot.png">processed_transcript (boxplot)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#tRNA_pseudogene.png">tRNA_pseudogene</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#tRNA_pseudogene_boxplot.png">tRNA_pseudogene (boxplot)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#IG.png">IG</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#IG_boxplot.png">IG (boxplot)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#pseudogene.png">pseudogene</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#pseudogene_boxplot.png">pseudogene (boxplot)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#mitocondrial.png">mitocondrial</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#mitocondrial_boxplot.png">mitocondrial (boxplot)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#unknown.png">Unknown</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#unknown_boxplot.png">Unknown (boxplot)</a></li>
+</div> <!-- sidebar -->
+
+<div class="clearer"></div>
+</div>
+
+</div>
+
+
+<div class="footer-wrapper">
+<div class="footer">
+<div class="left">
+<div class="footer">
+2012/04/24 19:50:20
+</div>
+</div>
+<div class="right">
+<div class="footer">
+Generated by QualiMap
+</div
+</div>
+<div class="clearer"></div>
+</div> <!-- footer -->
+</div>
+</body>
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+.. _faq:
+
+
+Frequently Asked Questions
+==========================
+
+
+General
+-------
+
+**Q**: *How to cite Qualimap?*
+
+**A**: If you use Qualimap 2 for your research, please cite the following:
+
+**Okonechnikov, K., Conesa, A., & García-Alcalde, F. (2015). "Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data." Bioinformatics, btv566**
+
+|
+
+.. _heapsize:
+
+**Q**: *How to increase maximum Java heap memory size?*
+
+**A**: The Qualimap launching script allows to set desired memory size using special command line argument :samp:`--java-mem-size`. Here are some usage examples:
+
+ :samp:`qualimap --java-mem-size=1200M`
+
+ :samp:`qualimap bamqc -bam very_large_alignment.bam --java-mem-size=4G`
+
+Note that there should be **no whitespace** between argument and its value.
+
+Alternatively one can change default memory size parameter by modifying the following line in the launching script:
+
+ JAVA_MEM_DEFAULT_SIZE="1200M"
+
+
+Also one can override this parameter by setting environment variable $JAVA_OPTS.
+
+
+|
+
+**Q**: *Does Qualimap run on MS Windows?*
+
+**A**: Qualimap can be launched on Windows using script :file:`qualimap.bat`. However, officially we do not support MS Windows.
+
+|
+
+**Q**: *Does Qualimap work with R version 3?*
+
+**A**: Yes, Qualimap works with R v3. There was a bug with R-version recogintion GUI, but starting from version 0.8 the bug was fixed.
+
+
+|
+
+**Q**: *Counts QC* mode launched on MacOS doesn't produce any results. Some of the following errors are reported:
+
+ :samp:`unable to load shared object ../libs/cairo.so`
+
+ or
+
+ :samp:`libpng warning: Application built with libpng-1.5.18 but running with 1.6.17`
+
+
+**A**: Issue is related to the update of R package structure on MacOS. The error can be fixed by updating R to version >= 3.2.2 and installation of a specific library XQuartz. More details can be found in the following `discussion <https://groups.google.com/forum/#!topic/qualimap/3EGtIdgojNc>`_.
+
+|
+
+
+**Q**: *I always get a message "Out of Memory". What should I do?*
+
+**A**: You can try decreasing the number of reads in chunk or increasing :ref:`maximum Java heap memory size <heapsize>`.
+
+|
+
+Command line
+------------
+.. _x11problem:
+
+**Q**: *I launch Qualimap command-line tool on my big and powerful Linux server. However it doesn't finish properly and outputs some strange message like*:
+
+| **Exception in thread "main" java.lang.InternalError: Can't connect to X11**
+| **window server using 'foo:42.0' as the value of the DISPLAY variable.**
+
+*What is going on?*
+
+**A**: Java virtual machine uses **DISPLAY** environment variable to detect if the X11 system is available. Sometimes this variable is set incorrectly by the operating system or some applications. To make Qualimap work simply unset this variable:
+ :samp:`unset DISPLAY`
+or like this:
+ :samp:`export DISPLAY=:0`
+
+Additionally it's possible to use a special option of Java **-Djava.awt.headless=true** to disable display requirement.
+
+Enabling this option can be performed by setting **JAVA_OPTS** variable in system or by changing **java_options** variable in the *qualimap* script:
+
+ :samp:`java_options="-Djava.awt.headless=true -Xmx$JAVA_MEM_SIZE -XX:MaxPermSize=1024m"`
+
+
+|
+
+Performance
+-----------
+
+
+**Q**: *Does Qualimap make use of multicore systems to improve computation speed?*
+
+**A**: Yes, Qualimap uses threads to perform BAM QC analysis.
+
+In short, reads are processed in chunks and each chunk is analyzed in parallel.
+
+Below you can find a schema, depicting the applied algorithm.
+
+
+.. image:: images/parallel.png
+ :width: 450pt
+ :align: center
+
+Here each block denotes a certain algorithm step. The analysis starts dividing the reference genome into windows. The first window is set to be the current one. Then the analysis continues processing BAM records belonging to the current window.
+
+When all the reads belonging to the current window are processed, the window is finalized in a newly created thread.
+
+The analysis is finished when all windows are processed.
+
+|
+
+**Q**: *What is the scalability of QualiMap? Can it run on a cluster?*
+
+**A**: Currently qualimap is designed to run in a single multicore machine. In the future we plan to support cluster and computational cloud execution for BAM QC.
+
+|
+
+**Q**: *I have a powerful computer with a lot of memory. Can I make Qualimap run faster?*
+
+**A**: Sure, just increase your :ref:`maximum JAVA heap size <heapsize>`.
+
+|
+
+
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+.. Qualimap documentation master file, created by
+ sphinx-quickstart on Mon Mar 12 11:54:43 2012.
+ You can adapt this file completely to your liking, but it should at least
+ contain the root `toctree` directive.
+
+.. _index:
+
+Contents
+====================
+
+.. toctree::
+ :maxdepth: 4
+
+ intro
+ workflow
+ analysis
+ tools
+ command_line
+ samples
+ faq
+
+.. Indices and tables
+ ==================
+
+.. * :ref:`genindex`
+ * :ref:`modindex`
+ * :ref:`search`
+
diff --git a/doc/intro.rst b/doc/intro.rst
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+.. _intro:
+
+Introduction
+============
+
+What is Qualimap?
+-----------------
+
+**Qualimap** is a platform-independent application written in Java and R that provides both a Graphical User Interface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data. Shortly, Qualimap:
+
+1. Examines sequencing **alignment data** according to the features of the mapped reads and their **genomic properties**
+2. Povides an **overall view** of the data that helps to to the **detect biases** in the sequencing and/or mapping of the data and eases **decision-making** for further analysis.
+
+The main features offered by Qualimap are:
+
+* fast analysis across the reference genome of mapping coverage and nucleotide distribution;
+* easy-to-interpret summary of the main properties of the alignment data;
+* analysis of the reads mapped inside/outside of the regions defined in an annotation reference;
+* computation and analysis of read counts obtained from intersting of read alignments with genomic features;
+* analysis of the adequacy of the sequencing depth in RNA-seq experiments;
+* support for multi-sample comparison for alignment data and counts data;
+* clustering of epigenomic profiles.
+
+Installation
+------------
+
+Download the ZIP file from the `Qualimap web page <http://qualimap.org>`_.
+
+Unpack it to desired directory.
+
+Run Qualimap from this directory using the prebuilt script:
+
+:samp:`./qualimap`
+
+Qualimap was tested on GNU Linux and MacOS.
+
+.. note:: On MS Windows use script :samp:`qualimap.bat` to launch Qualimap.
+
+Requirements
+------------
+
+Qualimap requires:
+
+* `JAVA <http://www.java.com>`_ runtime version 6 or above.
+* `R <http://www.r-project.org>`_ enviroment version 2.14 or above.
+
+The JAVA runtime can be downloaded from the `official web-site <http://www.java.com>`_.
+There are prebuilt binaries available for many platforms.
+
+R enviroment can be downloaded from `R project web-site <http://www.r-project.org>`_.
+
+.. note:: In general the installation of R environment is platform-specific and may require additional efforts.
+
+Several Qualimap features are implemented in R, using a number of external packages.
+
+.. note:: If R environment is not available or required R-packages are missing, "Counts QC" and "Clustering" features will be disabled.
+
+Currently Qualimap requires the following R-packages:
+
+* optparse (available from `CRAN <http://cran.r-project.org>`_)
+* NOISeq, Repitools, Rsamtools, GenomicFeatures, rtracklayer (available from `Bioconductor <http://bioconductor.org>`_)
+
+One can install these packages `manually <http://cran.r-project.org/doc/manuals/R-admin.html#Installing-packages>`_ or by executing the script found in the installation folder:
+
+:samp:`Rscript scripts/installDependencies.r`
+
+Installing Qualimap on Ubuntu
+-----------------------------
+
+This manual is specific for Ubuntu(Debian) Linux distribution, however with slight differences this can be applied for other GNU Linux systems.
+
+Install JAVA
+^^^^^^^^^^^^
+
+It is possible to use openjdk:
+
+:samp:`sudo apt-get install openjdk-6-jre`
+
+Install R
+^^^^^^^^^
+
+The R latest version can be installed from public repos.
+
+The repos must be added to the sources file. Open sources.list:
+
+:samp:`sudo gedit /etc/apt/sources.list`
+
+Add the following line:
+
+:samp:`deb http://<my.favorite.cran.mirror>/bin/linux/ubuntu <name.of.your.distribution>/`
+
+List of cran mirrors can be found `here <http://cran.r-project.org/mirrors.html>`_
+
+Here is an example for Ubuntu 10.04 (Lucid):
+
+:samp:`deb http://cran.stat.ucla.edu/bin/linux/ubuntu lucid/`
+
+Then install R:
+
+:samp:`sudo apt-get update`
+
+:samp:`sudo apt-get install r-base-core`
+
+If you don't have the public key for the mirror add it:
+
+:samp:`gpg --keyserver subkeys.pgp.net --recv-key <required.key>`
+
+:samp:`gpg -a --export <required.key> | sudo apt-key add -`
+
+More details available here:
+
+ http://cran.r-project.org/bin/linux/ubuntu/README
+
+Qualimap needs R version 2.14 or above. This can be checked with the following command:
+
+:samp:`Rscript --version`
+
+.. note:: Alternatively it is possible to build R enviroment directly from sources downloaded from r-project.org.
+
+Install required R-packages
+^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Some packages depend on external libraries, so you might need to install them either:
+
+:samp:`sudo apt-get install libxml2-dev`
+
+:samp:`sudo apt-get install libcurl4-openssl-dev`
+
+
+You can install required packages manually or use special script from Qualimap installation folder:
+
+:samp:`sudo Rscript $QUALIMAP_HOME/scripts/installDependencies.r`
+
+where :samp:`$QUALIMAP_HOME` is the full path to the Qualimap installation folder.
+
+
+
+
+Citing Qualimap
+---------------
+
+If you use Qualimap 2 for your research, please cite the following:
+
+*Okonechnikov, K., Conesa, A., & García-Alcalde, F. (2015). "Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data." Bioinformatics, btv566*
+
+The first version of the tool was described in the following manuscript:
+
+*García-Alcalde, et al. "Qualimap: evaluating next generation sequencing alignment data." Bioinformatics(2012) 28 (20): 2678-2679*
+
+
+
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+div.document ul {
+ margin: 1.5em;
+ list-style-type: square;
+}
+
+div.document dd {
+ margin-left: 1.2em;
+ margin-top: .4em;
+ margin-bottom: 1em;
+}
+
+div.document .section {
+ margin-top: 1.7em;
+}
+div.document .section:first-child {
+ margin-top: 0px;
+}
+
+div.document div.highlight {
+ padding: 3px;
+ background-color: #eeeeec;
+ border-top: 2px solid #dddddd;
+ border-bottom: 2px solid #dddddd;
+ margin-top: .8em;
+ margin-bottom: .8em;
+}
+
+div.document h2 {
+ margin-top: .7em;
+}
+
+div.document p {
+ margin-bottom: .5em;
+}
+
+div.document li.toctree-l1 {
+ margin-bottom: 1em;
+}
+
+div.document .descname {
+ font-weight: bold;
+}
+
+div.document .docutils.literal {
+ background-color: #eeeeec;
+ padding: 1px;
+}
+
+div.document .docutils.xref.literal {
+ background-color: transparent;
+ padding: 0px;
+}
+
+div.document blockquote {
+ margin: 1em;
+}
+
+div.document ol {
+ margin: 1.5em;
+}
+
+
+/* Sidebar */
+
+div.sidebar {
+ width: 20em;
+ float: right;
+ font-size: .9em;
+}
+
+div.sidebar a, div.header a {
+ text-decoration: none;
+}
+
+div.sidebar a:hover, div.header a:hover {
+ text-decoration: underline;
+}
+
+div.sidebar h3 {
+ color: #2e3436;
+ text-transform: uppercase;
+ font-size: 130%;
+ letter-spacing: .1em;
+}
+
+div.sidebar ul {
+ list-style-type: none;
+}
+
+div.sidebar li.toctree-l1 a {
+ display: block;
+ padding: 1px;
+ border: 1px solid #dddddd;
+ background-color: #eeeeec;
+ margin-bottom: .4em;
+ padding-left: 3px;
+ color: #2e3436;
+}
+
+div.sidebar li.toctree-l2 a {
+ background-color: transparent;
+ border: none;
+ margin-left: 1em;
+ border-bottom: 1px solid #dddddd;
+}
+
+div.sidebar li.toctree-l3 a {
+ background-color: transparent;
+ border: none;
+ margin-left: 2em;
+ border-bottom: 1px solid #dddddd;
+}
+
+div.sidebar li.toctree-l2:last-child a {
+ border-bottom: none;
+}
+
+div.sidebar li.toctree-l1.current a {
+ border-right: 5px solid #fcaf3e;
+}
+
+div.sidebar li.toctree-l1.current li.toctree-l2 a {
+ border-right: none;
+}
+
+div.sidebar input[type="text"] {
+ width: 170px;
+}
+
+div.sidebar input[type="submit"] {
+ width: 30px;
+}
+
+
+/* Footer */
+
+div.footer-wrapper {
+ background: url(bgfooter.png) top left repeat-x;
+ border-top: 4px solid #babdb6;
+ padding-top: 10px;
+ padding-bottom: 10px;
+ min-height: 80px;
+}
+
+div.footer, div.footer a {
+ color: #888a85;
+}
+
+div.footer .right {
+ text-align: right;
+}
+
+div.footer .left {
+ text-transform: uppercase;
+}
+
+
+/* Styles copied from basic theme */
+
+img.align-left, .figure.align-left, object.align-left {
+ clear: left;
+ float: left;
+ margin-right: 1em;
+}
+
+img.align-right, .figure.align-right, object.align-right {
+ clear: right;
+ float: right;
+ margin-left: 1em;
+}
+
+img.align-center, .figure.align-center, object.align-center {
+ display: block;
+ margin-left: auto;
+ margin-right: auto;
+}
+
+img.align-center-qualimap {
+ display: block;
+ margin-left: auto;
+ margin-right: auto;
+ width: 100%
+}
+
+.align-left {
+ text-align: left;
+}
+
+.align-center {
+ text-align: center;
+}
+
+.align-right {
+ text-align: right;
+}
+
+/* -- search page ----------------------------------------------------------- */
+
+ul.search {
+ margin: 10px 0 0 20px;
+ padding: 0;
+}
+
+ul.search li {
+ padding: 5px 0 5px 20px;
+ background-image: url(file.png);
+ background-repeat: no-repeat;
+ background-position: 0 7px;
+}
+
+ul.search li a {
+ font-weight: bold;
+}
+
+ul.search li div.context {
+ color: #888;
+ margin: 2px 0 0 30px;
+ text-align: left;
+}
+
+ul.keywordmatches li.goodmatch a {
+ font-weight: bold;
+}
+
+/* -- index page ------------------------------------------------------------ */
+
+table.contentstable {
+ width: 90%;
+}
+
+table.contentstable p.biglink {
+ line-height: 150%;
+}
+
+a.biglink {
+ font-size: 1.3em;
+}
+
+span.linkdescr {
+ font-style: italic;
+ padding-top: 5px;
+ font-size: 90%;
+}
+
+/* -- general index --------------------------------------------------------- */
+
+table.indextable td {
+ text-align: left;
+ vertical-align: top;
+}
+
+table.indextable dl, table.indextable dd {
+ margin-top: 0;
+ margin-bottom: 0;
+}
+
+table.indextable tr.pcap {
+ height: 10px;
+}
+
+table.indextable tr.cap {
+ margin-top: 10px;
+ background-color: #f2f2f2;
+}
+
+img.toggler {
+ margin-right: 3px;
+ margin-top: 3px;
+ cursor: pointer;
+}
+
+/* -- viewcode extension ---------------------------------------------------- */
+
+.viewcode-link {
+ float: right;
+}
+
+.viewcode-back {
+ float: right;
+ font-family:: "Verdana", Arial, sans-serif;
+}
+
+div.viewcode-block:target {
+ margin: -1px -3px;
+ padding: 0 3px;
+ background-color: #f4debf;
+ border-top: 1px solid #ac9;
+ border-bottom: 1px solid #ac9;
+}
diff --git a/doc/plasmodium/_static/ajax-loader.gif b/doc/plasmodium/_static/ajax-loader.gif
new file mode 100644
index 0000000..61faf8c
Binary files /dev/null and b/doc/plasmodium/_static/ajax-loader.gif differ
diff --git a/doc/plasmodium/_static/basic.css b/doc/plasmodium/_static/basic.css
new file mode 100644
index 0000000..1e02c5d
--- /dev/null
+++ b/doc/plasmodium/_static/basic.css
@@ -0,0 +1,540 @@
+/*
+ * basic.css
+ * ~~~~~~~~~
+ *
+ * Sphinx stylesheet -- basic theme.
+ *
+ * :copyright: Copyright 2007-2011 by the Sphinx team, see AUTHORS.
+ * :license: BSD, see LICENSE for details.
+ *
+ */
+
+/* -- main layout ----------------------------------------------------------- */
+
+div.clearer {
+ clear: both;
+}
+
+/* -- relbar ---------------------------------------------------------------- */
+
+div.related {
+ width: 100%;
+ font-size: 90%;
+}
+
+div.related h3 {
+ display: none;
+}
+
+div.related ul {
+ margin: 0;
+ padding: 0 0 0 10px;
+ list-style: none;
+}
+
+div.related li {
+ display: inline;
+}
+
+div.related li.right {
+ float: right;
+ margin-right: 5px;
+}
+
+/* -- sidebar --------------------------------------------------------------- */
+
+div.sphinxsidebarwrapper {
+ padding: 10px 5px 0 10px;
+}
+
+div.sphinxsidebar {
+ float: left;
+ width: 0px;
+ margin-left: -100%;
+ font-size: 90%;
+}
+
+div.sphinxsidebar ul {
+ list-style: none;
+}
+
+div.sphinxsidebar ul ul,
+div.sphinxsidebar ul.want-points {
+ margin-left: 20px;
+ list-style: square;
+}
+
+div.sphinxsidebar ul ul {
+ margin-top: 0;
+ margin-bottom: 0;
+}
+
+div.sphinxsidebar form {
+ margin-top: 10px;
+}
+
+div.sphinxsidebar input {
+ border: 1px solid #98dbcc;
+ font-family: sans-serif;
+ font-size: 1em;
+}
+
+div.sphinxsidebar #searchbox input[type="text"] {
+ width: 170px;
+}
+
+div.sphinxsidebar #searchbox input[type="submit"] {
+ width: 30px;
+}
+
+img {
+ border: 0;
+}
+
+/* -- search page ----------------------------------------------------------- */
+
+ul.search {
+ margin: 10px 0 0 20px;
+ padding: 0;
+}
+
+ul.search li {
+ padding: 5px 0 5px 20px;
+ background-image: url(file.png);
+ background-repeat: no-repeat;
+ background-position: 0 7px;
+}
+
+ul.search li a {
+ font-weight: bold;
+}
+
+ul.search li div.context {
+ color: #888;
+ margin: 2px 0 0 30px;
+ text-align: left;
+}
+
+ul.keywordmatches li.goodmatch a {
+ font-weight: bold;
+}
+
+/* -- index page ------------------------------------------------------------ */
+
+table.contentstable {
+ width: 90%;
+}
+
+table.contentstable p.biglink {
+ line-height: 150%;
+}
+
+a.biglink {
+ font-size: 1.3em;
+}
+
+span.linkdescr {
+ font-style: italic;
+ padding-top: 5px;
+ font-size: 90%;
+}
+
+/* -- general index --------------------------------------------------------- */
+
+table.indextable {
+ width: 100%;
+}
+
+table.indextable td {
+ text-align: left;
+ vertical-align: top;
+}
+
+table.indextable dl, table.indextable dd {
+ margin-top: 0;
+ margin-bottom: 0;
+}
+
+table.indextable tr.pcap {
+ height: 10px;
+}
+
+table.indextable tr.cap {
+ margin-top: 10px;
+ background-color: #f2f2f2;
+}
+
+img.toggler {
+ margin-right: 3px;
+ margin-top: 3px;
+ cursor: pointer;
+}
+
+div.modindex-jumpbox {
+ border-top: 1px solid #ddd;
+ border-bottom: 1px solid #ddd;
+ margin: 1em 0 1em 0;
+ padding: 0.4em;
+}
+
+div.genindex-jumpbox {
+ border-top: 1px solid #ddd;
+ border-bottom: 1px solid #ddd;
+ margin: 1em 0 1em 0;
+ padding: 0.4em;
+}
+
+/* -- general body styles --------------------------------------------------- */
+
+a.headerlink {
+ visibility: hidden;
+}
+
+h1:hover > a.headerlink,
+h2:hover > a.headerlink,
+h3:hover > a.headerlink,
+h4:hover > a.headerlink,
+h5:hover > a.headerlink,
+h6:hover > a.headerlink,
+dt:hover > a.headerlink {
+ visibility: visible;
+}
+
+div.body p.caption {
+ text-align: inherit;
+}
+
+div.body td {
+ text-align: left;
+}
+
+.field-list ul {
+ padding-left: 1em;
+}
+
+.first {
+ margin-top: 0 !important;
+}
+
+p.rubric {
+ margin-top: 30px;
+ font-weight: bold;
+}
+
+img.align-left, .figure.align-left, object.align-left {
+ clear: left;
+ float: left;
+ margin-right: 1em;
+}
+
+img.align-right, .figure.align-right, object.align-right {
+ clear: right;
+ float: right;
+ margin-left: 1em;
+}
+
+img.align-center, .figure.align-center, object.align-center {
+ display: block;
+ margin-left: auto;
+ margin-right: auto;
+}
+
+.align-left {
+ text-align: left;
+}
+
+.align-center {
+ text-align: center;
+}
+
+.align-right {
+ text-align: right;
+}
+
+/* -- sidebars -------------------------------------------------------------- */
+
+div.sidebar {
+ margin: 0 0 0.5em 1em;
+ border: 1px solid #ddb;
+ padding: 7px 7px 0 7px;
+ background-color: #ffe;
+ width: 40%;
+ float: right;
+}
+
+p.sidebar-title {
+ font-weight: bold;
+}
+
+/* -- topics ---------------------------------------------------------------- */
+
+div.topic {
+ border: 1px solid #ccc;
+ padding: 7px 7px 0 7px;
+ margin: 10px 0 10px 0;
+}
+
+p.topic-title {
+ font-size: 1.1em;
+ font-weight: bold;
+ margin-top: 10px;
+}
+
+/* -- admonitions ----------------------------------------------------------- */
+
+div.admonition {
+ margin-top: 10px;
+ margin-bottom: 10px;
+ padding: 7px;
+}
+
+div.admonition dt {
+ font-weight: bold;
+}
+
+div.admonition dl {
+ margin-bottom: 0;
+}
+
+p.admonition-title {
+ margin: 0px 10px 5px 0px;
+ font-weight: bold;
+}
+
+div.body p.centered {
+ text-align: center;
+ margin-top: 25px;
+}
+
+/* -- tables ---------------------------------------------------------------- */
+
+table.docutils {
+ border: 0;
+ border-collapse: collapse;
+}
+
+table.docutils td, table.docutils th {
+ padding: 1px 8px 1px 5px;
+ border-top: 0;
+ border-left: 0;
+ border-right: 0;
+ border-bottom: 1px solid #aaa;
+}
+
+table.field-list td, table.field-list th {
+ border: 0 !important;
+}
+
+table.footnote td, table.footnote th {
+ border: 0 !important;
+}
+
+th {
+ text-align: left;
+ padding-right: 5px;
+}
+
+table.citation {
+ border-left: solid 1px gray;
+ margin-left: 1px;
+}
+
+table.citation td {
+ border-bottom: none;
+}
+
+/* -- other body styles ----------------------------------------------------- */
+
+ol.arabic {
+ list-style: decimal;
+}
+
+ol.loweralpha {
+ list-style: lower-alpha;
+}
+
+ol.upperalpha {
+ list-style: upper-alpha;
+}
+
+ol.lowerroman {
+ list-style: lower-roman;
+}
+
+ol.upperroman {
+ list-style: upper-roman;
+}
+
+dl {
+ margin-bottom: 15px;
+}
+
+dd p {
+ margin-top: 0px;
+}
+
+dd ul, dd table {
+ margin-bottom: 10px;
+}
+
+dd {
+ margin-top: 3px;
+ margin-bottom: 10px;
+ margin-left: 30px;
+}
+
+dt:target, .highlighted {
+ background-color: #fbe54e;
+}
+
+dl.glossary dt {
+ font-weight: bold;
+ font-size: 1.1em;
+}
+
+.field-list ul {
+ margin: 0;
+ padding-left: 1em;
+}
+
+.field-list p {
+ margin: 0;
+}
+
+.refcount {
+ color: #060;
+}
+
+.optional {
+ font-size: 1.3em;
+}
+
+.versionmodified {
+ font-style: italic;
+}
+
+.system-message {
+ background-color: #fda;
+ padding: 5px;
+ border: 3px solid red;
+}
+
+.footnote:target {
+ background-color: #ffa;
+}
+
+.line-block {
+ display: block;
+ margin-top: 1em;
+ margin-bottom: 1em;
+}
+
+.line-block .line-block {
+ margin-top: 0;
+ margin-bottom: 0;
+ margin-left: 1.5em;
+}
+
+.guilabel, .menuselection {
+ font-family: sans-serif;
+}
+
+.accelerator {
+ text-decoration: underline;
+}
+
+.classifier {
+ font-style: oblique;
+}
+
+abbr, acronym {
+ border-bottom: dotted 1px;
+ cursor: help;
+}
+
+/* -- code displays --------------------------------------------------------- */
+
+pre {
+ overflow: auto;
+ overflow-y: hidden; /* fixes display issues on Chrome browsers */
+}
+
+td.linenos pre {
+ padding: 5px 0px;
+ border: 0;
+ background-color: transparent;
+ color: #aaa;
+}
+
+table.highlighttable {
+ margin-left: 0.5em;
+}
+
+table.highlighttable td {
+ padding: 0 0.5em 0 0.5em;
+}
+
+tt.descname {
+ background-color: transparent;
+ font-weight: bold;
+ font-size: 1.2em;
+}
+
+tt.descclassname {
+ background-color: transparent;
+}
+
+tt.xref, a tt {
+ background-color: transparent;
+ font-weight: bold;
+}
+
+h1 tt, h2 tt, h3 tt, h4 tt, h5 tt, h6 tt {
+ background-color: transparent;
+}
+
+.viewcode-link {
+ float: right;
+}
+
+.viewcode-back {
+ float: right;
+ font-family: sans-serif;
+}
+
+div.viewcode-block:target {
+ margin: -1px -10px;
+ padding: 0 10px;
+}
+
+/* -- math display ---------------------------------------------------------- */
+
+img.math {
+ vertical-align: middle;
+}
+
+div.body div.math p {
+ text-align: center;
+}
+
+span.eqno {
+ float: right;
+}
+
+/* -- printout stylesheet --------------------------------------------------- */
+
+ at media print {
+ div.document,
+ div.documentwrapper,
+ div.bodywrapper {
+ margin: 0 !important;
+ width: 100%;
+ }
+
+ div.sphinxsidebar,
+ div.related,
+ div.footer,
+ #top-link {
+ display: none;
+ }
+}
\ No newline at end of file
diff --git a/doc/plasmodium/_static/bgfooter.png b/doc/plasmodium/_static/bgfooter.png
new file mode 100644
index 0000000..9ce5bdd
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diff --git a/doc/plasmodium/_static/bgtop.png b/doc/plasmodium/_static/bgtop.png
new file mode 100644
index 0000000..a0d4709
Binary files /dev/null and b/doc/plasmodium/_static/bgtop.png differ
diff --git a/doc/plasmodium/_static/comment-bright.png b/doc/plasmodium/_static/comment-bright.png
new file mode 100644
index 0000000..551517b
Binary files /dev/null and b/doc/plasmodium/_static/comment-bright.png differ
diff --git a/doc/plasmodium/_static/comment-close.png b/doc/plasmodium/_static/comment-close.png
new file mode 100644
index 0000000..09b54be
Binary files /dev/null and b/doc/plasmodium/_static/comment-close.png differ
diff --git a/doc/plasmodium/_static/comment.png b/doc/plasmodium/_static/comment.png
new file mode 100644
index 0000000..92feb52
Binary files /dev/null and b/doc/plasmodium/_static/comment.png differ
diff --git a/doc/plasmodium/_static/doctools.js b/doc/plasmodium/_static/doctools.js
new file mode 100644
index 0000000..d4619fd
--- /dev/null
+++ b/doc/plasmodium/_static/doctools.js
@@ -0,0 +1,247 @@
+/*
+ * doctools.js
+ * ~~~~~~~~~~~
+ *
+ * Sphinx JavaScript utilities for all documentation.
+ *
+ * :copyright: Copyright 2007-2011 by the Sphinx team, see AUTHORS.
+ * :license: BSD, see LICENSE for details.
+ *
+ */
+
+/**
+ * select a different prefix for underscore
+ */
+$u = _.noConflict();
+
+/**
+ * make the code below compatible with browsers without
+ * an installed firebug like debugger
+if (!window.console || !console.firebug) {
+ var names = ["log", "debug", "info", "warn", "error", "assert", "dir",
+ "dirxml", "group", "groupEnd", "time", "timeEnd", "count", "trace",
+ "profile", "profileEnd"];
+ window.console = {};
+ for (var i = 0; i < names.length; ++i)
+ window.console[names[i]] = function() {};
+}
+ */
+
+/**
+ * small helper function to urldecode strings
+ */
+jQuery.urldecode = function(x) {
+ return decodeURIComponent(x).replace(/\+/g, ' ');
+}
+
+/**
+ * small helper function to urlencode strings
+ */
+jQuery.urlencode = encodeURIComponent;
+
+/**
+ * This function returns the parsed url parameters of the
+ * current request. Multiple values per key are supported,
+ * it will always return arrays of strings for the value parts.
+ */
+jQuery.getQueryParameters = function(s) {
+ if (typeof s == 'undefined')
+ s = document.location.search;
+ var parts = s.substr(s.indexOf('?') + 1).split('&');
+ var result = {};
+ for (var i = 0; i < parts.length; i++) {
+ var tmp = parts[i].split('=', 2);
+ var key = jQuery.urldecode(tmp[0]);
+ var value = jQuery.urldecode(tmp[1]);
+ if (key in result)
+ result[key].push(value);
+ else
+ result[key] = [value];
+ }
+ return result;
+};
+
+/**
+ * small function to check if an array contains
+ * a given item.
+ */
+jQuery.contains = function(arr, item) {
+ for (var i = 0; i < arr.length; i++) {
+ if (arr[i] == item)
+ return true;
+ }
+ return false;
+};
+
+/**
+ * highlight a given string on a jquery object by wrapping it in
+ * span elements with the given class name.
+ */
+jQuery.fn.highlightText = function(text, className) {
+ function highlight(node) {
+ if (node.nodeType == 3) {
+ var val = node.nodeValue;
+ var pos = val.toLowerCase().indexOf(text);
+ if (pos >= 0 && !jQuery(node.parentNode).hasClass(className)) {
+ var span = document.createElement("span");
+ span.className = className;
+ span.appendChild(document.createTextNode(val.substr(pos, text.length)));
+ node.parentNode.insertBefore(span, node.parentNode.insertBefore(
+ document.createTextNode(val.substr(pos + text.length)),
+ node.nextSibling));
+ node.nodeValue = val.substr(0, pos);
+ }
+ }
+ else if (!jQuery(node).is("button, select, textarea")) {
+ jQuery.each(node.childNodes, function() {
+ highlight(this);
+ });
+ }
+ }
+ return this.each(function() {
+ highlight(this);
+ });
+};
+
+/**
+ * Small JavaScript module for the documentation.
+ */
+var Documentation = {
+
+ init : function() {
+ this.fixFirefoxAnchorBug();
+ this.highlightSearchWords();
+ this.initIndexTable();
+ },
+
+ /**
+ * i18n support
+ */
+ TRANSLATIONS : {},
+ PLURAL_EXPR : function(n) { return n == 1 ? 0 : 1; },
+ LOCALE : 'unknown',
+
+ // gettext and ngettext don't access this so that the functions
+ // can safely bound to a different name (_ = Documentation.gettext)
+ gettext : function(string) {
+ var translated = Documentation.TRANSLATIONS[string];
+ if (typeof translated == 'undefined')
+ return string;
+ return (typeof translated == 'string') ? translated : translated[0];
+ },
+
+ ngettext : function(singular, plural, n) {
+ var translated = Documentation.TRANSLATIONS[singular];
+ if (typeof translated == 'undefined')
+ return (n == 1) ? singular : plural;
+ return translated[Documentation.PLURALEXPR(n)];
+ },
+
+ addTranslations : function(catalog) {
+ for (var key in catalog.messages)
+ this.TRANSLATIONS[key] = catalog.messages[key];
+ this.PLURAL_EXPR = new Function('n', 'return +(' + catalog.plural_expr + ')');
+ this.LOCALE = catalog.locale;
+ },
+
+ /**
+ * add context elements like header anchor links
+ */
+ addContextElements : function() {
+ $('div[id] > :header:first').each(function() {
+ $('<a class="headerlink">\u00B6</a>').
+ attr('href', '#' + this.id).
+ attr('title', _('Permalink to this headline')).
+ appendTo(this);
+ });
+ $('dt[id]').each(function() {
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+ }
+ },
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+ /**
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+ var idnum = $(this).attr('id').substr(7);
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+ }).css('display', '');
+ if (DOCUMENTATION_OPTIONS.COLLAPSE_INDEX) {
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+
+ /**
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+ hideSearchWords : function() {
+ $('#searchbox .highlight-link').fadeOut(300);
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+ },
+
+ /**
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+ */
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+ },
+
+ /**
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+ */
+ getCurrentURL : function() {
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+ var parts = path.split(/\//);
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+ });
+ var url = parts.join('/');
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+ }
+};
+
+// quick alias for translations
+_ = Documentation.gettext;
+
+$(document).ready(function() {
+ Documentation.init();
+});
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diff --git a/doc/plasmodium/_static/down.png b/doc/plasmodium/_static/down.png
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diff --git a/doc/plasmodium/_static/file.png b/doc/plasmodium/_static/file.png
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diff --git a/doc/plasmodium/_static/jquery.js b/doc/plasmodium/_static/jquery.js
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+f.top,left:d.left-f.left}},offsetParent:function(){return this.map(function(){for(var a=this.offsetParent||s.body;a&&!/^body|html$/i.test(a.nodeName)&&c.css(a,"position")==="static";)a=a.offsetParent;return a})}});c.each(["Left","Top"],function(a,b){var d="scroll"+b;c.fn[d]=function(f){var e=this[0],j;if(!e)return null;if(f!==w)return this.each(function(){if(j=wa(this))j.scrollTo(!a?f:c(j).scrollLeft(),a?f:c(j).scrollTop());else this[d]=f});else return(j=wa(e))?"pageXOffset"in j?j[a?"pag [...]
+"pageXOffset"]:c.support.boxModel&&j.document.documentElement[d]||j.document.body[d]:e[d]}});c.each(["Height","Width"],function(a,b){var d=b.toLowerCase();c.fn["inner"+b]=function(){return this[0]?c.css(this[0],d,false,"padding"):null};c.fn["outer"+b]=function(f){return this[0]?c.css(this[0],d,false,f?"margin":"border"):null};c.fn[d]=function(f){var e=this[0];if(!e)return f==null?null:this;if(c.isFunction(f))return this.each(function(j){var i=c(this);i[d](f.call(this,j,i[d]()))});return" [...]
+e&&e.document?e.document.compatMode==="CSS1Compat"&&e.document.documentElement["client"+b]||e.document.body["client"+b]:e.nodeType===9?Math.max(e.documentElement["client"+b],e.body["scroll"+b],e.documentElement["scroll"+b],e.body["offset"+b],e.documentElement["offset"+b]):f===w?c.css(e,d):this.css(d,typeof f==="string"?f:f+"px")}});A.jQuery=A.$=c})(window);
diff --git a/doc/plasmodium/_static/minus.png b/doc/plasmodium/_static/minus.png
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diff --git a/doc/plasmodium/_static/plus.png b/doc/plasmodium/_static/plus.png
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diff --git a/doc/plasmodium/_static/pygments.css b/doc/plasmodium/_static/pygments.css
new file mode 100644
index 0000000..1a14f2a
--- /dev/null
+++ b/doc/plasmodium/_static/pygments.css
@@ -0,0 +1,62 @@
+.highlight .hll { background-color: #ffffcc }
+.highlight { background: #eeffcc; }
+.highlight .c { color: #408090; font-style: italic } /* Comment */
+.highlight .err { border: 1px solid #FF0000 } /* Error */
+.highlight .k { color: #007020; font-weight: bold } /* Keyword */
+.highlight .o { color: #666666 } /* Operator */
+.highlight .cm { color: #408090; font-style: italic } /* Comment.Multiline */
+.highlight .cp { color: #007020 } /* Comment.Preproc */
+.highlight .c1 { color: #408090; font-style: italic } /* Comment.Single */
+.highlight .cs { color: #408090; background-color: #fff0f0 } /* Comment.Special */
+.highlight .gd { color: #A00000 } /* Generic.Deleted */
+.highlight .ge { font-style: italic } /* Generic.Emph */
+.highlight .gr { color: #FF0000 } /* Generic.Error */
+.highlight .gh { color: #000080; font-weight: bold } /* Generic.Heading */
+.highlight .gi { color: #00A000 } /* Generic.Inserted */
+.highlight .go { color: #303030 } /* Generic.Output */
+.highlight .gp { color: #c65d09; font-weight: bold } /* Generic.Prompt */
+.highlight .gs { font-weight: bold } /* Generic.Strong */
+.highlight .gu { color: #800080; font-weight: bold } /* Generic.Subheading */
+.highlight .gt { color: #0040D0 } /* Generic.Traceback */
+.highlight .kc { color: #007020; font-weight: bold } /* Keyword.Constant */
+.highlight .kd { color: #007020; font-weight: bold } /* Keyword.Declaration */
+.highlight .kn { color: #007020; font-weight: bold } /* Keyword.Namespace */
+.highlight .kp { color: #007020 } /* Keyword.Pseudo */
+.highlight .kr { color: #007020; font-weight: bold } /* Keyword.Reserved */
+.highlight .kt { color: #902000 } /* Keyword.Type */
+.highlight .m { color: #208050 } /* Literal.Number */
+.highlight .s { color: #4070a0 } /* Literal.String */
+.highlight .na { color: #4070a0 } /* Name.Attribute */
+.highlight .nb { color: #007020 } /* Name.Builtin */
+.highlight .nc { color: #0e84b5; font-weight: bold } /* Name.Class */
+.highlight .no { color: #60add5 } /* Name.Constant */
+.highlight .nd { color: #555555; font-weight: bold } /* Name.Decorator */
+.highlight .ni { color: #d55537; font-weight: bold } /* Name.Entity */
+.highlight .ne { color: #007020 } /* Name.Exception */
+.highlight .nf { color: #06287e } /* Name.Function */
+.highlight .nl { color: #002070; font-weight: bold } /* Name.Label */
+.highlight .nn { color: #0e84b5; font-weight: bold } /* Name.Namespace */
+.highlight .nt { color: #062873; font-weight: bold } /* Name.Tag */
+.highlight .nv { color: #bb60d5 } /* Name.Variable */
+.highlight .ow { color: #007020; font-weight: bold } /* Operator.Word */
+.highlight .w { color: #bbbbbb } /* Text.Whitespace */
+.highlight .mf { color: #208050 } /* Literal.Number.Float */
+.highlight .mh { color: #208050 } /* Literal.Number.Hex */
+.highlight .mi { color: #208050 } /* Literal.Number.Integer */
+.highlight .mo { color: #208050 } /* Literal.Number.Oct */
+.highlight .sb { color: #4070a0 } /* Literal.String.Backtick */
+.highlight .sc { color: #4070a0 } /* Literal.String.Char */
+.highlight .sd { color: #4070a0; font-style: italic } /* Literal.String.Doc */
+.highlight .s2 { color: #4070a0 } /* Literal.String.Double */
+.highlight .se { color: #4070a0; font-weight: bold } /* Literal.String.Escape */
+.highlight .sh { color: #4070a0 } /* Literal.String.Heredoc */
+.highlight .si { color: #70a0d0; font-style: italic } /* Literal.String.Interpol */
+.highlight .sx { color: #c65d09 } /* Literal.String.Other */
+.highlight .sr { color: #235388 } /* Literal.String.Regex */
+.highlight .s1 { color: #4070a0 } /* Literal.String.Single */
+.highlight .ss { color: #517918 } /* Literal.String.Symbol */
+.highlight .bp { color: #007020 } /* Name.Builtin.Pseudo */
+.highlight .vc { color: #bb60d5 } /* Name.Variable.Class */
+.highlight .vg { color: #bb60d5 } /* Name.Variable.Global */
+.highlight .vi { color: #bb60d5 } /* Name.Variable.Instance */
+.highlight .il { color: #208050 } /* Literal.Number.Integer.Long */
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diff --git a/doc/plasmodium/_static/qualimap_logo_small.png b/doc/plasmodium/_static/qualimap_logo_small.png
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diff --git a/doc/plasmodium/_static/report.css b/doc/plasmodium/_static/report.css
new file mode 100644
index 0000000..19ae268
--- /dev/null
+++ b/doc/plasmodium/_static/report.css
@@ -0,0 +1,50 @@
+div.summary{
+
+}
+
+table.summary{
+
+ border: 0px;
+ width: 100%;
+ vertical-align: top;
+
+}
+
+div.table-summary{
+ margin-left:auto;
+ margin-right:auto;
+ padding-bottom: 20px;
+}
+
+td.column1{
+ width: 60%;
+}
+
+table.hovertable {
+
+ font-size:14px;
+
+ border-width: 1px;
+ border-color: #999999;
+ border-collapse: collapse;
+}
+table.hovertable th {
+ background-color:#FFFFFF;
+ border-width: 1px;
+ padding: 8px;
+ border-style: solid;
+ border-color: #a9c6c9;
+}
+table.hovertable tr {
+ background-color:#FFFFFF;
+}
+table.hovertable td {
+ border-width: 1px;
+ padding: 8px;
+ border-style: solid;
+ border-color: #a9c6c9;
+}
+
+
+
+
diff --git a/doc/plasmodium/_static/searchtools.js b/doc/plasmodium/_static/searchtools.js
new file mode 100644
index 0000000..663be4c
--- /dev/null
+++ b/doc/plasmodium/_static/searchtools.js
@@ -0,0 +1,560 @@
+/*
+ * searchtools.js_t
+ * ~~~~~~~~~~~~~~~~
+ *
+ * Sphinx JavaScript utilties for the full-text search.
+ *
+ * :copyright: Copyright 2007-2011 by the Sphinx team, see AUTHORS.
+ * :license: BSD, see LICENSE for details.
+ *
+ */
+
+/**
+ * helper function to return a node containing the
+ * search summary for a given text. keywords is a list
+ * of stemmed words, hlwords is the list of normal, unstemmed
+ * words. the first one is used to find the occurance, the
+ * latter for highlighting it.
+ */
+
+jQuery.makeSearchSummary = function(text, keywords, hlwords) {
+ var textLower = text.toLowerCase();
+ var start = 0;
+ $.each(keywords, function() {
+ var i = textLower.indexOf(this.toLowerCase());
+ if (i > -1)
+ start = i;
+ });
+ start = Math.max(start - 120, 0);
+ var excerpt = ((start > 0) ? '...' : '') +
+ $.trim(text.substr(start, 240)) +
+ ((start + 240 - text.length) ? '...' : '');
+ var rv = $('<div class="context"></div>').text(excerpt);
+ $.each(hlwords, function() {
+ rv = rv.highlightText(this, 'highlighted');
+ });
+ return rv;
+}
+
+
+/**
+ * Porter Stemmer
+ */
+var Stemmer = function() {
+
+ var step2list = {
+ ational: 'ate',
+ tional: 'tion',
+ enci: 'ence',
+ anci: 'ance',
+ izer: 'ize',
+ bli: 'ble',
+ alli: 'al',
+ entli: 'ent',
+ eli: 'e',
+ ousli: 'ous',
+ ization: 'ize',
+ ation: 'ate',
+ ator: 'ate',
+ alism: 'al',
+ iveness: 'ive',
+ fulness: 'ful',
+ ousness: 'ous',
+ aliti: 'al',
+ iviti: 'ive',
+ biliti: 'ble',
+ logi: 'log'
+ };
+
+ var step3list = {
+ icate: 'ic',
+ ative: '',
+ alize: 'al',
+ iciti: 'ic',
+ ical: 'ic',
+ ful: '',
+ ness: ''
+ };
+
+ var c = "[^aeiou]"; // consonant
+ var v = "[aeiouy]"; // vowel
+ var C = c + "[^aeiouy]*"; // consonant sequence
+ var V = v + "[aeiou]*"; // vowel sequence
+
+ var mgr0 = "^(" + C + ")?" + V + C; // [C]VC... is m>0
+ var meq1 = "^(" + C + ")?" + V + C + "(" + V + ")?$"; // [C]VC[V] is m=1
+ var mgr1 = "^(" + C + ")?" + V + C + V + C; // [C]VCVC... is m>1
+ var s_v = "^(" + C + ")?" + v; // vowel in stem
+
+ this.stemWord = function (w) {
+ var stem;
+ var suffix;
+ var firstch;
+ var origword = w;
+
+ if (w.length < 3)
+ return w;
+
+ var re;
+ var re2;
+ var re3;
+ var re4;
+
+ firstch = w.substr(0,1);
+ if (firstch == "y")
+ w = firstch.toUpperCase() + w.substr(1);
+
+ // Step 1a
+ re = /^(.+?)(ss|i)es$/;
+ re2 = /^(.+?)([^s])s$/;
+
+ if (re.test(w))
+ w = w.replace(re,"$1$2");
+ else if (re2.test(w))
+ w = w.replace(re2,"$1$2");
+
+ // Step 1b
+ re = /^(.+?)eed$/;
+ re2 = /^(.+?)(ed|ing)$/;
+ if (re.test(w)) {
+ var fp = re.exec(w);
+ re = new RegExp(mgr0);
+ if (re.test(fp[1])) {
+ re = /.$/;
+ w = w.replace(re,"");
+ }
+ }
+ else if (re2.test(w)) {
+ var fp = re2.exec(w);
+ stem = fp[1];
+ re2 = new RegExp(s_v);
+ if (re2.test(stem)) {
+ w = stem;
+ re2 = /(at|bl|iz)$/;
+ re3 = new RegExp("([^aeiouylsz])\\1$");
+ re4 = new RegExp("^" + C + v + "[^aeiouwxy]$");
+ if (re2.test(w))
+ w = w + "e";
+ else if (re3.test(w)) {
+ re = /.$/;
+ w = w.replace(re,"");
+ }
+ else if (re4.test(w))
+ w = w + "e";
+ }
+ }
+
+ // Step 1c
+ re = /^(.+?)y$/;
+ if (re.test(w)) {
+ var fp = re.exec(w);
+ stem = fp[1];
+ re = new RegExp(s_v);
+ if (re.test(stem))
+ w = stem + "i";
+ }
+
+ // Step 2
+ re = /^(.+?)(ational|tional|enci|anci|izer|bli|alli|entli|eli|ousli|ization|ation|ator|alism|iveness|fulness|ousness|aliti|iviti|biliti|logi)$/;
+ if (re.test(w)) {
+ var fp = re.exec(w);
+ stem = fp[1];
+ suffix = fp[2];
+ re = new RegExp(mgr0);
+ if (re.test(stem))
+ w = stem + step2list[suffix];
+ }
+
+ // Step 3
+ re = /^(.+?)(icate|ative|alize|iciti|ical|ful|ness)$/;
+ if (re.test(w)) {
+ var fp = re.exec(w);
+ stem = fp[1];
+ suffix = fp[2];
+ re = new RegExp(mgr0);
+ if (re.test(stem))
+ w = stem + step3list[suffix];
+ }
+
+ // Step 4
+ re = /^(.+?)(al|ance|ence|er|ic|able|ible|ant|ement|ment|ent|ou|ism|ate|iti|ous|ive|ize)$/;
+ re2 = /^(.+?)(s|t)(ion)$/;
+ if (re.test(w)) {
+ var fp = re.exec(w);
+ stem = fp[1];
+ re = new RegExp(mgr1);
+ if (re.test(stem))
+ w = stem;
+ }
+ else if (re2.test(w)) {
+ var fp = re2.exec(w);
+ stem = fp[1] + fp[2];
+ re2 = new RegExp(mgr1);
+ if (re2.test(stem))
+ w = stem;
+ }
+
+ // Step 5
+ re = /^(.+?)e$/;
+ if (re.test(w)) {
+ var fp = re.exec(w);
+ stem = fp[1];
+ re = new RegExp(mgr1);
+ re2 = new RegExp(meq1);
+ re3 = new RegExp("^" + C + v + "[^aeiouwxy]$");
+ if (re.test(stem) || (re2.test(stem) && !(re3.test(stem))))
+ w = stem;
+ }
+ re = /ll$/;
+ re2 = new RegExp(mgr1);
+ if (re.test(w) && re2.test(w)) {
+ re = /.$/;
+ w = w.replace(re,"");
+ }
+
+ // and turn initial Y back to y
+ if (firstch == "y")
+ w = firstch.toLowerCase() + w.substr(1);
+ return w;
+ }
+}
+
+
+/**
+ * Search Module
+ */
+var Search = {
+
+ _index : null,
+ _queued_query : null,
+ _pulse_status : -1,
+
+ init : function() {
+ var params = $.getQueryParameters();
+ if (params.q) {
+ var query = params.q[0];
+ $('input[name="q"]')[0].value = query;
+ this.performSearch(query);
+ }
+ },
+
+ loadIndex : function(url) {
+ $.ajax({type: "GET", url: url, data: null, success: null,
+ dataType: "script", cache: true});
+ },
+
+ setIndex : function(index) {
+ var q;
+ this._index = index;
+ if ((q = this._queued_query) !== null) {
+ this._queued_query = null;
+ Search.query(q);
+ }
+ },
+
+ hasIndex : function() {
+ return this._index !== null;
+ },
+
+ deferQuery : function(query) {
+ this._queued_query = query;
+ },
+
+ stopPulse : function() {
+ this._pulse_status = 0;
+ },
+
+ startPulse : function() {
+ if (this._pulse_status >= 0)
+ return;
+ function pulse() {
+ Search._pulse_status = (Search._pulse_status + 1) % 4;
+ var dotString = '';
+ for (var i = 0; i < Search._pulse_status; i++)
+ dotString += '.';
+ Search.dots.text(dotString);
+ if (Search._pulse_status > -1)
+ window.setTimeout(pulse, 500);
+ };
+ pulse();
+ },
+
+ /**
+ * perform a search for something
+ */
+ performSearch : function(query) {
+ // create the required interface elements
+ this.out = $('#search-results');
+ this.title = $('<h2>' + _('Searching') + '</h2>').appendTo(this.out);
+ this.dots = $('<span></span>').appendTo(this.title);
+ this.status = $('<p style="display: none"></p>').appendTo(this.out);
+ this.output = $('<ul class="search"/>').appendTo(this.out);
+
+ $('#search-progress').text(_('Preparing search...'));
+ this.startPulse();
+
+ // index already loaded, the browser was quick!
+ if (this.hasIndex())
+ this.query(query);
+ else
+ this.deferQuery(query);
+ },
+
+ query : function(query) {
+ var stopwords = ["and","then","into","it","as","are","in","if","for","no","there","their","was","is","be","to","that","but","they","not","such","with","by","a","on","these","of","will","this","near","the","or","at"];
+
+ // Stem the searchterms and add them to the correct list
+ var stemmer = new Stemmer();
+ var searchterms = [];
+ var excluded = [];
+ var hlterms = [];
+ var tmp = query.split(/\s+/);
+ var objectterms = [];
+ for (var i = 0; i < tmp.length; i++) {
+ if (tmp[i] != "") {
+ objectterms.push(tmp[i].toLowerCase());
+ }
+
+ if ($u.indexOf(stopwords, tmp[i]) != -1 || tmp[i].match(/^\d+$/) ||
+ tmp[i] == "") {
+ // skip this "word"
+ continue;
+ }
+ // stem the word
+ var word = stemmer.stemWord(tmp[i]).toLowerCase();
+ // select the correct list
+ if (word[0] == '-') {
+ var toAppend = excluded;
+ word = word.substr(1);
+ }
+ else {
+ var toAppend = searchterms;
+ hlterms.push(tmp[i].toLowerCase());
+ }
+ // only add if not already in the list
+ if (!$.contains(toAppend, word))
+ toAppend.push(word);
+ };
+ var highlightstring = '?highlight=' + $.urlencode(hlterms.join(" "));
+
+ // console.debug('SEARCH: searching for:');
+ // console.info('required: ', searchterms);
+ // console.info('excluded: ', excluded);
+
+ // prepare search
+ var filenames = this._index.filenames;
+ var titles = this._index.titles;
+ var terms = this._index.terms;
+ var fileMap = {};
+ var files = null;
+ // different result priorities
+ var importantResults = [];
+ var objectResults = [];
+ var regularResults = [];
+ var unimportantResults = [];
+ $('#search-progress').empty();
+
+ // lookup as object
+ for (var i = 0; i < objectterms.length; i++) {
+ var others = [].concat(objectterms.slice(0,i),
+ objectterms.slice(i+1, objectterms.length))
+ var results = this.performObjectSearch(objectterms[i], others);
+ // Assume first word is most likely to be the object,
+ // other words more likely to be in description.
+ // Therefore put matches for earlier words first.
+ // (Results are eventually used in reverse order).
+ objectResults = results[0].concat(objectResults);
+ importantResults = results[1].concat(importantResults);
+ unimportantResults = results[2].concat(unimportantResults);
+ }
+
+ // perform the search on the required terms
+ for (var i = 0; i < searchterms.length; i++) {
+ var word = searchterms[i];
+ // no match but word was a required one
+ if ((files = terms[word]) == null)
+ break;
+ if (files.length == undefined) {
+ files = [files];
+ }
+ // create the mapping
+ for (var j = 0; j < files.length; j++) {
+ var file = files[j];
+ if (file in fileMap)
+ fileMap[file].push(word);
+ else
+ fileMap[file] = [word];
+ }
+ }
+
+ // now check if the files don't contain excluded terms
+ for (var file in fileMap) {
+ var valid = true;
+
+ // check if all requirements are matched
+ if (fileMap[file].length != searchterms.length)
+ continue;
+
+ // ensure that none of the excluded terms is in the
+ // search result.
+ for (var i = 0; i < excluded.length; i++) {
+ if (terms[excluded[i]] == file ||
+ $.contains(terms[excluded[i]] || [], file)) {
+ valid = false;
+ break;
+ }
+ }
+
+ // if we have still a valid result we can add it
+ // to the result list
+ if (valid)
+ regularResults.push([filenames[file], titles[file], '', null]);
+ }
+
+ // delete unused variables in order to not waste
+ // memory until list is retrieved completely
+ delete filenames, titles, terms;
+
+ // now sort the regular results descending by title
+ regularResults.sort(function(a, b) {
+ var left = a[1].toLowerCase();
+ var right = b[1].toLowerCase();
+ return (left > right) ? -1 : ((left < right) ? 1 : 0);
+ });
+
+ // combine all results
+ var results = unimportantResults.concat(regularResults)
+ .concat(objectResults).concat(importantResults);
+
+ // print the results
+ var resultCount = results.length;
+ function displayNextItem() {
+ // results left, load the summary and display it
+ if (results.length) {
+ var item = results.pop();
+ var listItem = $('<li style="display:none"></li>');
+ if (DOCUMENTATION_OPTIONS.FILE_SUFFIX == '') {
+ // dirhtml builder
+ var dirname = item[0] + '/';
+ if (dirname.match(/\/index\/$/)) {
+ dirname = dirname.substring(0, dirname.length-6);
+ } else if (dirname == 'index/') {
+ dirname = '';
+ }
+ listItem.append($('<a/>').attr('href',
+ DOCUMENTATION_OPTIONS.URL_ROOT + dirname +
+ highlightstring + item[2]).html(item[1]));
+ } else {
+ // normal html builders
+ listItem.append($('<a/>').attr('href',
+ item[0] + DOCUMENTATION_OPTIONS.FILE_SUFFIX +
+ highlightstring + item[2]).html(item[1]));
+ }
+ if (item[3]) {
+ listItem.append($('<span> (' + item[3] + ')</span>'));
+ Search.output.append(listItem);
+ listItem.slideDown(5, function() {
+ displayNextItem();
+ });
+ } else if (DOCUMENTATION_OPTIONS.HAS_SOURCE) {
+ $.get(DOCUMENTATION_OPTIONS.URL_ROOT + '_sources/' +
+ item[0] + '.txt', function(data) {
+ if (data != '') {
+ listItem.append($.makeSearchSummary(data, searchterms, hlterms));
+ Search.output.append(listItem);
+ }
+ listItem.slideDown(5, function() {
+ displayNextItem();
+ });
+ }, "text");
+ } else {
+ // no source available, just display title
+ Search.output.append(listItem);
+ listItem.slideDown(5, function() {
+ displayNextItem();
+ });
+ }
+ }
+ // search finished, update title and status message
+ else {
+ Search.stopPulse();
+ Search.title.text(_('Search Results'));
+ if (!resultCount)
+ Search.status.text(_('Your search did not match any documents. Please make sure that all words are spelled correctly and that you\'ve selected enough categories.'));
+ else
+ Search.status.text(_('Search finished, found %s page(s) matching the search query.').replace('%s', resultCount));
+ Search.status.fadeIn(500);
+ }
+ }
+ displayNextItem();
+ },
+
+ performObjectSearch : function(object, otherterms) {
+ var filenames = this._index.filenames;
+ var objects = this._index.objects;
+ var objnames = this._index.objnames;
+ var titles = this._index.titles;
+
+ var importantResults = [];
+ var objectResults = [];
+ var unimportantResults = [];
+
+ for (var prefix in objects) {
+ for (var name in objects[prefix]) {
+ var fullname = (prefix ? prefix + '.' : '') + name;
+ if (fullname.toLowerCase().indexOf(object) > -1) {
+ var match = objects[prefix][name];
+ var objname = objnames[match[1]][2];
+ var title = titles[match[0]];
+ // If more than one term searched for, we require other words to be
+ // found in the name/title/description
+ if (otherterms.length > 0) {
+ var haystack = (prefix + ' ' + name + ' ' +
+ objname + ' ' + title).toLowerCase();
+ var allfound = true;
+ for (var i = 0; i < otherterms.length; i++) {
+ if (haystack.indexOf(otherterms[i]) == -1) {
+ allfound = false;
+ break;
+ }
+ }
+ if (!allfound) {
+ continue;
+ }
+ }
+ var descr = objname + _(', in ') + title;
+ anchor = match[3];
+ if (anchor == '')
+ anchor = fullname;
+ else if (anchor == '-')
+ anchor = objnames[match[1]][1] + '-' + fullname;
+ result = [filenames[match[0]], fullname, '#'+anchor, descr];
+ switch (match[2]) {
+ case 1: objectResults.push(result); break;
+ case 0: importantResults.push(result); break;
+ case 2: unimportantResults.push(result); break;
+ }
+ }
+ }
+ }
+
+ // sort results descending
+ objectResults.sort(function(a, b) {
+ return (a[1] > b[1]) ? -1 : ((a[1] < b[1]) ? 1 : 0);
+ });
+
+ importantResults.sort(function(a, b) {
+ return (a[1] > b[1]) ? -1 : ((a[1] < b[1]) ? 1 : 0);
+ });
+
+ unimportantResults.sort(function(a, b) {
+ return (a[1] > b[1]) ? -1 : ((a[1] < b[1]) ? 1 : 0);
+ });
+
+ return [importantResults, objectResults, unimportantResults]
+ }
+}
+
+$(document).ready(function() {
+ Search.init();
+});
\ No newline at end of file
diff --git a/doc/plasmodium/_static/underscore.js b/doc/plasmodium/_static/underscore.js
new file mode 100644
index 0000000..5d89914
--- /dev/null
+++ b/doc/plasmodium/_static/underscore.js
@@ -0,0 +1,23 @@
+// Underscore.js 0.5.5
+// (c) 2009 Jeremy Ashkenas, DocumentCloud Inc.
+// Underscore is freely distributable under the terms of the MIT license.
+// Portions of Underscore are inspired by or borrowed from Prototype.js,
+// Oliver Steele's Functional, and John Resig's Micro-Templating.
+// For all details and documentation:
+// http://documentcloud.github.com/underscore/
+(function(){var j=this,n=j._,i=function(a){this._wrapped=a},m=typeof StopIteration!=="undefined"?StopIteration:"__break__",b=j._=function(a){return new i(a)};if(typeof exports!=="undefined")exports._=b;var k=Array.prototype.slice,o=Array.prototype.unshift,p=Object.prototype.toString,q=Object.prototype.hasOwnProperty,r=Object.prototype.propertyIsEnumerable;b.VERSION="0.5.5";b.each=function(a,c,d){try{if(a.forEach)a.forEach(c,d);else if(b.isArray(a)||b.isArguments(a))for(var e=0,f=a.length [...]
+a[e],e,a);else{var g=b.keys(a);f=g.length;for(e=0;e<f;e++)c.call(d,a[g[e]],g[e],a)}}catch(h){if(h!=m)throw h;}return a};b.map=function(a,c,d){if(a&&b.isFunction(a.map))return a.map(c,d);var e=[];b.each(a,function(f,g,h){e.push(c.call(d,f,g,h))});return e};b.reduce=function(a,c,d,e){if(a&&b.isFunction(a.reduce))return a.reduce(b.bind(d,e),c);b.each(a,function(f,g,h){c=d.call(e,c,f,g,h)});return c};b.reduceRight=function(a,c,d,e){if(a&&b.isFunction(a.reduceRight))return a.reduceRight(b.bin [...]
+var f=b.clone(b.toArray(a)).reverse();b.each(f,function(g,h){c=d.call(e,c,g,h,a)});return c};b.detect=function(a,c,d){var e;b.each(a,function(f,g,h){if(c.call(d,f,g,h)){e=f;b.breakLoop()}});return e};b.select=function(a,c,d){if(a&&b.isFunction(a.filter))return a.filter(c,d);var e=[];b.each(a,function(f,g,h){c.call(d,f,g,h)&&e.push(f)});return e};b.reject=function(a,c,d){var e=[];b.each(a,function(f,g,h){!c.call(d,f,g,h)&&e.push(f)});return e};b.all=function(a,c,d){c=c||b.identity;if(a&&b [...]
+d);var e=true;b.each(a,function(f,g,h){(e=e&&c.call(d,f,g,h))||b.breakLoop()});return e};b.any=function(a,c,d){c=c||b.identity;if(a&&b.isFunction(a.some))return a.some(c,d);var e=false;b.each(a,function(f,g,h){if(e=c.call(d,f,g,h))b.breakLoop()});return e};b.include=function(a,c){if(b.isArray(a))return b.indexOf(a,c)!=-1;var d=false;b.each(a,function(e){if(d=e===c)b.breakLoop()});return d};b.invoke=function(a,c){var d=b.rest(arguments,2);return b.map(a,function(e){return(c?e[c]:e).apply( [...]
+function(a,c){return b.map(a,function(d){return d[c]})};b.max=function(a,c,d){if(!c&&b.isArray(a))return Math.max.apply(Math,a);var e={computed:-Infinity};b.each(a,function(f,g,h){g=c?c.call(d,f,g,h):f;g>=e.computed&&(e={value:f,computed:g})});return e.value};b.min=function(a,c,d){if(!c&&b.isArray(a))return Math.min.apply(Math,a);var e={computed:Infinity};b.each(a,function(f,g,h){g=c?c.call(d,f,g,h):f;g<e.computed&&(e={value:f,computed:g})});return e.value};b.sortBy=function(a,c,d){retur [...]
+function(e,f,g){return{value:e,criteria:c.call(d,e,f,g)}}).sort(function(e,f){e=e.criteria;f=f.criteria;return e<f?-1:e>f?1:0}),"value")};b.sortedIndex=function(a,c,d){d=d||b.identity;for(var e=0,f=a.length;e<f;){var g=e+f>>1;d(a[g])<d(c)?(e=g+1):(f=g)}return e};b.toArray=function(a){if(!a)return[];if(a.toArray)return a.toArray();if(b.isArray(a))return a;if(b.isArguments(a))return k.call(a);return b.values(a)};b.size=function(a){return b.toArray(a).length};b.first=function(a,c,d){return [...]
+0,c):a[0]};b.rest=function(a,c,d){return k.call(a,b.isUndefined(c)||d?1:c)};b.last=function(a){return a[a.length-1]};b.compact=function(a){return b.select(a,function(c){return!!c})};b.flatten=function(a){return b.reduce(a,[],function(c,d){if(b.isArray(d))return c.concat(b.flatten(d));c.push(d);return c})};b.without=function(a){var c=b.rest(arguments);return b.select(a,function(d){return!b.include(c,d)})};b.uniq=function(a,c){return b.reduce(a,[],function(d,e,f){if(0==f||(c===true?b.last( [...]
+e)))d.push(e);return d})};b.intersect=function(a){var c=b.rest(arguments);return b.select(b.uniq(a),function(d){return b.all(c,function(e){return b.indexOf(e,d)>=0})})};b.zip=function(){for(var a=b.toArray(arguments),c=b.max(b.pluck(a,"length")),d=new Array(c),e=0;e<c;e++)d[e]=b.pluck(a,String(e));return d};b.indexOf=function(a,c){if(a.indexOf)return a.indexOf(c);for(var d=0,e=a.length;d<e;d++)if(a[d]===c)return d;return-1};b.lastIndexOf=function(a,c){if(a.lastIndexOf)return a.lastIndexO [...]
+a.length;d--;)if(a[d]===c)return d;return-1};b.range=function(a,c,d){var e=b.toArray(arguments),f=e.length<=1;a=f?0:e[0];c=f?e[0]:e[1];d=e[2]||1;e=Math.ceil((c-a)/d);if(e<=0)return[];e=new Array(e);f=a;for(var g=0;1;f+=d){if((d>0?f-c:c-f)>=0)return e;e[g++]=f}};b.bind=function(a,c){var d=b.rest(arguments,2);return function(){return a.apply(c||j,d.concat(b.toArray(arguments)))}};b.bindAll=function(a){var c=b.rest(arguments);if(c.length==0)c=b.functions(a);b.each(c,function(d){a[d]=b.bind( [...]
+return a};b.delay=function(a,c){var d=b.rest(arguments,2);return setTimeout(function(){return a.apply(a,d)},c)};b.defer=function(a){return b.delay.apply(b,[a,1].concat(b.rest(arguments)))};b.wrap=function(a,c){return function(){var d=[a].concat(b.toArray(arguments));return c.apply(c,d)}};b.compose=function(){var a=b.toArray(arguments);return function(){for(var c=b.toArray(arguments),d=a.length-1;d>=0;d--)c=[a[d].apply(this,c)];return c[0]}};b.keys=function(a){if(b.isArray(a))return b.ran [...]
+var c=[];for(var d in a)q.call(a,d)&&c.push(d);return c};b.values=function(a){return b.map(a,b.identity)};b.functions=function(a){return b.select(b.keys(a),function(c){return b.isFunction(a[c])}).sort()};b.extend=function(a,c){for(var d in c)a[d]=c[d];return a};b.clone=function(a){if(b.isArray(a))return a.slice(0);return b.extend({},a)};b.tap=function(a,c){c(a);return a};b.isEqual=function(a,c){if(a===c)return true;var d=typeof a;if(d!=typeof c)return false;if(a==c)return true;if(!a&&c|| [...]
+if(a.isEqual)return a.isEqual(c);if(b.isDate(a)&&b.isDate(c))return a.getTime()===c.getTime();if(b.isNaN(a)&&b.isNaN(c))return true;if(b.isRegExp(a)&&b.isRegExp(c))return a.source===c.source&&a.global===c.global&&a.ignoreCase===c.ignoreCase&&a.multiline===c.multiline;if(d!=="object")return false;if(a.length&&a.length!==c.length)return false;d=b.keys(a);var e=b.keys(c);if(d.length!=e.length)return false;for(var f in a)if(!b.isEqual(a[f],c[f]))return false;return true};b.isEmpty=function(a [...]
+0};b.isElement=function(a){return!!(a&&a.nodeType==1)};b.isArray=function(a){return!!(a&&a.concat&&a.unshift)};b.isArguments=function(a){return a&&b.isNumber(a.length)&&!b.isArray(a)&&!r.call(a,"length")};b.isFunction=function(a){return!!(a&&a.constructor&&a.call&&a.apply)};b.isString=function(a){return!!(a===""||a&&a.charCodeAt&&a.substr)};b.isNumber=function(a){return p.call(a)==="[object Number]"};b.isDate=function(a){return!!(a&&a.getTimezoneOffset&&a.setUTCFullYear)};b.isRegExp=func [...]
+a.test&&a.exec&&(a.ignoreCase||a.ignoreCase===false))};b.isNaN=function(a){return b.isNumber(a)&&isNaN(a)};b.isNull=function(a){return a===null};b.isUndefined=function(a){return typeof a=="undefined"};b.noConflict=function(){j._=n;return this};b.identity=function(a){return a};b.breakLoop=function(){throw m;};var s=0;b.uniqueId=function(a){var c=s++;return a?a+c:c};b.template=function(a,c){a=new Function("obj","var p=[],print=function(){p.push.apply(p,arguments);};with(obj){p.push('"+a.re [...]
+" ").replace(/'(?=[^%]*%>)/g,"\t").split("'").join("\\'").split("\t").join("'").replace(/<%=(.+?)%>/g,"',$1,'").split("<%").join("');").split("%>").join("p.push('")+"');}return p.join('');");return c?a(c):a};b.forEach=b.each;b.foldl=b.inject=b.reduce;b.foldr=b.reduceRight;b.filter=b.select;b.every=b.all;b.some=b.any;b.head=b.first;b.tail=b.rest;b.methods=b.functions;var l=function(a,c){return c?b(a).chain():a};b.each(b.functions(b),function(a){var c=b[a];i.prototype[a]=function(){var d=b [...]
+o.call(d,this._wrapped);return l(c.apply(b,d),this._chain)}});b.each(["pop","push","reverse","shift","sort","splice","unshift"],function(a){var c=Array.prototype[a];i.prototype[a]=function(){c.apply(this._wrapped,arguments);return l(this._wrapped,this._chain)}});b.each(["concat","join","slice"],function(a){var c=Array.prototype[a];i.prototype[a]=function(){return l(c.apply(this._wrapped,arguments),this._chain)}});i.prototype.chain=function(){this._chain=true;return this};i.prototype.valu [...]
diff --git a/doc/plasmodium/_static/up-pressed.png b/doc/plasmodium/_static/up-pressed.png
new file mode 100644
index 0000000..8bd587a
Binary files /dev/null and b/doc/plasmodium/_static/up-pressed.png differ
diff --git a/doc/plasmodium/_static/up.png b/doc/plasmodium/_static/up.png
new file mode 100644
index 0000000..b946256
Binary files /dev/null and b/doc/plasmodium/_static/up.png differ
diff --git a/doc/plasmodium/_static/websupport.js b/doc/plasmodium/_static/websupport.js
new file mode 100644
index 0000000..e9bd1b8
--- /dev/null
+++ b/doc/plasmodium/_static/websupport.js
@@ -0,0 +1,808 @@
+/*
+ * websupport.js
+ * ~~~~~~~~~~~~~
+ *
+ * sphinx.websupport utilties for all documentation.
+ *
+ * :copyright: Copyright 2007-2011 by the Sphinx team, see AUTHORS.
+ * :license: BSD, see LICENSE for details.
+ *
+ */
+
+(function($) {
+ $.fn.autogrow = function() {
+ return this.each(function() {
+ var textarea = this;
+
+ $.fn.autogrow.resize(textarea);
+
+ $(textarea)
+ .focus(function() {
+ textarea.interval = setInterval(function() {
+ $.fn.autogrow.resize(textarea);
+ }, 500);
+ })
+ .blur(function() {
+ clearInterval(textarea.interval);
+ });
+ });
+ };
+
+ $.fn.autogrow.resize = function(textarea) {
+ var lineHeight = parseInt($(textarea).css('line-height'), 10);
+ var lines = textarea.value.split('\n');
+ var columns = textarea.cols;
+ var lineCount = 0;
+ $.each(lines, function() {
+ lineCount += Math.ceil(this.length / columns) || 1;
+ });
+ var height = lineHeight * (lineCount + 1);
+ $(textarea).css('height', height);
+ };
+})(jQuery);
+
+(function($) {
+ var comp, by;
+
+ function init() {
+ initEvents();
+ initComparator();
+ }
+
+ function initEvents() {
+ $('a.comment-close').live("click", function(event) {
+ event.preventDefault();
+ hide($(this).attr('id').substring(2));
+ });
+ $('a.vote').live("click", function(event) {
+ event.preventDefault();
+ handleVote($(this));
+ });
+ $('a.reply').live("click", function(event) {
+ event.preventDefault();
+ openReply($(this).attr('id').substring(2));
+ });
+ $('a.close-reply').live("click", function(event) {
+ event.preventDefault();
+ closeReply($(this).attr('id').substring(2));
+ });
+ $('a.sort-option').live("click", function(event) {
+ event.preventDefault();
+ handleReSort($(this));
+ });
+ $('a.show-proposal').live("click", function(event) {
+ event.preventDefault();
+ showProposal($(this).attr('id').substring(2));
+ });
+ $('a.hide-proposal').live("click", function(event) {
+ event.preventDefault();
+ hideProposal($(this).attr('id').substring(2));
+ });
+ $('a.show-propose-change').live("click", function(event) {
+ event.preventDefault();
+ showProposeChange($(this).attr('id').substring(2));
+ });
+ $('a.hide-propose-change').live("click", function(event) {
+ event.preventDefault();
+ hideProposeChange($(this).attr('id').substring(2));
+ });
+ $('a.accept-comment').live("click", function(event) {
+ event.preventDefault();
+ acceptComment($(this).attr('id').substring(2));
+ });
+ $('a.delete-comment').live("click", function(event) {
+ event.preventDefault();
+ deleteComment($(this).attr('id').substring(2));
+ });
+ $('a.comment-markup').live("click", function(event) {
+ event.preventDefault();
+ toggleCommentMarkupBox($(this).attr('id').substring(2));
+ });
+ }
+
+ /**
+ * Set comp, which is a comparator function used for sorting and
+ * inserting comments into the list.
+ */
+ function setComparator() {
+ // If the first three letters are "asc", sort in ascending order
+ // and remove the prefix.
+ if (by.substring(0,3) == 'asc') {
+ var i = by.substring(3);
+ comp = function(a, b) { return a[i] - b[i]; };
+ } else {
+ // Otherwise sort in descending order.
+ comp = function(a, b) { return b[by] - a[by]; };
+ }
+
+ // Reset link styles and format the selected sort option.
+ $('a.sel').attr('href', '#').removeClass('sel');
+ $('a.by' + by).removeAttr('href').addClass('sel');
+ }
+
+ /**
+ * Create a comp function. If the user has preferences stored in
+ * the sortBy cookie, use those, otherwise use the default.
+ */
+ function initComparator() {
+ by = 'rating'; // Default to sort by rating.
+ // If the sortBy cookie is set, use that instead.
+ if (document.cookie.length > 0) {
+ var start = document.cookie.indexOf('sortBy=');
+ if (start != -1) {
+ start = start + 7;
+ var end = document.cookie.indexOf(";", start);
+ if (end == -1) {
+ end = document.cookie.length;
+ by = unescape(document.cookie.substring(start, end));
+ }
+ }
+ }
+ setComparator();
+ }
+
+ /**
+ * Show a comment div.
+ */
+ function show(id) {
+ $('#ao' + id).hide();
+ $('#ah' + id).show();
+ var context = $.extend({id: id}, opts);
+ var popup = $(renderTemplate(popupTemplate, context)).hide();
+ popup.find('textarea[name="proposal"]').hide();
+ popup.find('a.by' + by).addClass('sel');
+ var form = popup.find('#cf' + id);
+ form.submit(function(event) {
+ event.preventDefault();
+ addComment(form);
+ });
+ $('#s' + id).after(popup);
+ popup.slideDown('fast', function() {
+ getComments(id);
+ });
+ }
+
+ /**
+ * Hide a comment div.
+ */
+ function hide(id) {
+ $('#ah' + id).hide();
+ $('#ao' + id).show();
+ var div = $('#sc' + id);
+ div.slideUp('fast', function() {
+ div.remove();
+ });
+ }
+
+ /**
+ * Perform an ajax request to get comments for a node
+ * and insert the comments into the comments tree.
+ */
+ function getComments(id) {
+ $.ajax({
+ type: 'GET',
+ url: opts.getCommentsURL,
+ data: {node: id},
+ success: function(data, textStatus, request) {
+ var ul = $('#cl' + id);
+ var speed = 100;
+ $('#cf' + id)
+ .find('textarea[name="proposal"]')
+ .data('source', data.source);
+
+ if (data.comments.length === 0) {
+ ul.html('<li>No comments yet.</li>');
+ ul.data('empty', true);
+ } else {
+ // If there are comments, sort them and put them in the list.
+ var comments = sortComments(data.comments);
+ speed = data.comments.length * 100;
+ appendComments(comments, ul);
+ ul.data('empty', false);
+ }
+ $('#cn' + id).slideUp(speed + 200);
+ ul.slideDown(speed);
+ },
+ error: function(request, textStatus, error) {
+ showError('Oops, there was a problem retrieving the comments.');
+ },
+ dataType: 'json'
+ });
+ }
+
+ /**
+ * Add a comment via ajax and insert the comment into the comment tree.
+ */
+ function addComment(form) {
+ var node_id = form.find('input[name="node"]').val();
+ var parent_id = form.find('input[name="parent"]').val();
+ var text = form.find('textarea[name="comment"]').val();
+ var proposal = form.find('textarea[name="proposal"]').val();
+
+ if (text == '') {
+ showError('Please enter a comment.');
+ return;
+ }
+
+ // Disable the form that is being submitted.
+ form.find('textarea,input').attr('disabled', 'disabled');
+
+ // Send the comment to the server.
+ $.ajax({
+ type: "POST",
+ url: opts.addCommentURL,
+ dataType: 'json',
+ data: {
+ node: node_id,
+ parent: parent_id,
+ text: text,
+ proposal: proposal
+ },
+ success: function(data, textStatus, error) {
+ // Reset the form.
+ if (node_id) {
+ hideProposeChange(node_id);
+ }
+ form.find('textarea')
+ .val('')
+ .add(form.find('input'))
+ .removeAttr('disabled');
+ var ul = $('#cl' + (node_id || parent_id));
+ if (ul.data('empty')) {
+ $(ul).empty();
+ ul.data('empty', false);
+ }
+ insertComment(data.comment);
+ var ao = $('#ao' + node_id);
+ ao.find('img').attr({'src': opts.commentBrightImage});
+ if (node_id) {
+ // if this was a "root" comment, remove the commenting box
+ // (the user can get it back by reopening the comment popup)
+ $('#ca' + node_id).slideUp();
+ }
+ },
+ error: function(request, textStatus, error) {
+ form.find('textarea,input').removeAttr('disabled');
+ showError('Oops, there was a problem adding the comment.');
+ }
+ });
+ }
+
+ /**
+ * Recursively append comments to the main comment list and children
+ * lists, creating the comment tree.
+ */
+ function appendComments(comments, ul) {
+ $.each(comments, function() {
+ var div = createCommentDiv(this);
+ ul.append($(document.createElement('li')).html(div));
+ appendComments(this.children, div.find('ul.comment-children'));
+ // To avoid stagnating data, don't store the comments children in data.
+ this.children = null;
+ div.data('comment', this);
+ });
+ }
+
+ /**
+ * After adding a new comment, it must be inserted in the correct
+ * location in the comment tree.
+ */
+ function insertComment(comment) {
+ var div = createCommentDiv(comment);
+
+ // To avoid stagnating data, don't store the comments children in data.
+ comment.children = null;
+ div.data('comment', comment);
+
+ var ul = $('#cl' + (comment.node || comment.parent));
+ var siblings = getChildren(ul);
+
+ var li = $(document.createElement('li'));
+ li.hide();
+
+ // Determine where in the parents children list to insert this comment.
+ for(i=0; i < siblings.length; i++) {
+ if (comp(comment, siblings[i]) <= 0) {
+ $('#cd' + siblings[i].id)
+ .parent()
+ .before(li.html(div));
+ li.slideDown('fast');
+ return;
+ }
+ }
+
+ // If we get here, this comment rates lower than all the others,
+ // or it is the only comment in the list.
+ ul.append(li.html(div));
+ li.slideDown('fast');
+ }
+
+ function acceptComment(id) {
+ $.ajax({
+ type: 'POST',
+ url: opts.acceptCommentURL,
+ data: {id: id},
+ success: function(data, textStatus, request) {
+ $('#cm' + id).fadeOut('fast');
+ $('#cd' + id).removeClass('moderate');
+ },
+ error: function(request, textStatus, error) {
+ showError('Oops, there was a problem accepting the comment.');
+ }
+ });
+ }
+
+ function deleteComment(id) {
+ $.ajax({
+ type: 'POST',
+ url: opts.deleteCommentURL,
+ data: {id: id},
+ success: function(data, textStatus, request) {
+ var div = $('#cd' + id);
+ if (data == 'delete') {
+ // Moderator mode: remove the comment and all children immediately
+ div.slideUp('fast', function() {
+ div.remove();
+ });
+ return;
+ }
+ // User mode: only mark the comment as deleted
+ div
+ .find('span.user-id:first')
+ .text('[deleted]').end()
+ .find('div.comment-text:first')
+ .text('[deleted]').end()
+ .find('#cm' + id + ', #dc' + id + ', #ac' + id + ', #rc' + id +
+ ', #sp' + id + ', #hp' + id + ', #cr' + id + ', #rl' + id)
+ .remove();
+ var comment = div.data('comment');
+ comment.username = '[deleted]';
+ comment.text = '[deleted]';
+ div.data('comment', comment);
+ },
+ error: function(request, textStatus, error) {
+ showError('Oops, there was a problem deleting the comment.');
+ }
+ });
+ }
+
+ function showProposal(id) {
+ $('#sp' + id).hide();
+ $('#hp' + id).show();
+ $('#pr' + id).slideDown('fast');
+ }
+
+ function hideProposal(id) {
+ $('#hp' + id).hide();
+ $('#sp' + id).show();
+ $('#pr' + id).slideUp('fast');
+ }
+
+ function showProposeChange(id) {
+ $('#pc' + id).hide();
+ $('#hc' + id).show();
+ var textarea = $('#pt' + id);
+ textarea.val(textarea.data('source'));
+ $.fn.autogrow.resize(textarea[0]);
+ textarea.slideDown('fast');
+ }
+
+ function hideProposeChange(id) {
+ $('#hc' + id).hide();
+ $('#pc' + id).show();
+ var textarea = $('#pt' + id);
+ textarea.val('').removeAttr('disabled');
+ textarea.slideUp('fast');
+ }
+
+ function toggleCommentMarkupBox(id) {
+ $('#mb' + id).toggle();
+ }
+
+ /** Handle when the user clicks on a sort by link. */
+ function handleReSort(link) {
+ var classes = link.attr('class').split(/\s+/);
+ for (var i=0; i<classes.length; i++) {
+ if (classes[i] != 'sort-option') {
+ by = classes[i].substring(2);
+ }
+ }
+ setComparator();
+ // Save/update the sortBy cookie.
+ var expiration = new Date();
+ expiration.setDate(expiration.getDate() + 365);
+ document.cookie= 'sortBy=' + escape(by) +
+ ';expires=' + expiration.toUTCString();
+ $('ul.comment-ul').each(function(index, ul) {
+ var comments = getChildren($(ul), true);
+ comments = sortComments(comments);
+ appendComments(comments, $(ul).empty());
+ });
+ }
+
+ /**
+ * Function to process a vote when a user clicks an arrow.
+ */
+ function handleVote(link) {
+ if (!opts.voting) {
+ showError("You'll need to login to vote.");
+ return;
+ }
+
+ var id = link.attr('id');
+ if (!id) {
+ // Didn't click on one of the voting arrows.
+ return;
+ }
+ // If it is an unvote, the new vote value is 0,
+ // Otherwise it's 1 for an upvote, or -1 for a downvote.
+ var value = 0;
+ if (id.charAt(1) != 'u') {
+ value = id.charAt(0) == 'u' ? 1 : -1;
+ }
+ // The data to be sent to the server.
+ var d = {
+ comment_id: id.substring(2),
+ value: value
+ };
+
+ // Swap the vote and unvote links.
+ link.hide();
+ $('#' + id.charAt(0) + (id.charAt(1) == 'u' ? 'v' : 'u') + d.comment_id)
+ .show();
+
+ // The div the comment is displayed in.
+ var div = $('div#cd' + d.comment_id);
+ var data = div.data('comment');
+
+ // If this is not an unvote, and the other vote arrow has
+ // already been pressed, unpress it.
+ if ((d.value !== 0) && (data.vote === d.value * -1)) {
+ $('#' + (d.value == 1 ? 'd' : 'u') + 'u' + d.comment_id).hide();
+ $('#' + (d.value == 1 ? 'd' : 'u') + 'v' + d.comment_id).show();
+ }
+
+ // Update the comments rating in the local data.
+ data.rating += (data.vote === 0) ? d.value : (d.value - data.vote);
+ data.vote = d.value;
+ div.data('comment', data);
+
+ // Change the rating text.
+ div.find('.rating:first')
+ .text(data.rating + ' point' + (data.rating == 1 ? '' : 's'));
+
+ // Send the vote information to the server.
+ $.ajax({
+ type: "POST",
+ url: opts.processVoteURL,
+ data: d,
+ error: function(request, textStatus, error) {
+ showError('Oops, there was a problem casting that vote.');
+ }
+ });
+ }
+
+ /**
+ * Open a reply form used to reply to an existing comment.
+ */
+ function openReply(id) {
+ // Swap out the reply link for the hide link
+ $('#rl' + id).hide();
+ $('#cr' + id).show();
+
+ // Add the reply li to the children ul.
+ var div = $(renderTemplate(replyTemplate, {id: id})).hide();
+ $('#cl' + id)
+ .prepend(div)
+ // Setup the submit handler for the reply form.
+ .find('#rf' + id)
+ .submit(function(event) {
+ event.preventDefault();
+ addComment($('#rf' + id));
+ closeReply(id);
+ })
+ .find('input[type=button]')
+ .click(function() {
+ closeReply(id);
+ });
+ div.slideDown('fast', function() {
+ $('#rf' + id).find('textarea').focus();
+ });
+ }
+
+ /**
+ * Close the reply form opened with openReply.
+ */
+ function closeReply(id) {
+ // Remove the reply div from the DOM.
+ $('#rd' + id).slideUp('fast', function() {
+ $(this).remove();
+ });
+
+ // Swap out the hide link for the reply link
+ $('#cr' + id).hide();
+ $('#rl' + id).show();
+ }
+
+ /**
+ * Recursively sort a tree of comments using the comp comparator.
+ */
+ function sortComments(comments) {
+ comments.sort(comp);
+ $.each(comments, function() {
+ this.children = sortComments(this.children);
+ });
+ return comments;
+ }
+
+ /**
+ * Get the children comments from a ul. If recursive is true,
+ * recursively include childrens' children.
+ */
+ function getChildren(ul, recursive) {
+ var children = [];
+ ul.children().children("[id^='cd']")
+ .each(function() {
+ var comment = $(this).data('comment');
+ if (recursive)
+ comment.children = getChildren($(this).find('#cl' + comment.id), true);
+ children.push(comment);
+ });
+ return children;
+ }
+
+ /** Create a div to display a comment in. */
+ function createCommentDiv(comment) {
+ if (!comment.displayed && !opts.moderator) {
+ return $('<div class="moderate">Thank you! Your comment will show up '
+ + 'once it is has been approved by a moderator.</div>');
+ }
+ // Prettify the comment rating.
+ comment.pretty_rating = comment.rating + ' point' +
+ (comment.rating == 1 ? '' : 's');
+ // Make a class (for displaying not yet moderated comments differently)
+ comment.css_class = comment.displayed ? '' : ' moderate';
+ // Create a div for this comment.
+ var context = $.extend({}, opts, comment);
+ var div = $(renderTemplate(commentTemplate, context));
+
+ // If the user has voted on this comment, highlight the correct arrow.
+ if (comment.vote) {
+ var direction = (comment.vote == 1) ? 'u' : 'd';
+ div.find('#' + direction + 'v' + comment.id).hide();
+ div.find('#' + direction + 'u' + comment.id).show();
+ }
+
+ if (opts.moderator || comment.text != '[deleted]') {
+ div.find('a.reply').show();
+ if (comment.proposal_diff)
+ div.find('#sp' + comment.id).show();
+ if (opts.moderator && !comment.displayed)
+ div.find('#cm' + comment.id).show();
+ if (opts.moderator || (opts.username == comment.username))
+ div.find('#dc' + comment.id).show();
+ }
+ return div;
+ }
+
+ /**
+ * A simple template renderer. Placeholders such as <%id%> are replaced
+ * by context['id'] with items being escaped. Placeholders such as <#id#>
+ * are not escaped.
+ */
+ function renderTemplate(template, context) {
+ var esc = $(document.createElement('div'));
+
+ function handle(ph, escape) {
+ var cur = context;
+ $.each(ph.split('.'), function() {
+ cur = cur[this];
+ });
+ return escape ? esc.text(cur || "").html() : cur;
+ }
+
+ return template.replace(/<([%#])([\w\.]*)\1>/g, function() {
+ return handle(arguments[2], arguments[1] == '%' ? true : false);
+ });
+ }
+
+ /** Flash an error message briefly. */
+ function showError(message) {
+ $(document.createElement('div')).attr({'class': 'popup-error'})
+ .append($(document.createElement('div'))
+ .attr({'class': 'error-message'}).text(message))
+ .appendTo('body')
+ .fadeIn("slow")
+ .delay(2000)
+ .fadeOut("slow");
+ }
+
+ /** Add a link the user uses to open the comments popup. */
+ $.fn.comment = function() {
+ return this.each(function() {
+ var id = $(this).attr('id').substring(1);
+ var count = COMMENT_METADATA[id];
+ var title = count + ' comment' + (count == 1 ? '' : 's');
+ var image = count > 0 ? opts.commentBrightImage : opts.commentImage;
+ var addcls = count == 0 ? ' nocomment' : '';
+ $(this)
+ .append(
+ $(document.createElement('a')).attr({
+ href: '#',
+ 'class': 'sphinx-comment-open' + addcls,
+ id: 'ao' + id
+ })
+ .append($(document.createElement('img')).attr({
+ src: image,
+ alt: 'comment',
+ title: title
+ }))
+ .click(function(event) {
+ event.preventDefault();
+ show($(this).attr('id').substring(2));
+ })
+ )
+ .append(
+ $(document.createElement('a')).attr({
+ href: '#',
+ 'class': 'sphinx-comment-close hidden',
+ id: 'ah' + id
+ })
+ .append($(document.createElement('img')).attr({
+ src: opts.closeCommentImage,
+ alt: 'close',
+ title: 'close'
+ }))
+ .click(function(event) {
+ event.preventDefault();
+ hide($(this).attr('id').substring(2));
+ })
+ );
+ });
+ };
+
+ var opts = {
+ processVoteURL: '/_process_vote',
+ addCommentURL: '/_add_comment',
+ getCommentsURL: '/_get_comments',
+ acceptCommentURL: '/_accept_comment',
+ deleteCommentURL: '/_delete_comment',
+ commentImage: '/static/_static/comment.png',
+ closeCommentImage: '/static/_static/comment-close.png',
+ loadingImage: '/static/_static/ajax-loader.gif',
+ commentBrightImage: '/static/_static/comment-bright.png',
+ upArrow: '/static/_static/up.png',
+ downArrow: '/static/_static/down.png',
+ upArrowPressed: '/static/_static/up-pressed.png',
+ downArrowPressed: '/static/_static/down-pressed.png',
+ voting: false,
+ moderator: false
+ };
+
+ if (typeof COMMENT_OPTIONS != "undefined") {
+ opts = jQuery.extend(opts, COMMENT_OPTIONS);
+ }
+
+ var popupTemplate = '\
+ <div class="sphinx-comments" id="sc<%id%>">\
+ <p class="sort-options">\
+ Sort by:\
+ <a href="#" class="sort-option byrating">best rated</a>\
+ <a href="#" class="sort-option byascage">newest</a>\
+ <a href="#" class="sort-option byage">oldest</a>\
+ </p>\
+ <div class="comment-header">Comments</div>\
+ <div class="comment-loading" id="cn<%id%>">\
+ loading comments... <img src="<%loadingImage%>" alt="" /></div>\
+ <ul id="cl<%id%>" class="comment-ul"></ul>\
+ <div id="ca<%id%>">\
+ <p class="add-a-comment">Add a comment\
+ (<a href="#" class="comment-markup" id="ab<%id%>">markup</a>):</p>\
+ <div class="comment-markup-box" id="mb<%id%>">\
+ reStructured text markup: <i>*emph*</i>, <b>**strong**</b>, \
+ <tt>``code``</tt>, \
+ code blocks: <tt>::</tt> and an indented block after blank line</div>\
+ <form method="post" id="cf<%id%>" class="comment-form" action="">\
+ <textarea name="comment" cols="80"></textarea>\
+ <p class="propose-button">\
+ <a href="#" id="pc<%id%>" class="show-propose-change">\
+ Propose a change ▹\
+ </a>\
+ <a href="#" id="hc<%id%>" class="hide-propose-change">\
+ Propose a change ▿\
+ </a>\
+ </p>\
+ <textarea name="proposal" id="pt<%id%>" cols="80"\
+ spellcheck="false"></textarea>\
+ <input type="submit" value="Add comment" />\
+ <input type="hidden" name="node" value="<%id%>" />\
+ <input type="hidden" name="parent" value="" />\
+ </form>\
+ </div>\
+ </div>';
+
+ var commentTemplate = '\
+ <div id="cd<%id%>" class="sphinx-comment<%css_class%>">\
+ <div class="vote">\
+ <div class="arrow">\
+ <a href="#" id="uv<%id%>" class="vote" title="vote up">\
+ <img src="<%upArrow%>" />\
+ </a>\
+ <a href="#" id="uu<%id%>" class="un vote" title="vote up">\
+ <img src="<%upArrowPressed%>" />\
+ </a>\
+ </div>\
+ <div class="arrow">\
+ <a href="#" id="dv<%id%>" class="vote" title="vote down">\
+ <img src="<%downArrow%>" id="da<%id%>" />\
+ </a>\
+ <a href="#" id="du<%id%>" class="un vote" title="vote down">\
+ <img src="<%downArrowPressed%>" />\
+ </a>\
+ </div>\
+ </div>\
+ <div class="comment-content">\
+ <p class="tagline comment">\
+ <span class="user-id"><%username%></span>\
+ <span class="rating"><%pretty_rating%></span>\
+ <span class="delta"><%time.delta%></span>\
+ </p>\
+ <div class="comment-text comment"><#text#></div>\
+ <p class="comment-opts comment">\
+ <a href="#" class="reply hidden" id="rl<%id%>">reply ▹</a>\
+ <a href="#" class="close-reply" id="cr<%id%>">reply ▿</a>\
+ <a href="#" id="sp<%id%>" class="show-proposal">proposal ▹</a>\
+ <a href="#" id="hp<%id%>" class="hide-proposal">proposal ▿</a>\
+ <a href="#" id="dc<%id%>" class="delete-comment hidden">delete</a>\
+ <span id="cm<%id%>" class="moderation hidden">\
+ <a href="#" id="ac<%id%>" class="accept-comment">accept</a>\
+ </span>\
+ </p>\
+ <pre class="proposal" id="pr<%id%>">\
+<#proposal_diff#>\
+ </pre>\
+ <ul class="comment-children" id="cl<%id%>"></ul>\
+ </div>\
+ <div class="clearleft"></div>\
+ </div>\
+ </div>';
+
+ var replyTemplate = '\
+ <li>\
+ <div class="reply-div" id="rd<%id%>">\
+ <form id="rf<%id%>">\
+ <textarea name="comment" cols="80"></textarea>\
+ <input type="submit" value="Add reply" />\
+ <input type="button" value="Cancel" />\
+ <input type="hidden" name="parent" value="<%id%>" />\
+ <input type="hidden" name="node" value="" />\
+ </form>\
+ </div>\
+ </li>';
+
+ $(document).ready(function() {
+ init();
+ });
+})(jQuery);
+
+$(document).ready(function() {
+ // add comment anchors for all paragraphs that are commentable
+ $('.sphinx-has-comment').comment();
+
+ // highlight search words in search results
+ $("div.context").each(function() {
+ var params = $.getQueryParameters();
+ var terms = (params.q) ? params.q[0].split(/\s+/) : [];
+ var result = $(this);
+ $.each(terms, function() {
+ result.highlightText(this.toLowerCase(), 'highlighted');
+ });
+ });
+
+ // directly open comment window if requested
+ var anchor = document.location.hash;
+ if (anchor.substring(0, 9) == '#comment-') {
+ $('#ao' + anchor.substring(9)).click();
+ document.location.hash = '#s' + anchor.substring(9);
+ }
+});
diff --git a/doc/plasmodium/genome_coverage_0to50_histogram.png b/doc/plasmodium/genome_coverage_0to50_histogram.png
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diff --git a/doc/plasmodium/genome_coverage_across_reference.png b/doc/plasmodium/genome_coverage_across_reference.png
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index 0000000..a93b384
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diff --git a/doc/plasmodium/genome_coverage_histogram.png b/doc/plasmodium/genome_coverage_histogram.png
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diff --git a/doc/plasmodium/genome_coverage_quotes.png b/doc/plasmodium/genome_coverage_quotes.png
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diff --git a/doc/plasmodium/genome_gc_content_per_window.png b/doc/plasmodium/genome_gc_content_per_window.png
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index 0000000..4816e3e
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diff --git a/doc/plasmodium/genome_insert_size_across_reference.png b/doc/plasmodium/genome_insert_size_across_reference.png
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diff --git a/doc/plasmodium/genome_insert_size_histogram.png b/doc/plasmodium/genome_insert_size_histogram.png
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diff --git a/doc/plasmodium/genome_mapping_quality_across_reference.png b/doc/plasmodium/genome_mapping_quality_across_reference.png
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diff --git a/doc/plasmodium/genome_mapping_quality_histogram.png b/doc/plasmodium/genome_mapping_quality_histogram.png
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diff --git a/doc/plasmodium/genome_reads_content_per_read_position.png b/doc/plasmodium/genome_reads_content_per_read_position.png
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index 0000000..086aebf
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diff --git a/doc/plasmodium/genome_uniq_read_starts_histogram.png b/doc/plasmodium/genome_uniq_read_starts_histogram.png
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diff --git a/doc/plasmodium/qualimapReport.html b/doc/plasmodium/qualimapReport.html
new file mode 100644
index 0000000..e1347e5
--- /dev/null
+++ b/doc/plasmodium/qualimapReport.html
@@ -0,0 +1,438 @@
+<!DOCTYPE HTML>
+<html>
+ <head>
+ <link rel="stylesheet" href="_static/agogo.css" type="text/css" />
+ <link rel="stylesheet" href="_static/report.css" type="text/css" />
+ <title>Qualimap report: Genomic analysis</title>
+
+ </head>
+<body>
+ <div class="header-wrapper">
+ <div class="header">
+ <p class="logo"><a href="http://qualimap.bioinfo.cipf.es/">
+ <img class="logo" src="_static/qualimap_logo_small.png" alt="Logo"/>
+ </a></p>
+<div class="headertitle"><a href="">Qualimap Report</a></div>
+ </div>
+</div>
+
+<div class="content-wrapper">
+<div class="content">
+<div class="document">
+<div class="documentwrapper">
+<div class="bodywrapper">
+<div class="body">
+<div class=section>
+<h2>Summary<a class="headerlink" name="summary" title="Permalink to this headline"> </a></h2>
+<div class=summary>
+
+
+<div class=table-summary>
+<h3>Globals</h3>
+<table class="summary hovertable">
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Reference size</td>
+<td class=column2>23,264,337</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Number of reads</td>
+<td class=column2>6,649,159</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Number/percentage of mapped reads</td>
+<td class=column2>6,481,948 / 97.49%</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Number/percentage of unmapped reads</td>
+<td class=column2>167,211/2.51%</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Number/percentage of paired reads</td>
+<td class=column2>6,481,948/97.49%</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Number/percentage of reads both mates paired</td>
+<td class=column2>6,442,507/96.89%</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Number/percentage of singletons</td>
+<td class=column2>39,441/0.59%</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Read min/max/mean size</td>
+<td class=column2>76/76/76</td>
+</tr>
+</table>
+</div>
+
+
+<div class=table-summary>
+<h3>ACGT Content</h3>
+<table class="summary hovertable">
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Number/percentage of A's</td>
+<td class=column2>193,766,502 / 39.6%</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Number/percentage of C's</td>
+<td class=column2>50,669,578 / 10.36%</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Number/percentage of T's</td>
+<td class=column2>193,981,319 / 39.65%</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Number/percentage of G's</td>
+<td class=column2>50,870,741 / 10.4%</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Number/percentage of N's</td>
+<td class=column2>0 / 0%</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>GC Percentage</td>
+<td class=column2>20.75%</td>
+</tr>
+</table>
+</div>
+
+
+<div class=table-summary>
+<h3>Coverage</h3>
+<table class="summary hovertable">
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Mean</td>
+<td class=column2>21.03</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Standard Deviation</td>
+<td class=column2>10</td>
+</tr>
+</table>
+</div>
+
+
+<div class=table-summary>
+<h3>Mapping Quality</h3>
+<table class="summary hovertable">
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Mean Mapping Quality</td>
+<td class=column2>53.73</td>
+</tr>
+</table>
+</div>
+
+
+<div class=table-summary>
+<h3>Insert size</h3>
+<table class="summary hovertable">
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Mean</td>
+<td class=column2>177.13</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Median Estimation</td>
+<td class=column2>354</td>
+</tr>
+</table>
+</div>
+
+
+<div class=table-summary>
+<h3>Per chromosome statistics</h3>
+<table class="summary hovertable">
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td><b>Name</b></td>
+<td><b>Length</b></td>
+<td><b>Mapped bases</b></td>
+<td><b>Mean coverage</b></td>
+<td><b>Standard deviation</b></td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>MAL1</td>
+<td>643292</td>
+<td>14156303</td>
+<td>22.01</td>
+<td>10.1</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>MAL2</td>
+<td>947102</td>
+<td>19638269</td>
+<td>20.74</td>
+<td>9.71</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>MAL3</td>
+<td>1060087</td>
+<td>23125362</td>
+<td>21.81</td>
+<td>9.83</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>MAL4</td>
+<td>1204112</td>
+<td>26691925</td>
+<td>22.17</td>
+<td>13.5</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>MAL5</td>
+<td>1343552</td>
+<td>28354233</td>
+<td>21.1</td>
+<td>9.95</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>MAL6</td>
+<td>1418244</td>
+<td>30426474</td>
+<td>21.45</td>
+<td>9.91</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>MAL7</td>
+<td>1501717</td>
+<td>32782891</td>
+<td>21.83</td>
+<td>9.55</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>MAL8</td>
+<td>1419563</td>
+<td>29538054</td>
+<td>20.81</td>
+<td>9.62</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>MAL9</td>
+<td>1541723</td>
+<td>31382882</td>
+<td>20.36</td>
+<td>9.71</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>MAL10</td>
+<td>1687655</td>
+<td>35633830</td>
+<td>21.11</td>
+<td>10.2</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>MAL11</td>
+<td>2038337</td>
+<td>41616969</td>
+<td>20.42</td>
+<td>9.52</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>MAL12</td>
+<td>2271477</td>
+<td>47845286</td>
+<td>21.06</td>
+<td>10.07</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>MAL13</td>
+<td>2895605</td>
+<td>60752044</td>
+<td>20.98</td>
+<td>9.67</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>MAL14</td>
+<td>3291871</td>
+<td>67343618</td>
+<td>20.46</td>
+<td>9.46</td>
+</tr>
+</table>
+</div>
+
+</div>
+</div> <!-- summary section -->
+
+<div class=section>
+<h2>Input data and parameters<a class="headerlink" name="input" title="Permalink to this headline"> </a></h2>
+<div class=summary>
+
+
+<div class=table-summary>
+<h3>Alignment</h3>
+<table class="summary hovertable">
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>BAM file: </td>
+<td class=column2>/home/fgarcia/qualimapLatestBuild/dataRelease/genomics/Plasmodium-falciparum-3D7.bam</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Program: </td>
+<td class=column2>RTA (1.8.70.0)</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Number of windows: </td>
+<td class=column2>400</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Analysis date: </td>
+<td class=column2>Tue Apr 24 19:44:07 CEST 2012</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Draw chromosome limits: </td>
+<td class=column2>yes
+</td>
+</tr>
+</table>
+</div>
+
+</div>
+</div> <!-- summary section -->
+
+
+
+<div class=section>
+
+<h2>Coverage across reference<a class="headerlink" name="genome_coverage_across_reference.png" title="Permalink to this headline"> </a></h2>
+
+<div><img width=100% src="genome_coverage_across_reference.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>Coverage Histogram<a class="headerlink" name="genome_coverage_histogram.png" title="Permalink to this headline"> </a></h2>
+
+<div><img width=100% src="genome_coverage_histogram.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>Coverage Histogram (0-50X)<a class="headerlink" name="genome_coverage_0to50_histogram.png" title="Permalink to this headline"> </a></h2>
+
+<div><img width=100% src="genome_coverage_0to50_histogram.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>Duplication Rate Histogram<a class="headerlink" name="genome_uniq_read_starts_histogram.png" title="Permalink to this headline"> </a></h2>
+
+<div><img width=100% src="genome_uniq_read_starts_histogram.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>Genome Fraction Coverage<a class="headerlink" name="genome_coverage_quotes.png" title="Permalink to this headline"> </a></h2>
+
+<div><img width=100% src="genome_coverage_quotes.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>Mapped Reads Nucleotide Content<a class="headerlink" name="genome_reads_content_per_read_position.png" title="Permalink to this headline"> </a></h2>
+
+<div><img width=100% src="genome_reads_content_per_read_position.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>Mapped Reads GC-content Distribution<a class="headerlink" name="genome_gc_content_per_window.png" title="Permalink to this headline"> </a></h2>
+
+<div><img width=100% src="genome_gc_content_per_window.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>Mapping Quality Across Reference<a class="headerlink" name="genome_mapping_quality_across_reference.png" title="Permalink to this headline"> </a></h2>
+
+<div><img width=100% src="genome_mapping_quality_across_reference.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>Mapping Quality Histogram<a class="headerlink" name="genome_mapping_quality_histogram.png" title="Permalink to this headline"> </a></h2>
+
+<div><img width=100% src="genome_mapping_quality_histogram.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>Insert Size Across Reference<a class="headerlink" name="genome_insert_size_across_reference.png" title="Permalink to this headline"> </a></h2>
+
+<div><img width=100% src="genome_insert_size_across_reference.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>Insert Size Histogram<a class="headerlink" name="genome_insert_size_histogram.png" title="Permalink to this headline"> </a></h2>
+
+<div><img width=100% src="genome_insert_size_histogram.png"></div>
+
+</div><!-- graph section -->
+
+
+</div>
+
+</div>
+
+</div>
+
+</div>
+
+
+<div class="sidebar">
+<h3>Contents</h3>
+<li class="toctree-l1"><a class="reference internal" href="#summary">Summary</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#input">Input data & parameters</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#genome_coverage_across_reference.png">Coverage across reference</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#genome_coverage_histogram.png">Coverage Histogram</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#genome_coverage_0to50_histogram.png">Coverage Histogram (0-50X)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#genome_uniq_read_starts_histogram.png">Duplication Rate Histogram</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#genome_coverage_quotes.png">Genome Fraction Coverage</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#genome_reads_content_per_read_position.png">Mapped Reads Nucleotide Content</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#genome_gc_content_per_window.png">Mapped Reads GC-content Distribution</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#genome_mapping_quality_across_reference.png">Mapping Quality Across Reference</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#genome_mapping_quality_histogram.png">Mapping Quality Histogram</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#genome_insert_size_across_reference.png">Insert Size Across Reference</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#genome_insert_size_histogram.png">Insert Size Histogram</a></li>
+</div> <!-- sidebar -->
+
+<div class="clearer"></div>
+</div>
+
+</div>
+
+
+<div class="footer-wrapper">
+<div class="footer">
+<div class="left">
+<div class="footer">
+2012/04/24 19:44:41
+</div>
+</div>
+<div class="right">
+<div class="footer">
+Generated by QualiMap
+</div
+</div>
+<div class="clearer"></div>
+</div> <!-- footer -->
+</div>
+</body>
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+ text-align: left;
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+ font-weight: bold;
+}
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+ width: 90%;
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+ padding-top: 5px;
+ font-size: 90%;
+}
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+ vertical-align: top;
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+ margin-top: 0;
+ margin-bottom: 0;
+}
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+ height: 10px;
+}
+
+table.indextable tr.cap {
+ margin-top: 10px;
+ background-color: #f2f2f2;
+}
+
+img.toggler {
+ margin-right: 3px;
+ margin-top: 3px;
+ cursor: pointer;
+}
+
+/* -- viewcode extension ---------------------------------------------------- */
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+ float: right;
+}
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+}
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+ padding: 0 3px;
+ background-color: #f4debf;
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new file mode 100644
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+}
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+ font-size: 90%;
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+ font-size: 90%;
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+ list-style: square;
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+}
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+ background-image: url(file.png);
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+ background-position: 0 7px;
+}
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+}
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+ color: #888;
+ margin: 2px 0 0 30px;
+ text-align: left;
+}
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+ul.keywordmatches li.goodmatch a {
+ font-weight: bold;
+}
+
+/* -- index page ------------------------------------------------------------ */
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+table.contentstable {
+ width: 90%;
+}
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+table.contentstable p.biglink {
+ line-height: 150%;
+}
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+a.biglink {
+ font-size: 1.3em;
+}
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+span.linkdescr {
+ font-style: italic;
+ padding-top: 5px;
+ font-size: 90%;
+}
+
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+table.indextable {
+ width: 100%;
+}
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+ vertical-align: top;
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+}
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+}
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+}
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+img.toggler {
+ margin-right: 3px;
+ margin-top: 3px;
+ cursor: pointer;
+}
+
+div.modindex-jumpbox {
+ border-top: 1px solid #ddd;
+ border-bottom: 1px solid #ddd;
+ margin: 1em 0 1em 0;
+ padding: 0.4em;
+}
+
+div.genindex-jumpbox {
+ border-top: 1px solid #ddd;
+ border-bottom: 1px solid #ddd;
+ margin: 1em 0 1em 0;
+ padding: 0.4em;
+}
+
+/* -- general body styles --------------------------------------------------- */
+
+a.headerlink {
+ visibility: hidden;
+}
+
+h1:hover > a.headerlink,
+h2:hover > a.headerlink,
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+h4:hover > a.headerlink,
+h5:hover > a.headerlink,
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+dt:hover > a.headerlink {
+ visibility: visible;
+}
+
+div.body p.caption {
+ text-align: inherit;
+}
+
+div.body td {
+ text-align: left;
+}
+
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+ padding-left: 1em;
+}
+
+.first {
+ margin-top: 0 !important;
+}
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+p.rubric {
+ margin-top: 30px;
+ font-weight: bold;
+}
+
+img.align-left, .figure.align-left, object.align-left {
+ clear: left;
+ float: left;
+ margin-right: 1em;
+}
+
+img.align-right, .figure.align-right, object.align-right {
+ clear: right;
+ float: right;
+ margin-left: 1em;
+}
+
+img.align-center, .figure.align-center, object.align-center {
+ display: block;
+ margin-left: auto;
+ margin-right: auto;
+}
+
+.align-left {
+ text-align: left;
+}
+
+.align-center {
+ text-align: center;
+}
+
+.align-right {
+ text-align: right;
+}
+
+/* -- sidebars -------------------------------------------------------------- */
+
+div.sidebar {
+ margin: 0 0 0.5em 1em;
+ border: 1px solid #ddb;
+ padding: 7px 7px 0 7px;
+ background-color: #ffe;
+ width: 40%;
+ float: right;
+}
+
+p.sidebar-title {
+ font-weight: bold;
+}
+
+/* -- topics ---------------------------------------------------------------- */
+
+div.topic {
+ border: 1px solid #ccc;
+ padding: 7px 7px 0 7px;
+ margin: 10px 0 10px 0;
+}
+
+p.topic-title {
+ font-size: 1.1em;
+ font-weight: bold;
+ margin-top: 10px;
+}
+
+/* -- admonitions ----------------------------------------------------------- */
+
+div.admonition {
+ margin-top: 10px;
+ margin-bottom: 10px;
+ padding: 7px;
+}
+
+div.admonition dt {
+ font-weight: bold;
+}
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+ margin-bottom: 0;
+}
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+ font-weight: bold;
+}
+
+div.body p.centered {
+ text-align: center;
+ margin-top: 25px;
+}
+
+/* -- tables ---------------------------------------------------------------- */
+
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+ border: 0;
+ border-collapse: collapse;
+}
+
+table.docutils td, table.docutils th {
+ padding: 1px 8px 1px 5px;
+ border-top: 0;
+ border-left: 0;
+ border-right: 0;
+ border-bottom: 1px solid #aaa;
+}
+
+table.field-list td, table.field-list th {
+ border: 0 !important;
+}
+
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+ border: 0 !important;
+}
+
+th {
+ text-align: left;
+ padding-right: 5px;
+}
+
+table.citation {
+ border-left: solid 1px gray;
+ margin-left: 1px;
+}
+
+table.citation td {
+ border-bottom: none;
+}
+
+/* -- other body styles ----------------------------------------------------- */
+
+ol.arabic {
+ list-style: decimal;
+}
+
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+ list-style: lower-alpha;
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+ list-style: upper-alpha;
+}
+
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+ list-style: lower-roman;
+}
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+ list-style: upper-roman;
+}
+
+dl {
+ margin-bottom: 15px;
+}
+
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+ margin-top: 0px;
+}
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+ margin-bottom: 10px;
+}
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+dd {
+ margin-top: 3px;
+ margin-bottom: 10px;
+ margin-left: 30px;
+}
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+dt:target, .highlighted {
+ background-color: #fbe54e;
+}
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+ font-weight: bold;
+ font-size: 1.1em;
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+ margin: 0;
+ padding-left: 1em;
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+ margin: 0;
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+ font-style: italic;
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+ background-color: #fda;
+ padding: 5px;
+ border: 3px solid red;
+}
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+ background-color: #ffa;
+}
+
+.line-block {
+ display: block;
+ margin-top: 1em;
+ margin-bottom: 1em;
+}
+
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+ margin-top: 0;
+ margin-bottom: 0;
+ margin-left: 1.5em;
+}
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+ font-family: sans-serif;
+}
+
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+ text-decoration: underline;
+}
+
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+ font-style: oblique;
+}
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+ border-bottom: dotted 1px;
+ cursor: help;
+}
+
+/* -- code displays --------------------------------------------------------- */
+
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+ overflow: auto;
+ overflow-y: hidden; /* fixes display issues on Chrome browsers */
+}
+
+td.linenos pre {
+ padding: 5px 0px;
+ border: 0;
+ background-color: transparent;
+ color: #aaa;
+}
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+}
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+}
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+}
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+ padding: 0 10px;
+}
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+/* -- math display ---------------------------------------------------------- */
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+img.math {
+ vertical-align: middle;
+}
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+ text-align: center;
+}
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+ float: right;
+}
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+/* -- printout stylesheet --------------------------------------------------- */
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+ div.bodywrapper {
+ margin: 0 !important;
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+ div.related,
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diff --git a/doc/plasmodium_RNA-seq/_static/doctools.js b/doc/plasmodium_RNA-seq/_static/doctools.js
new file mode 100644
index 0000000..d4619fd
--- /dev/null
+++ b/doc/plasmodium_RNA-seq/_static/doctools.js
@@ -0,0 +1,247 @@
+/*
+ * doctools.js
+ * ~~~~~~~~~~~
+ *
+ * Sphinx JavaScript utilities for all documentation.
+ *
+ * :copyright: Copyright 2007-2011 by the Sphinx team, see AUTHORS.
+ * :license: BSD, see LICENSE for details.
+ *
+ */
+
+/**
+ * select a different prefix for underscore
+ */
+$u = _.noConflict();
+
+/**
+ * make the code below compatible with browsers without
+ * an installed firebug like debugger
+if (!window.console || !console.firebug) {
+ var names = ["log", "debug", "info", "warn", "error", "assert", "dir",
+ "dirxml", "group", "groupEnd", "time", "timeEnd", "count", "trace",
+ "profile", "profileEnd"];
+ window.console = {};
+ for (var i = 0; i < names.length; ++i)
+ window.console[names[i]] = function() {};
+}
+ */
+
+/**
+ * small helper function to urldecode strings
+ */
+jQuery.urldecode = function(x) {
+ return decodeURIComponent(x).replace(/\+/g, ' ');
+}
+
+/**
+ * small helper function to urlencode strings
+ */
+jQuery.urlencode = encodeURIComponent;
+
+/**
+ * This function returns the parsed url parameters of the
+ * current request. Multiple values per key are supported,
+ * it will always return arrays of strings for the value parts.
+ */
+jQuery.getQueryParameters = function(s) {
+ if (typeof s == 'undefined')
+ s = document.location.search;
+ var parts = s.substr(s.indexOf('?') + 1).split('&');
+ var result = {};
+ for (var i = 0; i < parts.length; i++) {
+ var tmp = parts[i].split('=', 2);
+ var key = jQuery.urldecode(tmp[0]);
+ var value = jQuery.urldecode(tmp[1]);
+ if (key in result)
+ result[key].push(value);
+ else
+ result[key] = [value];
+ }
+ return result;
+};
+
+/**
+ * small function to check if an array contains
+ * a given item.
+ */
+jQuery.contains = function(arr, item) {
+ for (var i = 0; i < arr.length; i++) {
+ if (arr[i] == item)
+ return true;
+ }
+ return false;
+};
+
+/**
+ * highlight a given string on a jquery object by wrapping it in
+ * span elements with the given class name.
+ */
+jQuery.fn.highlightText = function(text, className) {
+ function highlight(node) {
+ if (node.nodeType == 3) {
+ var val = node.nodeValue;
+ var pos = val.toLowerCase().indexOf(text);
+ if (pos >= 0 && !jQuery(node.parentNode).hasClass(className)) {
+ var span = document.createElement("span");
+ span.className = className;
+ span.appendChild(document.createTextNode(val.substr(pos, text.length)));
+ node.parentNode.insertBefore(span, node.parentNode.insertBefore(
+ document.createTextNode(val.substr(pos + text.length)),
+ node.nextSibling));
+ node.nodeValue = val.substr(0, pos);
+ }
+ }
+ else if (!jQuery(node).is("button, select, textarea")) {
+ jQuery.each(node.childNodes, function() {
+ highlight(this);
+ });
+ }
+ }
+ return this.each(function() {
+ highlight(this);
+ });
+};
+
+/**
+ * Small JavaScript module for the documentation.
+ */
+var Documentation = {
+
+ init : function() {
+ this.fixFirefoxAnchorBug();
+ this.highlightSearchWords();
+ this.initIndexTable();
+ },
+
+ /**
+ * i18n support
+ */
+ TRANSLATIONS : {},
+ PLURAL_EXPR : function(n) { return n == 1 ? 0 : 1; },
+ LOCALE : 'unknown',
+
+ // gettext and ngettext don't access this so that the functions
+ // can safely bound to a different name (_ = Documentation.gettext)
+ gettext : function(string) {
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+ if (typeof translated == 'undefined')
+ return string;
+ return (typeof translated == 'string') ? translated : translated[0];
+ },
+
+ ngettext : function(singular, plural, n) {
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+ if (typeof translated == 'undefined')
+ return (n == 1) ? singular : plural;
+ return translated[Documentation.PLURALEXPR(n)];
+ },
+
+ addTranslations : function(catalog) {
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+ this.PLURAL_EXPR = new Function('n', 'return +(' + catalog.plural_expr + ')');
+ this.LOCALE = catalog.locale;
+ },
+
+ /**
+ * add context elements like header anchor links
+ */
+ addContextElements : function() {
+ $('div[id] > :header:first').each(function() {
+ $('<a class="headerlink">\u00B6</a>').
+ attr('href', '#' + this.id).
+ attr('title', _('Permalink to this headline')).
+ appendTo(this);
+ });
+ $('dt[id]').each(function() {
+ $('<a class="headerlink">\u00B6</a>').
+ attr('href', '#' + this.id).
+ attr('title', _('Permalink to this definition')).
+ appendTo(this);
+ });
+ },
+
+ /**
+ * workaround a firefox stupidity
+ */
+ fixFirefoxAnchorBug : function() {
+ if (document.location.hash && $.browser.mozilla)
+ window.setTimeout(function() {
+ document.location.href += '';
+ }, 10);
+ },
+
+ /**
+ * highlight the search words provided in the url in the text
+ */
+ highlightSearchWords : function() {
+ var params = $.getQueryParameters();
+ var terms = (params.highlight) ? params.highlight[0].split(/\s+/) : [];
+ if (terms.length) {
+ var body = $('div.body');
+ window.setTimeout(function() {
+ $.each(terms, function() {
+ body.highlightText(this.toLowerCase(), 'highlighted');
+ });
+ }, 10);
+ $('<p class="highlight-link"><a href="javascript:Documentation.' +
+ 'hideSearchWords()">' + _('Hide Search Matches') + '</a></p>')
+ .appendTo($('#searchbox'));
+ }
+ },
+
+ /**
+ * init the domain index toggle buttons
+ */
+ initIndexTable : function() {
+ var togglers = $('img.toggler').click(function() {
+ var src = $(this).attr('src');
+ var idnum = $(this).attr('id').substr(7);
+ $('tr.cg-' + idnum).toggle();
+ if (src.substr(-9) == 'minus.png')
+ $(this).attr('src', src.substr(0, src.length-9) + 'plus.png');
+ else
+ $(this).attr('src', src.substr(0, src.length-8) + 'minus.png');
+ }).css('display', '');
+ if (DOCUMENTATION_OPTIONS.COLLAPSE_INDEX) {
+ togglers.click();
+ }
+ },
+
+ /**
+ * helper function to hide the search marks again
+ */
+ hideSearchWords : function() {
+ $('#searchbox .highlight-link').fadeOut(300);
+ $('span.highlighted').removeClass('highlighted');
+ },
+
+ /**
+ * make the url absolute
+ */
+ makeURL : function(relativeURL) {
+ return DOCUMENTATION_OPTIONS.URL_ROOT + '/' + relativeURL;
+ },
+
+ /**
+ * get the current relative url
+ */
+ getCurrentURL : function() {
+ var path = document.location.pathname;
+ var parts = path.split(/\//);
+ $.each(DOCUMENTATION_OPTIONS.URL_ROOT.split(/\//), function() {
+ if (this == '..')
+ parts.pop();
+ });
+ var url = parts.join('/');
+ return path.substring(url.lastIndexOf('/') + 1, path.length - 1);
+ }
+};
+
+// quick alias for translations
+_ = Documentation.gettext;
+
+$(document).ready(function() {
+ Documentation.init();
+});
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diff --git a/doc/plasmodium_RNA-seq/_static/jquery.js b/doc/plasmodium_RNA-seq/_static/jquery.js
new file mode 100644
index 0000000..7c24308
--- /dev/null
+++ b/doc/plasmodium_RNA-seq/_static/jquery.js
@@ -0,0 +1,154 @@
+/*!
+ * jQuery JavaScript Library v1.4.2
+ * http://jquery.com/
+ *
+ * Copyright 2010, John Resig
+ * Dual licensed under the MIT or GPL Version 2 licenses.
+ * http://jquery.org/license
+ *
+ * Includes Sizzle.js
+ * http://sizzlejs.com/
+ * Copyright 2010, The Dojo Foundation
+ * Released under the MIT, BSD, and GPL Licenses.
+ *
+ * Date: Sat Feb 13 22:33:48 2010 -0500
+ */
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+.highlight .gu { color: #800080; font-weight: bold } /* Generic.Subheading */
+.highlight .gt { color: #0040D0 } /* Generic.Traceback */
+.highlight .kc { color: #007020; font-weight: bold } /* Keyword.Constant */
+.highlight .kd { color: #007020; font-weight: bold } /* Keyword.Declaration */
+.highlight .kn { color: #007020; font-weight: bold } /* Keyword.Namespace */
+.highlight .kp { color: #007020 } /* Keyword.Pseudo */
+.highlight .kr { color: #007020; font-weight: bold } /* Keyword.Reserved */
+.highlight .kt { color: #902000 } /* Keyword.Type */
+.highlight .m { color: #208050 } /* Literal.Number */
+.highlight .s { color: #4070a0 } /* Literal.String */
+.highlight .na { color: #4070a0 } /* Name.Attribute */
+.highlight .nb { color: #007020 } /* Name.Builtin */
+.highlight .nc { color: #0e84b5; font-weight: bold } /* Name.Class */
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+.highlight .nn { color: #0e84b5; font-weight: bold } /* Name.Namespace */
+.highlight .nt { color: #062873; font-weight: bold } /* Name.Tag */
+.highlight .nv { color: #bb60d5 } /* Name.Variable */
+.highlight .ow { color: #007020; font-weight: bold } /* Operator.Word */
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+.highlight .mo { color: #208050 } /* Literal.Number.Oct */
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+.highlight .se { color: #4070a0; font-weight: bold } /* Literal.String.Escape */
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diff --git a/doc/plasmodium_RNA-seq/_static/report.css b/doc/plasmodium_RNA-seq/_static/report.css
new file mode 100644
index 0000000..19ae268
--- /dev/null
+++ b/doc/plasmodium_RNA-seq/_static/report.css
@@ -0,0 +1,50 @@
+div.summary{
+
+}
+
+table.summary{
+
+ border: 0px;
+ width: 100%;
+ vertical-align: top;
+
+}
+
+div.table-summary{
+ margin-left:auto;
+ margin-right:auto;
+ padding-bottom: 20px;
+}
+
+td.column1{
+ width: 60%;
+}
+
+table.hovertable {
+
+ font-size:14px;
+
+ border-width: 1px;
+ border-color: #999999;
+ border-collapse: collapse;
+}
+table.hovertable th {
+ background-color:#FFFFFF;
+ border-width: 1px;
+ padding: 8px;
+ border-style: solid;
+ border-color: #a9c6c9;
+}
+table.hovertable tr {
+ background-color:#FFFFFF;
+}
+table.hovertable td {
+ border-width: 1px;
+ padding: 8px;
+ border-style: solid;
+ border-color: #a9c6c9;
+}
+
+
+
+
diff --git a/doc/plasmodium_RNA-seq/_static/searchtools.js b/doc/plasmodium_RNA-seq/_static/searchtools.js
new file mode 100644
index 0000000..663be4c
--- /dev/null
+++ b/doc/plasmodium_RNA-seq/_static/searchtools.js
@@ -0,0 +1,560 @@
+/*
+ * searchtools.js_t
+ * ~~~~~~~~~~~~~~~~
+ *
+ * Sphinx JavaScript utilties for the full-text search.
+ *
+ * :copyright: Copyright 2007-2011 by the Sphinx team, see AUTHORS.
+ * :license: BSD, see LICENSE for details.
+ *
+ */
+
+/**
+ * helper function to return a node containing the
+ * search summary for a given text. keywords is a list
+ * of stemmed words, hlwords is the list of normal, unstemmed
+ * words. the first one is used to find the occurance, the
+ * latter for highlighting it.
+ */
+
+jQuery.makeSearchSummary = function(text, keywords, hlwords) {
+ var textLower = text.toLowerCase();
+ var start = 0;
+ $.each(keywords, function() {
+ var i = textLower.indexOf(this.toLowerCase());
+ if (i > -1)
+ start = i;
+ });
+ start = Math.max(start - 120, 0);
+ var excerpt = ((start > 0) ? '...' : '') +
+ $.trim(text.substr(start, 240)) +
+ ((start + 240 - text.length) ? '...' : '');
+ var rv = $('<div class="context"></div>').text(excerpt);
+ $.each(hlwords, function() {
+ rv = rv.highlightText(this, 'highlighted');
+ });
+ return rv;
+}
+
+
+/**
+ * Porter Stemmer
+ */
+var Stemmer = function() {
+
+ var step2list = {
+ ational: 'ate',
+ tional: 'tion',
+ enci: 'ence',
+ anci: 'ance',
+ izer: 'ize',
+ bli: 'ble',
+ alli: 'al',
+ entli: 'ent',
+ eli: 'e',
+ ousli: 'ous',
+ ization: 'ize',
+ ation: 'ate',
+ ator: 'ate',
+ alism: 'al',
+ iveness: 'ive',
+ fulness: 'ful',
+ ousness: 'ous',
+ aliti: 'al',
+ iviti: 'ive',
+ biliti: 'ble',
+ logi: 'log'
+ };
+
+ var step3list = {
+ icate: 'ic',
+ ative: '',
+ alize: 'al',
+ iciti: 'ic',
+ ical: 'ic',
+ ful: '',
+ ness: ''
+ };
+
+ var c = "[^aeiou]"; // consonant
+ var v = "[aeiouy]"; // vowel
+ var C = c + "[^aeiouy]*"; // consonant sequence
+ var V = v + "[aeiou]*"; // vowel sequence
+
+ var mgr0 = "^(" + C + ")?" + V + C; // [C]VC... is m>0
+ var meq1 = "^(" + C + ")?" + V + C + "(" + V + ")?$"; // [C]VC[V] is m=1
+ var mgr1 = "^(" + C + ")?" + V + C + V + C; // [C]VCVC... is m>1
+ var s_v = "^(" + C + ")?" + v; // vowel in stem
+
+ this.stemWord = function (w) {
+ var stem;
+ var suffix;
+ var firstch;
+ var origword = w;
+
+ if (w.length < 3)
+ return w;
+
+ var re;
+ var re2;
+ var re3;
+ var re4;
+
+ firstch = w.substr(0,1);
+ if (firstch == "y")
+ w = firstch.toUpperCase() + w.substr(1);
+
+ // Step 1a
+ re = /^(.+?)(ss|i)es$/;
+ re2 = /^(.+?)([^s])s$/;
+
+ if (re.test(w))
+ w = w.replace(re,"$1$2");
+ else if (re2.test(w))
+ w = w.replace(re2,"$1$2");
+
+ // Step 1b
+ re = /^(.+?)eed$/;
+ re2 = /^(.+?)(ed|ing)$/;
+ if (re.test(w)) {
+ var fp = re.exec(w);
+ re = new RegExp(mgr0);
+ if (re.test(fp[1])) {
+ re = /.$/;
+ w = w.replace(re,"");
+ }
+ }
+ else if (re2.test(w)) {
+ var fp = re2.exec(w);
+ stem = fp[1];
+ re2 = new RegExp(s_v);
+ if (re2.test(stem)) {
+ w = stem;
+ re2 = /(at|bl|iz)$/;
+ re3 = new RegExp("([^aeiouylsz])\\1$");
+ re4 = new RegExp("^" + C + v + "[^aeiouwxy]$");
+ if (re2.test(w))
+ w = w + "e";
+ else if (re3.test(w)) {
+ re = /.$/;
+ w = w.replace(re,"");
+ }
+ else if (re4.test(w))
+ w = w + "e";
+ }
+ }
+
+ // Step 1c
+ re = /^(.+?)y$/;
+ if (re.test(w)) {
+ var fp = re.exec(w);
+ stem = fp[1];
+ re = new RegExp(s_v);
+ if (re.test(stem))
+ w = stem + "i";
+ }
+
+ // Step 2
+ re = /^(.+?)(ational|tional|enci|anci|izer|bli|alli|entli|eli|ousli|ization|ation|ator|alism|iveness|fulness|ousness|aliti|iviti|biliti|logi)$/;
+ if (re.test(w)) {
+ var fp = re.exec(w);
+ stem = fp[1];
+ suffix = fp[2];
+ re = new RegExp(mgr0);
+ if (re.test(stem))
+ w = stem + step2list[suffix];
+ }
+
+ // Step 3
+ re = /^(.+?)(icate|ative|alize|iciti|ical|ful|ness)$/;
+ if (re.test(w)) {
+ var fp = re.exec(w);
+ stem = fp[1];
+ suffix = fp[2];
+ re = new RegExp(mgr0);
+ if (re.test(stem))
+ w = stem + step3list[suffix];
+ }
+
+ // Step 4
+ re = /^(.+?)(al|ance|ence|er|ic|able|ible|ant|ement|ment|ent|ou|ism|ate|iti|ous|ive|ize)$/;
+ re2 = /^(.+?)(s|t)(ion)$/;
+ if (re.test(w)) {
+ var fp = re.exec(w);
+ stem = fp[1];
+ re = new RegExp(mgr1);
+ if (re.test(stem))
+ w = stem;
+ }
+ else if (re2.test(w)) {
+ var fp = re2.exec(w);
+ stem = fp[1] + fp[2];
+ re2 = new RegExp(mgr1);
+ if (re2.test(stem))
+ w = stem;
+ }
+
+ // Step 5
+ re = /^(.+?)e$/;
+ if (re.test(w)) {
+ var fp = re.exec(w);
+ stem = fp[1];
+ re = new RegExp(mgr1);
+ re2 = new RegExp(meq1);
+ re3 = new RegExp("^" + C + v + "[^aeiouwxy]$");
+ if (re.test(stem) || (re2.test(stem) && !(re3.test(stem))))
+ w = stem;
+ }
+ re = /ll$/;
+ re2 = new RegExp(mgr1);
+ if (re.test(w) && re2.test(w)) {
+ re = /.$/;
+ w = w.replace(re,"");
+ }
+
+ // and turn initial Y back to y
+ if (firstch == "y")
+ w = firstch.toLowerCase() + w.substr(1);
+ return w;
+ }
+}
+
+
+/**
+ * Search Module
+ */
+var Search = {
+
+ _index : null,
+ _queued_query : null,
+ _pulse_status : -1,
+
+ init : function() {
+ var params = $.getQueryParameters();
+ if (params.q) {
+ var query = params.q[0];
+ $('input[name="q"]')[0].value = query;
+ this.performSearch(query);
+ }
+ },
+
+ loadIndex : function(url) {
+ $.ajax({type: "GET", url: url, data: null, success: null,
+ dataType: "script", cache: true});
+ },
+
+ setIndex : function(index) {
+ var q;
+ this._index = index;
+ if ((q = this._queued_query) !== null) {
+ this._queued_query = null;
+ Search.query(q);
+ }
+ },
+
+ hasIndex : function() {
+ return this._index !== null;
+ },
+
+ deferQuery : function(query) {
+ this._queued_query = query;
+ },
+
+ stopPulse : function() {
+ this._pulse_status = 0;
+ },
+
+ startPulse : function() {
+ if (this._pulse_status >= 0)
+ return;
+ function pulse() {
+ Search._pulse_status = (Search._pulse_status + 1) % 4;
+ var dotString = '';
+ for (var i = 0; i < Search._pulse_status; i++)
+ dotString += '.';
+ Search.dots.text(dotString);
+ if (Search._pulse_status > -1)
+ window.setTimeout(pulse, 500);
+ };
+ pulse();
+ },
+
+ /**
+ * perform a search for something
+ */
+ performSearch : function(query) {
+ // create the required interface elements
+ this.out = $('#search-results');
+ this.title = $('<h2>' + _('Searching') + '</h2>').appendTo(this.out);
+ this.dots = $('<span></span>').appendTo(this.title);
+ this.status = $('<p style="display: none"></p>').appendTo(this.out);
+ this.output = $('<ul class="search"/>').appendTo(this.out);
+
+ $('#search-progress').text(_('Preparing search...'));
+ this.startPulse();
+
+ // index already loaded, the browser was quick!
+ if (this.hasIndex())
+ this.query(query);
+ else
+ this.deferQuery(query);
+ },
+
+ query : function(query) {
+ var stopwords = ["and","then","into","it","as","are","in","if","for","no","there","their","was","is","be","to","that","but","they","not","such","with","by","a","on","these","of","will","this","near","the","or","at"];
+
+ // Stem the searchterms and add them to the correct list
+ var stemmer = new Stemmer();
+ var searchterms = [];
+ var excluded = [];
+ var hlterms = [];
+ var tmp = query.split(/\s+/);
+ var objectterms = [];
+ for (var i = 0; i < tmp.length; i++) {
+ if (tmp[i] != "") {
+ objectterms.push(tmp[i].toLowerCase());
+ }
+
+ if ($u.indexOf(stopwords, tmp[i]) != -1 || tmp[i].match(/^\d+$/) ||
+ tmp[i] == "") {
+ // skip this "word"
+ continue;
+ }
+ // stem the word
+ var word = stemmer.stemWord(tmp[i]).toLowerCase();
+ // select the correct list
+ if (word[0] == '-') {
+ var toAppend = excluded;
+ word = word.substr(1);
+ }
+ else {
+ var toAppend = searchterms;
+ hlterms.push(tmp[i].toLowerCase());
+ }
+ // only add if not already in the list
+ if (!$.contains(toAppend, word))
+ toAppend.push(word);
+ };
+ var highlightstring = '?highlight=' + $.urlencode(hlterms.join(" "));
+
+ // console.debug('SEARCH: searching for:');
+ // console.info('required: ', searchterms);
+ // console.info('excluded: ', excluded);
+
+ // prepare search
+ var filenames = this._index.filenames;
+ var titles = this._index.titles;
+ var terms = this._index.terms;
+ var fileMap = {};
+ var files = null;
+ // different result priorities
+ var importantResults = [];
+ var objectResults = [];
+ var regularResults = [];
+ var unimportantResults = [];
+ $('#search-progress').empty();
+
+ // lookup as object
+ for (var i = 0; i < objectterms.length; i++) {
+ var others = [].concat(objectterms.slice(0,i),
+ objectterms.slice(i+1, objectterms.length))
+ var results = this.performObjectSearch(objectterms[i], others);
+ // Assume first word is most likely to be the object,
+ // other words more likely to be in description.
+ // Therefore put matches for earlier words first.
+ // (Results are eventually used in reverse order).
+ objectResults = results[0].concat(objectResults);
+ importantResults = results[1].concat(importantResults);
+ unimportantResults = results[2].concat(unimportantResults);
+ }
+
+ // perform the search on the required terms
+ for (var i = 0; i < searchterms.length; i++) {
+ var word = searchterms[i];
+ // no match but word was a required one
+ if ((files = terms[word]) == null)
+ break;
+ if (files.length == undefined) {
+ files = [files];
+ }
+ // create the mapping
+ for (var j = 0; j < files.length; j++) {
+ var file = files[j];
+ if (file in fileMap)
+ fileMap[file].push(word);
+ else
+ fileMap[file] = [word];
+ }
+ }
+
+ // now check if the files don't contain excluded terms
+ for (var file in fileMap) {
+ var valid = true;
+
+ // check if all requirements are matched
+ if (fileMap[file].length != searchterms.length)
+ continue;
+
+ // ensure that none of the excluded terms is in the
+ // search result.
+ for (var i = 0; i < excluded.length; i++) {
+ if (terms[excluded[i]] == file ||
+ $.contains(terms[excluded[i]] || [], file)) {
+ valid = false;
+ break;
+ }
+ }
+
+ // if we have still a valid result we can add it
+ // to the result list
+ if (valid)
+ regularResults.push([filenames[file], titles[file], '', null]);
+ }
+
+ // delete unused variables in order to not waste
+ // memory until list is retrieved completely
+ delete filenames, titles, terms;
+
+ // now sort the regular results descending by title
+ regularResults.sort(function(a, b) {
+ var left = a[1].toLowerCase();
+ var right = b[1].toLowerCase();
+ return (left > right) ? -1 : ((left < right) ? 1 : 0);
+ });
+
+ // combine all results
+ var results = unimportantResults.concat(regularResults)
+ .concat(objectResults).concat(importantResults);
+
+ // print the results
+ var resultCount = results.length;
+ function displayNextItem() {
+ // results left, load the summary and display it
+ if (results.length) {
+ var item = results.pop();
+ var listItem = $('<li style="display:none"></li>');
+ if (DOCUMENTATION_OPTIONS.FILE_SUFFIX == '') {
+ // dirhtml builder
+ var dirname = item[0] + '/';
+ if (dirname.match(/\/index\/$/)) {
+ dirname = dirname.substring(0, dirname.length-6);
+ } else if (dirname == 'index/') {
+ dirname = '';
+ }
+ listItem.append($('<a/>').attr('href',
+ DOCUMENTATION_OPTIONS.URL_ROOT + dirname +
+ highlightstring + item[2]).html(item[1]));
+ } else {
+ // normal html builders
+ listItem.append($('<a/>').attr('href',
+ item[0] + DOCUMENTATION_OPTIONS.FILE_SUFFIX +
+ highlightstring + item[2]).html(item[1]));
+ }
+ if (item[3]) {
+ listItem.append($('<span> (' + item[3] + ')</span>'));
+ Search.output.append(listItem);
+ listItem.slideDown(5, function() {
+ displayNextItem();
+ });
+ } else if (DOCUMENTATION_OPTIONS.HAS_SOURCE) {
+ $.get(DOCUMENTATION_OPTIONS.URL_ROOT + '_sources/' +
+ item[0] + '.txt', function(data) {
+ if (data != '') {
+ listItem.append($.makeSearchSummary(data, searchterms, hlterms));
+ Search.output.append(listItem);
+ }
+ listItem.slideDown(5, function() {
+ displayNextItem();
+ });
+ }, "text");
+ } else {
+ // no source available, just display title
+ Search.output.append(listItem);
+ listItem.slideDown(5, function() {
+ displayNextItem();
+ });
+ }
+ }
+ // search finished, update title and status message
+ else {
+ Search.stopPulse();
+ Search.title.text(_('Search Results'));
+ if (!resultCount)
+ Search.status.text(_('Your search did not match any documents. Please make sure that all words are spelled correctly and that you\'ve selected enough categories.'));
+ else
+ Search.status.text(_('Search finished, found %s page(s) matching the search query.').replace('%s', resultCount));
+ Search.status.fadeIn(500);
+ }
+ }
+ displayNextItem();
+ },
+
+ performObjectSearch : function(object, otherterms) {
+ var filenames = this._index.filenames;
+ var objects = this._index.objects;
+ var objnames = this._index.objnames;
+ var titles = this._index.titles;
+
+ var importantResults = [];
+ var objectResults = [];
+ var unimportantResults = [];
+
+ for (var prefix in objects) {
+ for (var name in objects[prefix]) {
+ var fullname = (prefix ? prefix + '.' : '') + name;
+ if (fullname.toLowerCase().indexOf(object) > -1) {
+ var match = objects[prefix][name];
+ var objname = objnames[match[1]][2];
+ var title = titles[match[0]];
+ // If more than one term searched for, we require other words to be
+ // found in the name/title/description
+ if (otherterms.length > 0) {
+ var haystack = (prefix + ' ' + name + ' ' +
+ objname + ' ' + title).toLowerCase();
+ var allfound = true;
+ for (var i = 0; i < otherterms.length; i++) {
+ if (haystack.indexOf(otherterms[i]) == -1) {
+ allfound = false;
+ break;
+ }
+ }
+ if (!allfound) {
+ continue;
+ }
+ }
+ var descr = objname + _(', in ') + title;
+ anchor = match[3];
+ if (anchor == '')
+ anchor = fullname;
+ else if (anchor == '-')
+ anchor = objnames[match[1]][1] + '-' + fullname;
+ result = [filenames[match[0]], fullname, '#'+anchor, descr];
+ switch (match[2]) {
+ case 1: objectResults.push(result); break;
+ case 0: importantResults.push(result); break;
+ case 2: unimportantResults.push(result); break;
+ }
+ }
+ }
+ }
+
+ // sort results descending
+ objectResults.sort(function(a, b) {
+ return (a[1] > b[1]) ? -1 : ((a[1] < b[1]) ? 1 : 0);
+ });
+
+ importantResults.sort(function(a, b) {
+ return (a[1] > b[1]) ? -1 : ((a[1] < b[1]) ? 1 : 0);
+ });
+
+ unimportantResults.sort(function(a, b) {
+ return (a[1] > b[1]) ? -1 : ((a[1] < b[1]) ? 1 : 0);
+ });
+
+ return [importantResults, objectResults, unimportantResults]
+ }
+}
+
+$(document).ready(function() {
+ Search.init();
+});
\ No newline at end of file
diff --git a/doc/plasmodium_RNA-seq/_static/underscore.js b/doc/plasmodium_RNA-seq/_static/underscore.js
new file mode 100644
index 0000000..5d89914
--- /dev/null
+++ b/doc/plasmodium_RNA-seq/_static/underscore.js
@@ -0,0 +1,23 @@
+// Underscore.js 0.5.5
+// (c) 2009 Jeremy Ashkenas, DocumentCloud Inc.
+// Underscore is freely distributable under the terms of the MIT license.
+// Portions of Underscore are inspired by or borrowed from Prototype.js,
+// Oliver Steele's Functional, and John Resig's Micro-Templating.
+// For all details and documentation:
+// http://documentcloud.github.com/underscore/
+(function(){var j=this,n=j._,i=function(a){this._wrapped=a},m=typeof StopIteration!=="undefined"?StopIteration:"__break__",b=j._=function(a){return new i(a)};if(typeof exports!=="undefined")exports._=b;var k=Array.prototype.slice,o=Array.prototype.unshift,p=Object.prototype.toString,q=Object.prototype.hasOwnProperty,r=Object.prototype.propertyIsEnumerable;b.VERSION="0.5.5";b.each=function(a,c,d){try{if(a.forEach)a.forEach(c,d);else if(b.isArray(a)||b.isArguments(a))for(var e=0,f=a.length [...]
+a[e],e,a);else{var g=b.keys(a);f=g.length;for(e=0;e<f;e++)c.call(d,a[g[e]],g[e],a)}}catch(h){if(h!=m)throw h;}return a};b.map=function(a,c,d){if(a&&b.isFunction(a.map))return a.map(c,d);var e=[];b.each(a,function(f,g,h){e.push(c.call(d,f,g,h))});return e};b.reduce=function(a,c,d,e){if(a&&b.isFunction(a.reduce))return a.reduce(b.bind(d,e),c);b.each(a,function(f,g,h){c=d.call(e,c,f,g,h)});return c};b.reduceRight=function(a,c,d,e){if(a&&b.isFunction(a.reduceRight))return a.reduceRight(b.bin [...]
+var f=b.clone(b.toArray(a)).reverse();b.each(f,function(g,h){c=d.call(e,c,g,h,a)});return c};b.detect=function(a,c,d){var e;b.each(a,function(f,g,h){if(c.call(d,f,g,h)){e=f;b.breakLoop()}});return e};b.select=function(a,c,d){if(a&&b.isFunction(a.filter))return a.filter(c,d);var e=[];b.each(a,function(f,g,h){c.call(d,f,g,h)&&e.push(f)});return e};b.reject=function(a,c,d){var e=[];b.each(a,function(f,g,h){!c.call(d,f,g,h)&&e.push(f)});return e};b.all=function(a,c,d){c=c||b.identity;if(a&&b [...]
+d);var e=true;b.each(a,function(f,g,h){(e=e&&c.call(d,f,g,h))||b.breakLoop()});return e};b.any=function(a,c,d){c=c||b.identity;if(a&&b.isFunction(a.some))return a.some(c,d);var e=false;b.each(a,function(f,g,h){if(e=c.call(d,f,g,h))b.breakLoop()});return e};b.include=function(a,c){if(b.isArray(a))return b.indexOf(a,c)!=-1;var d=false;b.each(a,function(e){if(d=e===c)b.breakLoop()});return d};b.invoke=function(a,c){var d=b.rest(arguments,2);return b.map(a,function(e){return(c?e[c]:e).apply( [...]
+function(a,c){return b.map(a,function(d){return d[c]})};b.max=function(a,c,d){if(!c&&b.isArray(a))return Math.max.apply(Math,a);var e={computed:-Infinity};b.each(a,function(f,g,h){g=c?c.call(d,f,g,h):f;g>=e.computed&&(e={value:f,computed:g})});return e.value};b.min=function(a,c,d){if(!c&&b.isArray(a))return Math.min.apply(Math,a);var e={computed:Infinity};b.each(a,function(f,g,h){g=c?c.call(d,f,g,h):f;g<e.computed&&(e={value:f,computed:g})});return e.value};b.sortBy=function(a,c,d){retur [...]
+function(e,f,g){return{value:e,criteria:c.call(d,e,f,g)}}).sort(function(e,f){e=e.criteria;f=f.criteria;return e<f?-1:e>f?1:0}),"value")};b.sortedIndex=function(a,c,d){d=d||b.identity;for(var e=0,f=a.length;e<f;){var g=e+f>>1;d(a[g])<d(c)?(e=g+1):(f=g)}return e};b.toArray=function(a){if(!a)return[];if(a.toArray)return a.toArray();if(b.isArray(a))return a;if(b.isArguments(a))return k.call(a);return b.values(a)};b.size=function(a){return b.toArray(a).length};b.first=function(a,c,d){return [...]
+0,c):a[0]};b.rest=function(a,c,d){return k.call(a,b.isUndefined(c)||d?1:c)};b.last=function(a){return a[a.length-1]};b.compact=function(a){return b.select(a,function(c){return!!c})};b.flatten=function(a){return b.reduce(a,[],function(c,d){if(b.isArray(d))return c.concat(b.flatten(d));c.push(d);return c})};b.without=function(a){var c=b.rest(arguments);return b.select(a,function(d){return!b.include(c,d)})};b.uniq=function(a,c){return b.reduce(a,[],function(d,e,f){if(0==f||(c===true?b.last( [...]
+e)))d.push(e);return d})};b.intersect=function(a){var c=b.rest(arguments);return b.select(b.uniq(a),function(d){return b.all(c,function(e){return b.indexOf(e,d)>=0})})};b.zip=function(){for(var a=b.toArray(arguments),c=b.max(b.pluck(a,"length")),d=new Array(c),e=0;e<c;e++)d[e]=b.pluck(a,String(e));return d};b.indexOf=function(a,c){if(a.indexOf)return a.indexOf(c);for(var d=0,e=a.length;d<e;d++)if(a[d]===c)return d;return-1};b.lastIndexOf=function(a,c){if(a.lastIndexOf)return a.lastIndexO [...]
+a.length;d--;)if(a[d]===c)return d;return-1};b.range=function(a,c,d){var e=b.toArray(arguments),f=e.length<=1;a=f?0:e[0];c=f?e[0]:e[1];d=e[2]||1;e=Math.ceil((c-a)/d);if(e<=0)return[];e=new Array(e);f=a;for(var g=0;1;f+=d){if((d>0?f-c:c-f)>=0)return e;e[g++]=f}};b.bind=function(a,c){var d=b.rest(arguments,2);return function(){return a.apply(c||j,d.concat(b.toArray(arguments)))}};b.bindAll=function(a){var c=b.rest(arguments);if(c.length==0)c=b.functions(a);b.each(c,function(d){a[d]=b.bind( [...]
+return a};b.delay=function(a,c){var d=b.rest(arguments,2);return setTimeout(function(){return a.apply(a,d)},c)};b.defer=function(a){return b.delay.apply(b,[a,1].concat(b.rest(arguments)))};b.wrap=function(a,c){return function(){var d=[a].concat(b.toArray(arguments));return c.apply(c,d)}};b.compose=function(){var a=b.toArray(arguments);return function(){for(var c=b.toArray(arguments),d=a.length-1;d>=0;d--)c=[a[d].apply(this,c)];return c[0]}};b.keys=function(a){if(b.isArray(a))return b.ran [...]
+var c=[];for(var d in a)q.call(a,d)&&c.push(d);return c};b.values=function(a){return b.map(a,b.identity)};b.functions=function(a){return b.select(b.keys(a),function(c){return b.isFunction(a[c])}).sort()};b.extend=function(a,c){for(var d in c)a[d]=c[d];return a};b.clone=function(a){if(b.isArray(a))return a.slice(0);return b.extend({},a)};b.tap=function(a,c){c(a);return a};b.isEqual=function(a,c){if(a===c)return true;var d=typeof a;if(d!=typeof c)return false;if(a==c)return true;if(!a&&c|| [...]
+if(a.isEqual)return a.isEqual(c);if(b.isDate(a)&&b.isDate(c))return a.getTime()===c.getTime();if(b.isNaN(a)&&b.isNaN(c))return true;if(b.isRegExp(a)&&b.isRegExp(c))return a.source===c.source&&a.global===c.global&&a.ignoreCase===c.ignoreCase&&a.multiline===c.multiline;if(d!=="object")return false;if(a.length&&a.length!==c.length)return false;d=b.keys(a);var e=b.keys(c);if(d.length!=e.length)return false;for(var f in a)if(!b.isEqual(a[f],c[f]))return false;return true};b.isEmpty=function(a [...]
+0};b.isElement=function(a){return!!(a&&a.nodeType==1)};b.isArray=function(a){return!!(a&&a.concat&&a.unshift)};b.isArguments=function(a){return a&&b.isNumber(a.length)&&!b.isArray(a)&&!r.call(a,"length")};b.isFunction=function(a){return!!(a&&a.constructor&&a.call&&a.apply)};b.isString=function(a){return!!(a===""||a&&a.charCodeAt&&a.substr)};b.isNumber=function(a){return p.call(a)==="[object Number]"};b.isDate=function(a){return!!(a&&a.getTimezoneOffset&&a.setUTCFullYear)};b.isRegExp=func [...]
+a.test&&a.exec&&(a.ignoreCase||a.ignoreCase===false))};b.isNaN=function(a){return b.isNumber(a)&&isNaN(a)};b.isNull=function(a){return a===null};b.isUndefined=function(a){return typeof a=="undefined"};b.noConflict=function(){j._=n;return this};b.identity=function(a){return a};b.breakLoop=function(){throw m;};var s=0;b.uniqueId=function(a){var c=s++;return a?a+c:c};b.template=function(a,c){a=new Function("obj","var p=[],print=function(){p.push.apply(p,arguments);};with(obj){p.push('"+a.re [...]
+" ").replace(/'(?=[^%]*%>)/g,"\t").split("'").join("\\'").split("\t").join("'").replace(/<%=(.+?)%>/g,"',$1,'").split("<%").join("');").split("%>").join("p.push('")+"');}return p.join('');");return c?a(c):a};b.forEach=b.each;b.foldl=b.inject=b.reduce;b.foldr=b.reduceRight;b.filter=b.select;b.every=b.all;b.some=b.any;b.head=b.first;b.tail=b.rest;b.methods=b.functions;var l=function(a,c){return c?b(a).chain():a};b.each(b.functions(b),function(a){var c=b[a];i.prototype[a]=function(){var d=b [...]
+o.call(d,this._wrapped);return l(c.apply(b,d),this._chain)}});b.each(["pop","push","reverse","shift","sort","splice","unshift"],function(a){var c=Array.prototype[a];i.prototype[a]=function(){c.apply(this._wrapped,arguments);return l(this._wrapped,this._chain)}});b.each(["concat","join","slice"],function(a){var c=Array.prototype[a];i.prototype[a]=function(){return l(c.apply(this._wrapped,arguments),this._chain)}});i.prototype.chain=function(){this._chain=true;return this};i.prototype.valu [...]
diff --git a/doc/plasmodium_RNA-seq/_static/up-pressed.png b/doc/plasmodium_RNA-seq/_static/up-pressed.png
new file mode 100644
index 0000000..8bd587a
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diff --git a/doc/plasmodium_RNA-seq/_static/up.png b/doc/plasmodium_RNA-seq/_static/up.png
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diff --git a/doc/plasmodium_RNA-seq/_static/websupport.js b/doc/plasmodium_RNA-seq/_static/websupport.js
new file mode 100644
index 0000000..e9bd1b8
--- /dev/null
+++ b/doc/plasmodium_RNA-seq/_static/websupport.js
@@ -0,0 +1,808 @@
+/*
+ * websupport.js
+ * ~~~~~~~~~~~~~
+ *
+ * sphinx.websupport utilties for all documentation.
+ *
+ * :copyright: Copyright 2007-2011 by the Sphinx team, see AUTHORS.
+ * :license: BSD, see LICENSE for details.
+ *
+ */
+
+(function($) {
+ $.fn.autogrow = function() {
+ return this.each(function() {
+ var textarea = this;
+
+ $.fn.autogrow.resize(textarea);
+
+ $(textarea)
+ .focus(function() {
+ textarea.interval = setInterval(function() {
+ $.fn.autogrow.resize(textarea);
+ }, 500);
+ })
+ .blur(function() {
+ clearInterval(textarea.interval);
+ });
+ });
+ };
+
+ $.fn.autogrow.resize = function(textarea) {
+ var lineHeight = parseInt($(textarea).css('line-height'), 10);
+ var lines = textarea.value.split('\n');
+ var columns = textarea.cols;
+ var lineCount = 0;
+ $.each(lines, function() {
+ lineCount += Math.ceil(this.length / columns) || 1;
+ });
+ var height = lineHeight * (lineCount + 1);
+ $(textarea).css('height', height);
+ };
+})(jQuery);
+
+(function($) {
+ var comp, by;
+
+ function init() {
+ initEvents();
+ initComparator();
+ }
+
+ function initEvents() {
+ $('a.comment-close').live("click", function(event) {
+ event.preventDefault();
+ hide($(this).attr('id').substring(2));
+ });
+ $('a.vote').live("click", function(event) {
+ event.preventDefault();
+ handleVote($(this));
+ });
+ $('a.reply').live("click", function(event) {
+ event.preventDefault();
+ openReply($(this).attr('id').substring(2));
+ });
+ $('a.close-reply').live("click", function(event) {
+ event.preventDefault();
+ closeReply($(this).attr('id').substring(2));
+ });
+ $('a.sort-option').live("click", function(event) {
+ event.preventDefault();
+ handleReSort($(this));
+ });
+ $('a.show-proposal').live("click", function(event) {
+ event.preventDefault();
+ showProposal($(this).attr('id').substring(2));
+ });
+ $('a.hide-proposal').live("click", function(event) {
+ event.preventDefault();
+ hideProposal($(this).attr('id').substring(2));
+ });
+ $('a.show-propose-change').live("click", function(event) {
+ event.preventDefault();
+ showProposeChange($(this).attr('id').substring(2));
+ });
+ $('a.hide-propose-change').live("click", function(event) {
+ event.preventDefault();
+ hideProposeChange($(this).attr('id').substring(2));
+ });
+ $('a.accept-comment').live("click", function(event) {
+ event.preventDefault();
+ acceptComment($(this).attr('id').substring(2));
+ });
+ $('a.delete-comment').live("click", function(event) {
+ event.preventDefault();
+ deleteComment($(this).attr('id').substring(2));
+ });
+ $('a.comment-markup').live("click", function(event) {
+ event.preventDefault();
+ toggleCommentMarkupBox($(this).attr('id').substring(2));
+ });
+ }
+
+ /**
+ * Set comp, which is a comparator function used for sorting and
+ * inserting comments into the list.
+ */
+ function setComparator() {
+ // If the first three letters are "asc", sort in ascending order
+ // and remove the prefix.
+ if (by.substring(0,3) == 'asc') {
+ var i = by.substring(3);
+ comp = function(a, b) { return a[i] - b[i]; };
+ } else {
+ // Otherwise sort in descending order.
+ comp = function(a, b) { return b[by] - a[by]; };
+ }
+
+ // Reset link styles and format the selected sort option.
+ $('a.sel').attr('href', '#').removeClass('sel');
+ $('a.by' + by).removeAttr('href').addClass('sel');
+ }
+
+ /**
+ * Create a comp function. If the user has preferences stored in
+ * the sortBy cookie, use those, otherwise use the default.
+ */
+ function initComparator() {
+ by = 'rating'; // Default to sort by rating.
+ // If the sortBy cookie is set, use that instead.
+ if (document.cookie.length > 0) {
+ var start = document.cookie.indexOf('sortBy=');
+ if (start != -1) {
+ start = start + 7;
+ var end = document.cookie.indexOf(";", start);
+ if (end == -1) {
+ end = document.cookie.length;
+ by = unescape(document.cookie.substring(start, end));
+ }
+ }
+ }
+ setComparator();
+ }
+
+ /**
+ * Show a comment div.
+ */
+ function show(id) {
+ $('#ao' + id).hide();
+ $('#ah' + id).show();
+ var context = $.extend({id: id}, opts);
+ var popup = $(renderTemplate(popupTemplate, context)).hide();
+ popup.find('textarea[name="proposal"]').hide();
+ popup.find('a.by' + by).addClass('sel');
+ var form = popup.find('#cf' + id);
+ form.submit(function(event) {
+ event.preventDefault();
+ addComment(form);
+ });
+ $('#s' + id).after(popup);
+ popup.slideDown('fast', function() {
+ getComments(id);
+ });
+ }
+
+ /**
+ * Hide a comment div.
+ */
+ function hide(id) {
+ $('#ah' + id).hide();
+ $('#ao' + id).show();
+ var div = $('#sc' + id);
+ div.slideUp('fast', function() {
+ div.remove();
+ });
+ }
+
+ /**
+ * Perform an ajax request to get comments for a node
+ * and insert the comments into the comments tree.
+ */
+ function getComments(id) {
+ $.ajax({
+ type: 'GET',
+ url: opts.getCommentsURL,
+ data: {node: id},
+ success: function(data, textStatus, request) {
+ var ul = $('#cl' + id);
+ var speed = 100;
+ $('#cf' + id)
+ .find('textarea[name="proposal"]')
+ .data('source', data.source);
+
+ if (data.comments.length === 0) {
+ ul.html('<li>No comments yet.</li>');
+ ul.data('empty', true);
+ } else {
+ // If there are comments, sort them and put them in the list.
+ var comments = sortComments(data.comments);
+ speed = data.comments.length * 100;
+ appendComments(comments, ul);
+ ul.data('empty', false);
+ }
+ $('#cn' + id).slideUp(speed + 200);
+ ul.slideDown(speed);
+ },
+ error: function(request, textStatus, error) {
+ showError('Oops, there was a problem retrieving the comments.');
+ },
+ dataType: 'json'
+ });
+ }
+
+ /**
+ * Add a comment via ajax and insert the comment into the comment tree.
+ */
+ function addComment(form) {
+ var node_id = form.find('input[name="node"]').val();
+ var parent_id = form.find('input[name="parent"]').val();
+ var text = form.find('textarea[name="comment"]').val();
+ var proposal = form.find('textarea[name="proposal"]').val();
+
+ if (text == '') {
+ showError('Please enter a comment.');
+ return;
+ }
+
+ // Disable the form that is being submitted.
+ form.find('textarea,input').attr('disabled', 'disabled');
+
+ // Send the comment to the server.
+ $.ajax({
+ type: "POST",
+ url: opts.addCommentURL,
+ dataType: 'json',
+ data: {
+ node: node_id,
+ parent: parent_id,
+ text: text,
+ proposal: proposal
+ },
+ success: function(data, textStatus, error) {
+ // Reset the form.
+ if (node_id) {
+ hideProposeChange(node_id);
+ }
+ form.find('textarea')
+ .val('')
+ .add(form.find('input'))
+ .removeAttr('disabled');
+ var ul = $('#cl' + (node_id || parent_id));
+ if (ul.data('empty')) {
+ $(ul).empty();
+ ul.data('empty', false);
+ }
+ insertComment(data.comment);
+ var ao = $('#ao' + node_id);
+ ao.find('img').attr({'src': opts.commentBrightImage});
+ if (node_id) {
+ // if this was a "root" comment, remove the commenting box
+ // (the user can get it back by reopening the comment popup)
+ $('#ca' + node_id).slideUp();
+ }
+ },
+ error: function(request, textStatus, error) {
+ form.find('textarea,input').removeAttr('disabled');
+ showError('Oops, there was a problem adding the comment.');
+ }
+ });
+ }
+
+ /**
+ * Recursively append comments to the main comment list and children
+ * lists, creating the comment tree.
+ */
+ function appendComments(comments, ul) {
+ $.each(comments, function() {
+ var div = createCommentDiv(this);
+ ul.append($(document.createElement('li')).html(div));
+ appendComments(this.children, div.find('ul.comment-children'));
+ // To avoid stagnating data, don't store the comments children in data.
+ this.children = null;
+ div.data('comment', this);
+ });
+ }
+
+ /**
+ * After adding a new comment, it must be inserted in the correct
+ * location in the comment tree.
+ */
+ function insertComment(comment) {
+ var div = createCommentDiv(comment);
+
+ // To avoid stagnating data, don't store the comments children in data.
+ comment.children = null;
+ div.data('comment', comment);
+
+ var ul = $('#cl' + (comment.node || comment.parent));
+ var siblings = getChildren(ul);
+
+ var li = $(document.createElement('li'));
+ li.hide();
+
+ // Determine where in the parents children list to insert this comment.
+ for(i=0; i < siblings.length; i++) {
+ if (comp(comment, siblings[i]) <= 0) {
+ $('#cd' + siblings[i].id)
+ .parent()
+ .before(li.html(div));
+ li.slideDown('fast');
+ return;
+ }
+ }
+
+ // If we get here, this comment rates lower than all the others,
+ // or it is the only comment in the list.
+ ul.append(li.html(div));
+ li.slideDown('fast');
+ }
+
+ function acceptComment(id) {
+ $.ajax({
+ type: 'POST',
+ url: opts.acceptCommentURL,
+ data: {id: id},
+ success: function(data, textStatus, request) {
+ $('#cm' + id).fadeOut('fast');
+ $('#cd' + id).removeClass('moderate');
+ },
+ error: function(request, textStatus, error) {
+ showError('Oops, there was a problem accepting the comment.');
+ }
+ });
+ }
+
+ function deleteComment(id) {
+ $.ajax({
+ type: 'POST',
+ url: opts.deleteCommentURL,
+ data: {id: id},
+ success: function(data, textStatus, request) {
+ var div = $('#cd' + id);
+ if (data == 'delete') {
+ // Moderator mode: remove the comment and all children immediately
+ div.slideUp('fast', function() {
+ div.remove();
+ });
+ return;
+ }
+ // User mode: only mark the comment as deleted
+ div
+ .find('span.user-id:first')
+ .text('[deleted]').end()
+ .find('div.comment-text:first')
+ .text('[deleted]').end()
+ .find('#cm' + id + ', #dc' + id + ', #ac' + id + ', #rc' + id +
+ ', #sp' + id + ', #hp' + id + ', #cr' + id + ', #rl' + id)
+ .remove();
+ var comment = div.data('comment');
+ comment.username = '[deleted]';
+ comment.text = '[deleted]';
+ div.data('comment', comment);
+ },
+ error: function(request, textStatus, error) {
+ showError('Oops, there was a problem deleting the comment.');
+ }
+ });
+ }
+
+ function showProposal(id) {
+ $('#sp' + id).hide();
+ $('#hp' + id).show();
+ $('#pr' + id).slideDown('fast');
+ }
+
+ function hideProposal(id) {
+ $('#hp' + id).hide();
+ $('#sp' + id).show();
+ $('#pr' + id).slideUp('fast');
+ }
+
+ function showProposeChange(id) {
+ $('#pc' + id).hide();
+ $('#hc' + id).show();
+ var textarea = $('#pt' + id);
+ textarea.val(textarea.data('source'));
+ $.fn.autogrow.resize(textarea[0]);
+ textarea.slideDown('fast');
+ }
+
+ function hideProposeChange(id) {
+ $('#hc' + id).hide();
+ $('#pc' + id).show();
+ var textarea = $('#pt' + id);
+ textarea.val('').removeAttr('disabled');
+ textarea.slideUp('fast');
+ }
+
+ function toggleCommentMarkupBox(id) {
+ $('#mb' + id).toggle();
+ }
+
+ /** Handle when the user clicks on a sort by link. */
+ function handleReSort(link) {
+ var classes = link.attr('class').split(/\s+/);
+ for (var i=0; i<classes.length; i++) {
+ if (classes[i] != 'sort-option') {
+ by = classes[i].substring(2);
+ }
+ }
+ setComparator();
+ // Save/update the sortBy cookie.
+ var expiration = new Date();
+ expiration.setDate(expiration.getDate() + 365);
+ document.cookie= 'sortBy=' + escape(by) +
+ ';expires=' + expiration.toUTCString();
+ $('ul.comment-ul').each(function(index, ul) {
+ var comments = getChildren($(ul), true);
+ comments = sortComments(comments);
+ appendComments(comments, $(ul).empty());
+ });
+ }
+
+ /**
+ * Function to process a vote when a user clicks an arrow.
+ */
+ function handleVote(link) {
+ if (!opts.voting) {
+ showError("You'll need to login to vote.");
+ return;
+ }
+
+ var id = link.attr('id');
+ if (!id) {
+ // Didn't click on one of the voting arrows.
+ return;
+ }
+ // If it is an unvote, the new vote value is 0,
+ // Otherwise it's 1 for an upvote, or -1 for a downvote.
+ var value = 0;
+ if (id.charAt(1) != 'u') {
+ value = id.charAt(0) == 'u' ? 1 : -1;
+ }
+ // The data to be sent to the server.
+ var d = {
+ comment_id: id.substring(2),
+ value: value
+ };
+
+ // Swap the vote and unvote links.
+ link.hide();
+ $('#' + id.charAt(0) + (id.charAt(1) == 'u' ? 'v' : 'u') + d.comment_id)
+ .show();
+
+ // The div the comment is displayed in.
+ var div = $('div#cd' + d.comment_id);
+ var data = div.data('comment');
+
+ // If this is not an unvote, and the other vote arrow has
+ // already been pressed, unpress it.
+ if ((d.value !== 0) && (data.vote === d.value * -1)) {
+ $('#' + (d.value == 1 ? 'd' : 'u') + 'u' + d.comment_id).hide();
+ $('#' + (d.value == 1 ? 'd' : 'u') + 'v' + d.comment_id).show();
+ }
+
+ // Update the comments rating in the local data.
+ data.rating += (data.vote === 0) ? d.value : (d.value - data.vote);
+ data.vote = d.value;
+ div.data('comment', data);
+
+ // Change the rating text.
+ div.find('.rating:first')
+ .text(data.rating + ' point' + (data.rating == 1 ? '' : 's'));
+
+ // Send the vote information to the server.
+ $.ajax({
+ type: "POST",
+ url: opts.processVoteURL,
+ data: d,
+ error: function(request, textStatus, error) {
+ showError('Oops, there was a problem casting that vote.');
+ }
+ });
+ }
+
+ /**
+ * Open a reply form used to reply to an existing comment.
+ */
+ function openReply(id) {
+ // Swap out the reply link for the hide link
+ $('#rl' + id).hide();
+ $('#cr' + id).show();
+
+ // Add the reply li to the children ul.
+ var div = $(renderTemplate(replyTemplate, {id: id})).hide();
+ $('#cl' + id)
+ .prepend(div)
+ // Setup the submit handler for the reply form.
+ .find('#rf' + id)
+ .submit(function(event) {
+ event.preventDefault();
+ addComment($('#rf' + id));
+ closeReply(id);
+ })
+ .find('input[type=button]')
+ .click(function() {
+ closeReply(id);
+ });
+ div.slideDown('fast', function() {
+ $('#rf' + id).find('textarea').focus();
+ });
+ }
+
+ /**
+ * Close the reply form opened with openReply.
+ */
+ function closeReply(id) {
+ // Remove the reply div from the DOM.
+ $('#rd' + id).slideUp('fast', function() {
+ $(this).remove();
+ });
+
+ // Swap out the hide link for the reply link
+ $('#cr' + id).hide();
+ $('#rl' + id).show();
+ }
+
+ /**
+ * Recursively sort a tree of comments using the comp comparator.
+ */
+ function sortComments(comments) {
+ comments.sort(comp);
+ $.each(comments, function() {
+ this.children = sortComments(this.children);
+ });
+ return comments;
+ }
+
+ /**
+ * Get the children comments from a ul. If recursive is true,
+ * recursively include childrens' children.
+ */
+ function getChildren(ul, recursive) {
+ var children = [];
+ ul.children().children("[id^='cd']")
+ .each(function() {
+ var comment = $(this).data('comment');
+ if (recursive)
+ comment.children = getChildren($(this).find('#cl' + comment.id), true);
+ children.push(comment);
+ });
+ return children;
+ }
+
+ /** Create a div to display a comment in. */
+ function createCommentDiv(comment) {
+ if (!comment.displayed && !opts.moderator) {
+ return $('<div class="moderate">Thank you! Your comment will show up '
+ + 'once it is has been approved by a moderator.</div>');
+ }
+ // Prettify the comment rating.
+ comment.pretty_rating = comment.rating + ' point' +
+ (comment.rating == 1 ? '' : 's');
+ // Make a class (for displaying not yet moderated comments differently)
+ comment.css_class = comment.displayed ? '' : ' moderate';
+ // Create a div for this comment.
+ var context = $.extend({}, opts, comment);
+ var div = $(renderTemplate(commentTemplate, context));
+
+ // If the user has voted on this comment, highlight the correct arrow.
+ if (comment.vote) {
+ var direction = (comment.vote == 1) ? 'u' : 'd';
+ div.find('#' + direction + 'v' + comment.id).hide();
+ div.find('#' + direction + 'u' + comment.id).show();
+ }
+
+ if (opts.moderator || comment.text != '[deleted]') {
+ div.find('a.reply').show();
+ if (comment.proposal_diff)
+ div.find('#sp' + comment.id).show();
+ if (opts.moderator && !comment.displayed)
+ div.find('#cm' + comment.id).show();
+ if (opts.moderator || (opts.username == comment.username))
+ div.find('#dc' + comment.id).show();
+ }
+ return div;
+ }
+
+ /**
+ * A simple template renderer. Placeholders such as <%id%> are replaced
+ * by context['id'] with items being escaped. Placeholders such as <#id#>
+ * are not escaped.
+ */
+ function renderTemplate(template, context) {
+ var esc = $(document.createElement('div'));
+
+ function handle(ph, escape) {
+ var cur = context;
+ $.each(ph.split('.'), function() {
+ cur = cur[this];
+ });
+ return escape ? esc.text(cur || "").html() : cur;
+ }
+
+ return template.replace(/<([%#])([\w\.]*)\1>/g, function() {
+ return handle(arguments[2], arguments[1] == '%' ? true : false);
+ });
+ }
+
+ /** Flash an error message briefly. */
+ function showError(message) {
+ $(document.createElement('div')).attr({'class': 'popup-error'})
+ .append($(document.createElement('div'))
+ .attr({'class': 'error-message'}).text(message))
+ .appendTo('body')
+ .fadeIn("slow")
+ .delay(2000)
+ .fadeOut("slow");
+ }
+
+ /** Add a link the user uses to open the comments popup. */
+ $.fn.comment = function() {
+ return this.each(function() {
+ var id = $(this).attr('id').substring(1);
+ var count = COMMENT_METADATA[id];
+ var title = count + ' comment' + (count == 1 ? '' : 's');
+ var image = count > 0 ? opts.commentBrightImage : opts.commentImage;
+ var addcls = count == 0 ? ' nocomment' : '';
+ $(this)
+ .append(
+ $(document.createElement('a')).attr({
+ href: '#',
+ 'class': 'sphinx-comment-open' + addcls,
+ id: 'ao' + id
+ })
+ .append($(document.createElement('img')).attr({
+ src: image,
+ alt: 'comment',
+ title: title
+ }))
+ .click(function(event) {
+ event.preventDefault();
+ show($(this).attr('id').substring(2));
+ })
+ )
+ .append(
+ $(document.createElement('a')).attr({
+ href: '#',
+ 'class': 'sphinx-comment-close hidden',
+ id: 'ah' + id
+ })
+ .append($(document.createElement('img')).attr({
+ src: opts.closeCommentImage,
+ alt: 'close',
+ title: 'close'
+ }))
+ .click(function(event) {
+ event.preventDefault();
+ hide($(this).attr('id').substring(2));
+ })
+ );
+ });
+ };
+
+ var opts = {
+ processVoteURL: '/_process_vote',
+ addCommentURL: '/_add_comment',
+ getCommentsURL: '/_get_comments',
+ acceptCommentURL: '/_accept_comment',
+ deleteCommentURL: '/_delete_comment',
+ commentImage: '/static/_static/comment.png',
+ closeCommentImage: '/static/_static/comment-close.png',
+ loadingImage: '/static/_static/ajax-loader.gif',
+ commentBrightImage: '/static/_static/comment-bright.png',
+ upArrow: '/static/_static/up.png',
+ downArrow: '/static/_static/down.png',
+ upArrowPressed: '/static/_static/up-pressed.png',
+ downArrowPressed: '/static/_static/down-pressed.png',
+ voting: false,
+ moderator: false
+ };
+
+ if (typeof COMMENT_OPTIONS != "undefined") {
+ opts = jQuery.extend(opts, COMMENT_OPTIONS);
+ }
+
+ var popupTemplate = '\
+ <div class="sphinx-comments" id="sc<%id%>">\
+ <p class="sort-options">\
+ Sort by:\
+ <a href="#" class="sort-option byrating">best rated</a>\
+ <a href="#" class="sort-option byascage">newest</a>\
+ <a href="#" class="sort-option byage">oldest</a>\
+ </p>\
+ <div class="comment-header">Comments</div>\
+ <div class="comment-loading" id="cn<%id%>">\
+ loading comments... <img src="<%loadingImage%>" alt="" /></div>\
+ <ul id="cl<%id%>" class="comment-ul"></ul>\
+ <div id="ca<%id%>">\
+ <p class="add-a-comment">Add a comment\
+ (<a href="#" class="comment-markup" id="ab<%id%>">markup</a>):</p>\
+ <div class="comment-markup-box" id="mb<%id%>">\
+ reStructured text markup: <i>*emph*</i>, <b>**strong**</b>, \
+ <tt>``code``</tt>, \
+ code blocks: <tt>::</tt> and an indented block after blank line</div>\
+ <form method="post" id="cf<%id%>" class="comment-form" action="">\
+ <textarea name="comment" cols="80"></textarea>\
+ <p class="propose-button">\
+ <a href="#" id="pc<%id%>" class="show-propose-change">\
+ Propose a change ▹\
+ </a>\
+ <a href="#" id="hc<%id%>" class="hide-propose-change">\
+ Propose a change ▿\
+ </a>\
+ </p>\
+ <textarea name="proposal" id="pt<%id%>" cols="80"\
+ spellcheck="false"></textarea>\
+ <input type="submit" value="Add comment" />\
+ <input type="hidden" name="node" value="<%id%>" />\
+ <input type="hidden" name="parent" value="" />\
+ </form>\
+ </div>\
+ </div>';
+
+ var commentTemplate = '\
+ <div id="cd<%id%>" class="sphinx-comment<%css_class%>">\
+ <div class="vote">\
+ <div class="arrow">\
+ <a href="#" id="uv<%id%>" class="vote" title="vote up">\
+ <img src="<%upArrow%>" />\
+ </a>\
+ <a href="#" id="uu<%id%>" class="un vote" title="vote up">\
+ <img src="<%upArrowPressed%>" />\
+ </a>\
+ </div>\
+ <div class="arrow">\
+ <a href="#" id="dv<%id%>" class="vote" title="vote down">\
+ <img src="<%downArrow%>" id="da<%id%>" />\
+ </a>\
+ <a href="#" id="du<%id%>" class="un vote" title="vote down">\
+ <img src="<%downArrowPressed%>" />\
+ </a>\
+ </div>\
+ </div>\
+ <div class="comment-content">\
+ <p class="tagline comment">\
+ <span class="user-id"><%username%></span>\
+ <span class="rating"><%pretty_rating%></span>\
+ <span class="delta"><%time.delta%></span>\
+ </p>\
+ <div class="comment-text comment"><#text#></div>\
+ <p class="comment-opts comment">\
+ <a href="#" class="reply hidden" id="rl<%id%>">reply ▹</a>\
+ <a href="#" class="close-reply" id="cr<%id%>">reply ▿</a>\
+ <a href="#" id="sp<%id%>" class="show-proposal">proposal ▹</a>\
+ <a href="#" id="hp<%id%>" class="hide-proposal">proposal ▿</a>\
+ <a href="#" id="dc<%id%>" class="delete-comment hidden">delete</a>\
+ <span id="cm<%id%>" class="moderation hidden">\
+ <a href="#" id="ac<%id%>" class="accept-comment">accept</a>\
+ </span>\
+ </p>\
+ <pre class="proposal" id="pr<%id%>">\
+<#proposal_diff#>\
+ </pre>\
+ <ul class="comment-children" id="cl<%id%>"></ul>\
+ </div>\
+ <div class="clearleft"></div>\
+ </div>\
+ </div>';
+
+ var replyTemplate = '\
+ <li>\
+ <div class="reply-div" id="rd<%id%>">\
+ <form id="rf<%id%>">\
+ <textarea name="comment" cols="80"></textarea>\
+ <input type="submit" value="Add reply" />\
+ <input type="button" value="Cancel" />\
+ <input type="hidden" name="parent" value="<%id%>" />\
+ <input type="hidden" name="node" value="" />\
+ </form>\
+ </div>\
+ </li>';
+
+ $(document).ready(function() {
+ init();
+ });
+})(jQuery);
+
+$(document).ready(function() {
+ // add comment anchors for all paragraphs that are commentable
+ $('.sphinx-has-comment').comment();
+
+ // highlight search words in search results
+ $("div.context").each(function() {
+ var params = $.getQueryParameters();
+ var terms = (params.q) ? params.q[0].split(/\s+/) : [];
+ var result = $(this);
+ $.each(terms, function() {
+ result.highlightText(this.toLowerCase(), 'highlighted');
+ });
+ });
+
+ // directly open comment window if requested
+ var anchor = document.location.hash;
+ if (anchor.substring(0, 9) == '#comment-') {
+ $('#ao' + anchor.substring(9)).click();
+ document.location.hash = '#s' + anchor.substring(9);
+ }
+});
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diff --git a/doc/plasmodium_RNA-seq/qualimapReport.html b/doc/plasmodium_RNA-seq/qualimapReport.html
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index 0000000..cf9cda6
--- /dev/null
+++ b/doc/plasmodium_RNA-seq/qualimapReport.html
@@ -0,0 +1,484 @@
+<!DOCTYPE HTML>
+<html>
+ <head>
+ <link rel="stylesheet" href="_static/agogo.css" type="text/css" />
+ <link rel="stylesheet" href="_static/report.css" type="text/css" />
+ <title>Qualimap report: Genomic analysis</title>
+
+ </head>
+<body>
+ <div class="header-wrapper">
+ <div class="header">
+ <p class="logo"><a href="http://qualimap.bioinfo.cipf.es/">
+ <img class="logo" src="_static/qualimap_logo_small.png" alt="Logo"/>
+ </a></p>
+<div class="headertitle"><a href="">Qualimap Report</a></div>
+ </div>
+</div>
+
+<div class="content-wrapper">
+<div class="content">
+<div class="document">
+<div class="documentwrapper">
+<div class="bodywrapper">
+<div class="body">
+<div class=section>
+<h2>Summary<a class="headerlink" name="summary" title="Permalink to this headline"> </a></h2>
+<div class=summary>
+
+
+<div class=table-summary>
+<h3>Globals</h3>
+<table class="summary hovertable">
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Reference size</td>
+<td class=column2>23,299,734</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Number of selected regions</td>
+<td class=column2>5,452</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Size/percentage of selected regions</td>
+<td class=column2>13,711,554/58.85%</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Size/percentage of non-selected regions</td>
+<td class=column2>9,588,180/41.15%</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Number of reads</td>
+<td class=column2>8,386,304</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Number/percentage of mapped reads</td>
+<td class=column2>5,830,399 / 69.52%</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Number/percentage of mapped reads inside of regions</td>
+<td class=column2>4,552,567 / 78.08%</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Number/percentage of mapped reads outside of regions</td>
+<td class=column2>1,277,832 / 21.92%</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Number/percentage of unmapped reads</td>
+<td class=column2>2,555,905/30.48%</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Number/percentage of paired reads</td>
+<td class=column2>5,830,399/69.52%</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Number/percentage of reads both mates paired</td>
+<td class=column2>5,245,862/62.55%</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Number/percentage of singletons</td>
+<td class=column2>584,537/6.97%</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Read min/max/mean size</td>
+<td class=column2>12/54/49.65</td>
+</tr>
+</table>
+</div>
+
+
+<div class=table-summary>
+<h3>ACGT Content (inside of regions)</h3>
+<table class="summary hovertable">
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Number/percentage of A's</td>
+<td class=column2>77,753,463 / 36.36%</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Number/percentage of C's</td>
+<td class=column2>29,164,712 / 13.64%</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Number/percentage of T's</td>
+<td class=column2>77,522,187 / 36.25%</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Number/percentage of G's</td>
+<td class=column2>29,430,157 / 13.76%</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Number/percentage of N's</td>
+<td class=column2>0 / 0%</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>GC Percentage</td>
+<td class=column2>27.4%</td>
+</tr>
+</table>
+</div>
+
+
+<div class=table-summary>
+<h3>Coverage (inside of regions)</h3>
+<table class="summary hovertable">
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Mean</td>
+<td class=column2>15.6</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Standard Deviation</td>
+<td class=column2>138.99</td>
+</tr>
+</table>
+</div>
+
+
+<div class=table-summary>
+<h3>Mapping Quality (inside of regions)</h3>
+<table class="summary hovertable">
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Mean Mapping Quality</td>
+<td class=column2>42.21</td>
+</tr>
+</table>
+</div>
+
+
+<div class=table-summary>
+<h3>Insert size (inside of regions)</h3>
+<table class="summary hovertable">
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Mean</td>
+<td class=column2>81.77</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Median Estimation</td>
+<td class=column2>1</td>
+</tr>
+</table>
+</div>
+
+
+<div class=table-summary>
+<h3>Per chromosome statistics (inside of regions)</h3>
+<table class="summary hovertable">
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td><b>Name</b></td>
+<td><b>Length</b></td>
+<td><b>Mapped bases</b></td>
+<td><b>Mean coverage</b></td>
+<td><b>Standard deviation</b></td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>MAL1</td>
+<td>643292</td>
+<td>11465909</td>
+<td>35.84</td>
+<td>327.59</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>MAL10</td>
+<td>1687655</td>
+<td>15828953</td>
+<td>16.49</td>
+<td>81.73</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>MAL11</td>
+<td>2038337</td>
+<td>21220199</td>
+<td>17.51</td>
+<td>144.81</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>MAL12</td>
+<td>2271477</td>
+<td>20585179</td>
+<td>15.28</td>
+<td>52.69</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>MAL13</td>
+<td>2895605</td>
+<td>20438366</td>
+<td>11.57</td>
+<td>42.22</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>MAL14</td>
+<td>3291871</td>
+<td>34105226</td>
+<td>16.99</td>
+<td>219.82</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>MAL2</td>
+<td>947102</td>
+<td>10643889</td>
+<td>20.19</td>
+<td>106.42</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>MAL3</td>
+<td>1060087</td>
+<td>5228770</td>
+<td>8.02</td>
+<td>33.63</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>MAL4</td>
+<td>1204112</td>
+<td>4465238</td>
+<td>6.17</td>
+<td>23.84</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>MAL5</td>
+<td>1343552</td>
+<td>16960522</td>
+<td>20.78</td>
+<td>188.54</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>MAL6</td>
+<td>1418244</td>
+<td>12802513</td>
+<td>15.28</td>
+<td>93.51</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>MAL7</td>
+<td>1501717</td>
+<td>12943630</td>
+<td>14.02</td>
+<td>216.97</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>MAL8</td>
+<td>1419563</td>
+<td>9208669</td>
+<td>10.91</td>
+<td>65.71</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>MAL9</td>
+<td>1541723</td>
+<td>17973456</td>
+<td>19.81</td>
+<td>66</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>PF_apicoplast_genome_1</td>
+<td>29430</td>
+<td>0</td>
+<td>0</td>
+<td>0</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>Pf_mito</td>
+<td>5967</td>
+<td>0</td>
+<td>0</td>
+<td>0</td>
+</tr>
+</table>
+</div>
+
+</div>
+</div> <!-- summary section -->
+
+<div class=section>
+<h2>Input data and parameters<a class="headerlink" name="input" title="Permalink to this headline"> </a></h2>
+<div class=summary>
+
+
+<div class=table-summary>
+<h3>Alignment</h3>
+<table class="summary hovertable">
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>BAM file: </td>
+<td class=column2>/home/fgarcia/qualimapLatestBuild/dataRelease/genomics/Plasmodium-falciparum-3D7_RNASeq.bam</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Number of windows: </td>
+<td class=column2>400</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Analysis date: </td>
+<td class=column2>Tue Apr 24 19:45:34 CEST 2012</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Draw chromosome limits: </td>
+<td class=column2>yes
+</td>
+</tr>
+</table>
+</div>
+
+
+<div class=table-summary>
+<h3>GFF region</h3>
+<table class="summary hovertable">
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>GFF file: </td>
+<td class=column2>/home/fgarcia/qualimapLatestBuild/dataRelease/annotations/Plasmodium-falciparum-3D7.gff</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Outside statistics: </td>
+<td class=column2>yes
+</td>
+</tr>
+</table>
+</div>
+
+</div>
+</div> <!-- summary section -->
+
+
+
+<div class=section>
+
+<h2>Coverage across reference<a class="headerlink" name="genome_coverage_across_reference.png" title="Permalink to this headline"> </a></h2>
+
+<div><img width=100% src="genome_coverage_across_reference.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>Coverage Histogram<a class="headerlink" name="genome_coverage_histogram.png" title="Permalink to this headline"> </a></h2>
+
+<div><img width=100% src="genome_coverage_histogram.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>Coverage Histogram (0-50X)<a class="headerlink" name="genome_coverage_0to50_histogram.png" title="Permalink to this headline"> </a></h2>
+
+<div><img width=100% src="genome_coverage_0to50_histogram.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>Duplication Rate Histogram<a class="headerlink" name="genome_uniq_read_starts_histogram.png" title="Permalink to this headline"> </a></h2>
+
+<div><img width=100% src="genome_uniq_read_starts_histogram.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>Genome Fraction Coverage<a class="headerlink" name="genome_coverage_quotes.png" title="Permalink to this headline"> </a></h2>
+
+<div><img width=100% src="genome_coverage_quotes.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>Mapped Reads Nucleotide Content<a class="headerlink" name="genome_reads_content_per_read_position.png" title="Permalink to this headline"> </a></h2>
+
+<div><img width=100% src="genome_reads_content_per_read_position.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>Mapped Reads GC-content Distribution<a class="headerlink" name="genome_gc_content_per_window.png" title="Permalink to this headline"> </a></h2>
+
+<div><img width=100% src="genome_gc_content_per_window.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>Mapping Quality Across Reference<a class="headerlink" name="genome_mapping_quality_across_reference.png" title="Permalink to this headline"> </a></h2>
+
+<div><img width=100% src="genome_mapping_quality_across_reference.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>Mapping Quality Histogram<a class="headerlink" name="genome_mapping_quality_histogram.png" title="Permalink to this headline"> </a></h2>
+
+<div><img width=100% src="genome_mapping_quality_histogram.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>Insert Size Across Reference<a class="headerlink" name="genome_insert_size_across_reference.png" title="Permalink to this headline"> </a></h2>
+
+<div><img width=100% src="genome_insert_size_across_reference.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>Insert Size Histogram<a class="headerlink" name="genome_insert_size_histogram.png" title="Permalink to this headline"> </a></h2>
+
+<div><img width=100% src="genome_insert_size_histogram.png"></div>
+
+</div><!-- graph section -->
+
+
+</div>
+
+</div>
+
+</div>
+
+</div>
+
+
+<div class="sidebar">
+<h3>Contents</h3>
+<li class="toctree-l1"><a class="reference internal" href="#summary">Summary</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#input">Input data & parameters</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#genome_coverage_across_reference.png">Coverage across reference</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#genome_coverage_histogram.png">Coverage Histogram</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#genome_coverage_0to50_histogram.png">Coverage Histogram (0-50X)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#genome_uniq_read_starts_histogram.png">Duplication Rate Histogram</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#genome_coverage_quotes.png">Genome Fraction Coverage</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#genome_reads_content_per_read_position.png">Mapped Reads Nucleotide Content</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#genome_gc_content_per_window.png">Mapped Reads GC-content Distribution</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#genome_mapping_quality_across_reference.png">Mapping Quality Across Reference</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#genome_mapping_quality_histogram.png">Mapping Quality Histogram</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#genome_insert_size_across_reference.png">Insert Size Across Reference</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#genome_insert_size_histogram.png">Insert Size Histogram</a></li>
+</div> <!-- sidebar -->
+
+<div class="clearer"></div>
+</div>
+
+</div>
+
+
+<div class="footer-wrapper">
+<div class="footer">
+<div class="left">
+<div class="footer">
+2012/04/24 19:46:00
+</div>
+</div>
+<div class="right">
+<div class="footer">
+Generated by QualiMap
+</div
+</div>
+<div class="clearer"></div>
+</div> <!-- footer -->
+</div>
+</body>
diff --git a/doc/plasmodium_RNA-seq/qualimapReportOutsideOfRegions.html b/doc/plasmodium_RNA-seq/qualimapReportOutsideOfRegions.html
new file mode 100644
index 0000000..387a436
--- /dev/null
+++ b/doc/plasmodium_RNA-seq/qualimapReportOutsideOfRegions.html
@@ -0,0 +1,484 @@
+<!DOCTYPE HTML>
+<html>
+ <head>
+ <link rel="stylesheet" href="_static/agogo.css" type="text/css" />
+ <link rel="stylesheet" href="_static/report.css" type="text/css" />
+ <title>Qualimap report: Genomic analysis</title>
+
+ </head>
+<body>
+ <div class="header-wrapper">
+ <div class="header">
+ <p class="logo"><a href="http://qualimap.bioinfo.cipf.es/">
+ <img class="logo" src="_static/qualimap_logo_small.png" alt="Logo"/>
+ </a></p>
+<div class="headertitle"><a href="">Qualimap Report</a></div>
+ </div>
+</div>
+
+<div class="content-wrapper">
+<div class="content">
+<div class="document">
+<div class="documentwrapper">
+<div class="bodywrapper">
+<div class="body">
+<div class=section>
+<h2>Summary<a class="headerlink" name="summary" title="Permalink to this headline"> </a></h2>
+<div class=summary>
+
+
+<div class=table-summary>
+<h3>Globals</h3>
+<table class="summary hovertable">
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Reference size</td>
+<td class=column2>23,299,734</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Number of selected regions</td>
+<td class=column2>5,452</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Size/percentage of selected regions</td>
+<td class=column2>13,711,554/58.85%</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Size/percentage of non-selected regions</td>
+<td class=column2>9,588,180/41.15%</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Number of reads</td>
+<td class=column2>8,386,304</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Number/percentage of mapped reads</td>
+<td class=column2>5,830,399 / 69.52%</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Number/percentage of mapped reads inside of regions</td>
+<td class=column2>4,552,567 / 78.08%</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Number/percentage of mapped reads outside of regions</td>
+<td class=column2>1,277,832 / 21.92%</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Number/percentage of unmapped reads</td>
+<td class=column2>2,555,905/30.48%</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Number/percentage of paired reads</td>
+<td class=column2>5,830,399/69.52%</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Number/percentage of reads both mates paired</td>
+<td class=column2>5,245,862/62.55%</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Number/percentage of singletons</td>
+<td class=column2>584,537/6.97%</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Read min/max/mean size</td>
+<td class=column2>12/54/49.65</td>
+</tr>
+</table>
+</div>
+
+
+<div class=table-summary>
+<h3>ACGT Content (outside of regions)</h3>
+<table class="summary hovertable">
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Number/percentage of A's</td>
+<td class=column2>25,205,877 / 39.18%</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Number/percentage of C's</td>
+<td class=column2>7,353,985 / 11.43%</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Number/percentage of T's</td>
+<td class=column2>24,391,597 / 37.91%</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Number/percentage of G's</td>
+<td class=column2>7,388,859 / 11.48%</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Number/percentage of N's</td>
+<td class=column2>0 / 0%</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>GC Percentage</td>
+<td class=column2>22.91%</td>
+</tr>
+</table>
+</div>
+
+
+<div class=table-summary>
+<h3>Coverage (outside of regions)</h3>
+<table class="summary hovertable">
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Mean</td>
+<td class=column2>4.69</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Standard Deviation</td>
+<td class=column2>66.74</td>
+</tr>
+</table>
+</div>
+
+
+<div class=table-summary>
+<h3>Mapping Quality (outside of regions)</h3>
+<table class="summary hovertable">
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Mean Mapping Quality</td>
+<td class=column2>39.26</td>
+</tr>
+</table>
+</div>
+
+
+<div class=table-summary>
+<h3>Insert size (outside of regions)</h3>
+<table class="summary hovertable">
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Mean</td>
+<td class=column2>77.45</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Median Estimation</td>
+<td class=column2>1</td>
+</tr>
+</table>
+</div>
+
+
+<div class=table-summary>
+<h3>Per chromosome statistics (outside of regions)</h3>
+<table class="summary hovertable">
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td><b>Name</b></td>
+<td><b>Length</b></td>
+<td><b>Mapped bases</b></td>
+<td><b>Mean coverage</b></td>
+<td><b>Standard deviation</b></td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>MAL1</td>
+<td>643292</td>
+<td>1861740</td>
+<td>5.71</td>
+<td>55.73</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>MAL10</td>
+<td>1687655</td>
+<td>3184372</td>
+<td>4.37</td>
+<td>80.04</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>MAL11</td>
+<td>2038337</td>
+<td>6143140</td>
+<td>7.43</td>
+<td>172.05</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>MAL12</td>
+<td>2271477</td>
+<td>3572946</td>
+<td>3.87</td>
+<td>22.17</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>MAL13</td>
+<td>2895605</td>
+<td>8636941</td>
+<td>7.65</td>
+<td>35.96</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>MAL14</td>
+<td>3291871</td>
+<td>5548109</td>
+<td>4.32</td>
+<td>80.87</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>MAL2</td>
+<td>947102</td>
+<td>1410652</td>
+<td>3.36</td>
+<td>24.23</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>MAL3</td>
+<td>1060087</td>
+<td>3858930</td>
+<td>8.82</td>
+<td>34.08</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>MAL4</td>
+<td>1204112</td>
+<td>3664145</td>
+<td>7.05</td>
+<td>31.82</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>MAL5</td>
+<td>1343552</td>
+<td>1823439</td>
+<td>3.46</td>
+<td>21.64</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>MAL6</td>
+<td>1418244</td>
+<td>2014202</td>
+<td>3.47</td>
+<td>48.12</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>MAL7</td>
+<td>1501717</td>
+<td>11505051</td>
+<td>18.44</td>
+<td>151.8</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>MAL8</td>
+<td>1419563</td>
+<td>7993675</td>
+<td>13.9</td>
+<td>69.33</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>MAL9</td>
+<td>1541723</td>
+<td>2524665</td>
+<td>3.84</td>
+<td>19.55</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>PF_apicoplast_genome_1</td>
+<td>29430</td>
+<td>296884</td>
+<td>10.09</td>
+<td>29.14</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td>Pf_mito</td>
+<td>5967</td>
+<td>301427</td>
+<td>50.52</td>
+<td>18.52</td>
+</tr>
+</table>
+</div>
+
+</div>
+</div> <!-- summary section -->
+
+<div class=section>
+<h2>Input data and parameters<a class="headerlink" name="input" title="Permalink to this headline"> </a></h2>
+<div class=summary>
+
+
+<div class=table-summary>
+<h3>Alignment</h3>
+<table class="summary hovertable">
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>BAM file: </td>
+<td class=column2>/home/fgarcia/qualimapLatestBuild/dataRelease/genomics/Plasmodium-falciparum-3D7_RNASeq.bam</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Number of windows: </td>
+<td class=column2>400</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Analysis date: </td>
+<td class=column2>Tue Apr 24 19:45:34 CEST 2012</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Draw chromosome limits: </td>
+<td class=column2>yes
+</td>
+</tr>
+</table>
+</div>
+
+
+<div class=table-summary>
+<h3>GFF region</h3>
+<table class="summary hovertable">
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>GFF file: </td>
+<td class=column2>/home/fgarcia/qualimapLatestBuild/dataRelease/annotations/Plasmodium-falciparum-3D7.gff</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Outside statistics: </td>
+<td class=column2>yes
+</td>
+</tr>
+</table>
+</div>
+
+</div>
+</div> <!-- summary section -->
+
+
+
+<div class=section>
+
+<h2>Coverage across reference<a class="headerlink" name="outside_coverage_across_reference.png" title="Permalink to this headline"> </a></h2>
+
+<div><img width=100% src="outside_coverage_across_reference.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>Coverage Histogram<a class="headerlink" name="outside_coverage_histogram.png" title="Permalink to this headline"> </a></h2>
+
+<div><img width=100% src="outside_coverage_histogram.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>Coverage Histogram (0-50X)<a class="headerlink" name="outside_coverage_0to50_histogram.png" title="Permalink to this headline"> </a></h2>
+
+<div><img width=100% src="outside_coverage_0to50_histogram.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>Duplication Rate Histogram<a class="headerlink" name="outside_uniq_read_starts_histogram.png" title="Permalink to this headline"> </a></h2>
+
+<div><img width=100% src="outside_uniq_read_starts_histogram.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>Genome Fraction Coverage<a class="headerlink" name="outside_coverage_quotes.png" title="Permalink to this headline"> </a></h2>
+
+<div><img width=100% src="outside_coverage_quotes.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>Mapped Reads Nucleotide Content<a class="headerlink" name="outside_reads_content_per_read_position.png" title="Permalink to this headline"> </a></h2>
+
+<div><img width=100% src="outside_reads_content_per_read_position.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>Mapped Reads GC-content Distribution<a class="headerlink" name="outside_gc_content_per_window.png" title="Permalink to this headline"> </a></h2>
+
+<div><img width=100% src="outside_gc_content_per_window.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>Mapping Quality Across Reference<a class="headerlink" name="outside_mapping_quality_across_reference.png" title="Permalink to this headline"> </a></h2>
+
+<div><img width=100% src="outside_mapping_quality_across_reference.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>Mapping Quality Histogram<a class="headerlink" name="outside_mapping_quality_histogram.png" title="Permalink to this headline"> </a></h2>
+
+<div><img width=100% src="outside_mapping_quality_histogram.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>Insert Size Across Reference<a class="headerlink" name="outside_insert_size_across_reference.png" title="Permalink to this headline"> </a></h2>
+
+<div><img width=100% src="outside_insert_size_across_reference.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>Insert Size Histogram<a class="headerlink" name="outside_insert_size_histogram.png" title="Permalink to this headline"> </a></h2>
+
+<div><img width=100% src="outside_insert_size_histogram.png"></div>
+
+</div><!-- graph section -->
+
+
+</div>
+
+</div>
+
+</div>
+
+</div>
+
+
+<div class="sidebar">
+<h3>Contents</h3>
+<li class="toctree-l1"><a class="reference internal" href="#summary">Summary</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#input">Input data & parameters</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#outside_coverage_across_reference.png">Coverage across reference</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#outside_coverage_histogram.png">Coverage Histogram</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#outside_coverage_0to50_histogram.png">Coverage Histogram (0-50X)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#outside_uniq_read_starts_histogram.png">Duplication Rate Histogram</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#outside_coverage_quotes.png">Genome Fraction Coverage</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#outside_reads_content_per_read_position.png">Mapped Reads Nucleotide Content</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#outside_gc_content_per_window.png">Mapped Reads GC-content Distribution</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#outside_mapping_quality_across_reference.png">Mapping Quality Across Reference</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#outside_mapping_quality_histogram.png">Mapping Quality Histogram</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#outside_insert_size_across_reference.png">Insert Size Across Reference</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#outside_insert_size_histogram.png">Insert Size Histogram</a></li>
+</div> <!-- sidebar -->
+
+<div class="clearer"></div>
+</div>
+
+</div>
+
+
+<div class="footer-wrapper">
+<div class="footer">
+<div class="left">
+<div class="footer">
+2012/04/24 19:46:02
+</div>
+</div>
+<div class="right">
+<div class="footer">
+Generated by QualiMap
+</div
+</div>
+<div class="clearer"></div>
+</div> <!-- footer -->
+</div>
+</body>
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new file mode 100644
index 0000000..d4619fd
--- /dev/null
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new file mode 100644
index 0000000..7c24308
--- /dev/null
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+/*!
+ * jQuery JavaScript Library v1.4.2
+ * http://jquery.com/
+ *
+ * Copyright 2010, John Resig
+ * Dual licensed under the MIT or GPL Version 2 licenses.
+ * http://jquery.org/license
+ *
+ * Includes Sizzle.js
+ * http://sizzlejs.com/
+ * Copyright 2010, The Dojo Foundation
+ * Released under the MIT, BSD, and GPL Licenses.
+ *
+ * Date: Sat Feb 13 22:33:48 2010 -0500
+ */
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+.highlight .cs { color: #408090; background-color: #fff0f0 } /* Comment.Special */
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+.highlight .gu { color: #800080; font-weight: bold } /* Generic.Subheading */
+.highlight .gt { color: #0040D0 } /* Generic.Traceback */
+.highlight .kc { color: #007020; font-weight: bold } /* Keyword.Constant */
+.highlight .kd { color: #007020; font-weight: bold } /* Keyword.Declaration */
+.highlight .kn { color: #007020; font-weight: bold } /* Keyword.Namespace */
+.highlight .kp { color: #007020 } /* Keyword.Pseudo */
+.highlight .kr { color: #007020; font-weight: bold } /* Keyword.Reserved */
+.highlight .kt { color: #902000 } /* Keyword.Type */
+.highlight .m { color: #208050 } /* Literal.Number */
+.highlight .s { color: #4070a0 } /* Literal.String */
+.highlight .na { color: #4070a0 } /* Name.Attribute */
+.highlight .nb { color: #007020 } /* Name.Builtin */
+.highlight .nc { color: #0e84b5; font-weight: bold } /* Name.Class */
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+.highlight .nd { color: #555555; font-weight: bold } /* Name.Decorator */
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+.highlight .nn { color: #0e84b5; font-weight: bold } /* Name.Namespace */
+.highlight .nt { color: #062873; font-weight: bold } /* Name.Tag */
+.highlight .nv { color: #bb60d5 } /* Name.Variable */
+.highlight .ow { color: #007020; font-weight: bold } /* Operator.Word */
+.highlight .w { color: #bbbbbb } /* Text.Whitespace */
+.highlight .mf { color: #208050 } /* Literal.Number.Float */
+.highlight .mh { color: #208050 } /* Literal.Number.Hex */
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+.highlight .mo { color: #208050 } /* Literal.Number.Oct */
+.highlight .sb { color: #4070a0 } /* Literal.String.Backtick */
+.highlight .sc { color: #4070a0 } /* Literal.String.Char */
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+.highlight .s2 { color: #4070a0 } /* Literal.String.Double */
+.highlight .se { color: #4070a0; font-weight: bold } /* Literal.String.Escape */
+.highlight .sh { color: #4070a0 } /* Literal.String.Heredoc */
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diff --git a/doc/rna-seq-example/_static/qualimap_logo_small.png b/doc/rna-seq-example/_static/qualimap_logo_small.png
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diff --git a/doc/rna-seq-example/_static/report.css b/doc/rna-seq-example/_static/report.css
new file mode 100644
index 0000000..19ae268
--- /dev/null
+++ b/doc/rna-seq-example/_static/report.css
@@ -0,0 +1,50 @@
+div.summary{
+
+}
+
+table.summary{
+
+ border: 0px;
+ width: 100%;
+ vertical-align: top;
+
+}
+
+div.table-summary{
+ margin-left:auto;
+ margin-right:auto;
+ padding-bottom: 20px;
+}
+
+td.column1{
+ width: 60%;
+}
+
+table.hovertable {
+
+ font-size:14px;
+
+ border-width: 1px;
+ border-color: #999999;
+ border-collapse: collapse;
+}
+table.hovertable th {
+ background-color:#FFFFFF;
+ border-width: 1px;
+ padding: 8px;
+ border-style: solid;
+ border-color: #a9c6c9;
+}
+table.hovertable tr {
+ background-color:#FFFFFF;
+}
+table.hovertable td {
+ border-width: 1px;
+ padding: 8px;
+ border-style: solid;
+ border-color: #a9c6c9;
+}
+
+
+
+
diff --git a/doc/rna-seq-example/_static/searchtools.js b/doc/rna-seq-example/_static/searchtools.js
new file mode 100644
index 0000000..663be4c
--- /dev/null
+++ b/doc/rna-seq-example/_static/searchtools.js
@@ -0,0 +1,560 @@
+/*
+ * searchtools.js_t
+ * ~~~~~~~~~~~~~~~~
+ *
+ * Sphinx JavaScript utilties for the full-text search.
+ *
+ * :copyright: Copyright 2007-2011 by the Sphinx team, see AUTHORS.
+ * :license: BSD, see LICENSE for details.
+ *
+ */
+
+/**
+ * helper function to return a node containing the
+ * search summary for a given text. keywords is a list
+ * of stemmed words, hlwords is the list of normal, unstemmed
+ * words. the first one is used to find the occurance, the
+ * latter for highlighting it.
+ */
+
+jQuery.makeSearchSummary = function(text, keywords, hlwords) {
+ var textLower = text.toLowerCase();
+ var start = 0;
+ $.each(keywords, function() {
+ var i = textLower.indexOf(this.toLowerCase());
+ if (i > -1)
+ start = i;
+ });
+ start = Math.max(start - 120, 0);
+ var excerpt = ((start > 0) ? '...' : '') +
+ $.trim(text.substr(start, 240)) +
+ ((start + 240 - text.length) ? '...' : '');
+ var rv = $('<div class="context"></div>').text(excerpt);
+ $.each(hlwords, function() {
+ rv = rv.highlightText(this, 'highlighted');
+ });
+ return rv;
+}
+
+
+/**
+ * Porter Stemmer
+ */
+var Stemmer = function() {
+
+ var step2list = {
+ ational: 'ate',
+ tional: 'tion',
+ enci: 'ence',
+ anci: 'ance',
+ izer: 'ize',
+ bli: 'ble',
+ alli: 'al',
+ entli: 'ent',
+ eli: 'e',
+ ousli: 'ous',
+ ization: 'ize',
+ ation: 'ate',
+ ator: 'ate',
+ alism: 'al',
+ iveness: 'ive',
+ fulness: 'ful',
+ ousness: 'ous',
+ aliti: 'al',
+ iviti: 'ive',
+ biliti: 'ble',
+ logi: 'log'
+ };
+
+ var step3list = {
+ icate: 'ic',
+ ative: '',
+ alize: 'al',
+ iciti: 'ic',
+ ical: 'ic',
+ ful: '',
+ ness: ''
+ };
+
+ var c = "[^aeiou]"; // consonant
+ var v = "[aeiouy]"; // vowel
+ var C = c + "[^aeiouy]*"; // consonant sequence
+ var V = v + "[aeiou]*"; // vowel sequence
+
+ var mgr0 = "^(" + C + ")?" + V + C; // [C]VC... is m>0
+ var meq1 = "^(" + C + ")?" + V + C + "(" + V + ")?$"; // [C]VC[V] is m=1
+ var mgr1 = "^(" + C + ")?" + V + C + V + C; // [C]VCVC... is m>1
+ var s_v = "^(" + C + ")?" + v; // vowel in stem
+
+ this.stemWord = function (w) {
+ var stem;
+ var suffix;
+ var firstch;
+ var origword = w;
+
+ if (w.length < 3)
+ return w;
+
+ var re;
+ var re2;
+ var re3;
+ var re4;
+
+ firstch = w.substr(0,1);
+ if (firstch == "y")
+ w = firstch.toUpperCase() + w.substr(1);
+
+ // Step 1a
+ re = /^(.+?)(ss|i)es$/;
+ re2 = /^(.+?)([^s])s$/;
+
+ if (re.test(w))
+ w = w.replace(re,"$1$2");
+ else if (re2.test(w))
+ w = w.replace(re2,"$1$2");
+
+ // Step 1b
+ re = /^(.+?)eed$/;
+ re2 = /^(.+?)(ed|ing)$/;
+ if (re.test(w)) {
+ var fp = re.exec(w);
+ re = new RegExp(mgr0);
+ if (re.test(fp[1])) {
+ re = /.$/;
+ w = w.replace(re,"");
+ }
+ }
+ else if (re2.test(w)) {
+ var fp = re2.exec(w);
+ stem = fp[1];
+ re2 = new RegExp(s_v);
+ if (re2.test(stem)) {
+ w = stem;
+ re2 = /(at|bl|iz)$/;
+ re3 = new RegExp("([^aeiouylsz])\\1$");
+ re4 = new RegExp("^" + C + v + "[^aeiouwxy]$");
+ if (re2.test(w))
+ w = w + "e";
+ else if (re3.test(w)) {
+ re = /.$/;
+ w = w.replace(re,"");
+ }
+ else if (re4.test(w))
+ w = w + "e";
+ }
+ }
+
+ // Step 1c
+ re = /^(.+?)y$/;
+ if (re.test(w)) {
+ var fp = re.exec(w);
+ stem = fp[1];
+ re = new RegExp(s_v);
+ if (re.test(stem))
+ w = stem + "i";
+ }
+
+ // Step 2
+ re = /^(.+?)(ational|tional|enci|anci|izer|bli|alli|entli|eli|ousli|ization|ation|ator|alism|iveness|fulness|ousness|aliti|iviti|biliti|logi)$/;
+ if (re.test(w)) {
+ var fp = re.exec(w);
+ stem = fp[1];
+ suffix = fp[2];
+ re = new RegExp(mgr0);
+ if (re.test(stem))
+ w = stem + step2list[suffix];
+ }
+
+ // Step 3
+ re = /^(.+?)(icate|ative|alize|iciti|ical|ful|ness)$/;
+ if (re.test(w)) {
+ var fp = re.exec(w);
+ stem = fp[1];
+ suffix = fp[2];
+ re = new RegExp(mgr0);
+ if (re.test(stem))
+ w = stem + step3list[suffix];
+ }
+
+ // Step 4
+ re = /^(.+?)(al|ance|ence|er|ic|able|ible|ant|ement|ment|ent|ou|ism|ate|iti|ous|ive|ize)$/;
+ re2 = /^(.+?)(s|t)(ion)$/;
+ if (re.test(w)) {
+ var fp = re.exec(w);
+ stem = fp[1];
+ re = new RegExp(mgr1);
+ if (re.test(stem))
+ w = stem;
+ }
+ else if (re2.test(w)) {
+ var fp = re2.exec(w);
+ stem = fp[1] + fp[2];
+ re2 = new RegExp(mgr1);
+ if (re2.test(stem))
+ w = stem;
+ }
+
+ // Step 5
+ re = /^(.+?)e$/;
+ if (re.test(w)) {
+ var fp = re.exec(w);
+ stem = fp[1];
+ re = new RegExp(mgr1);
+ re2 = new RegExp(meq1);
+ re3 = new RegExp("^" + C + v + "[^aeiouwxy]$");
+ if (re.test(stem) || (re2.test(stem) && !(re3.test(stem))))
+ w = stem;
+ }
+ re = /ll$/;
+ re2 = new RegExp(mgr1);
+ if (re.test(w) && re2.test(w)) {
+ re = /.$/;
+ w = w.replace(re,"");
+ }
+
+ // and turn initial Y back to y
+ if (firstch == "y")
+ w = firstch.toLowerCase() + w.substr(1);
+ return w;
+ }
+}
+
+
+/**
+ * Search Module
+ */
+var Search = {
+
+ _index : null,
+ _queued_query : null,
+ _pulse_status : -1,
+
+ init : function() {
+ var params = $.getQueryParameters();
+ if (params.q) {
+ var query = params.q[0];
+ $('input[name="q"]')[0].value = query;
+ this.performSearch(query);
+ }
+ },
+
+ loadIndex : function(url) {
+ $.ajax({type: "GET", url: url, data: null, success: null,
+ dataType: "script", cache: true});
+ },
+
+ setIndex : function(index) {
+ var q;
+ this._index = index;
+ if ((q = this._queued_query) !== null) {
+ this._queued_query = null;
+ Search.query(q);
+ }
+ },
+
+ hasIndex : function() {
+ return this._index !== null;
+ },
+
+ deferQuery : function(query) {
+ this._queued_query = query;
+ },
+
+ stopPulse : function() {
+ this._pulse_status = 0;
+ },
+
+ startPulse : function() {
+ if (this._pulse_status >= 0)
+ return;
+ function pulse() {
+ Search._pulse_status = (Search._pulse_status + 1) % 4;
+ var dotString = '';
+ for (var i = 0; i < Search._pulse_status; i++)
+ dotString += '.';
+ Search.dots.text(dotString);
+ if (Search._pulse_status > -1)
+ window.setTimeout(pulse, 500);
+ };
+ pulse();
+ },
+
+ /**
+ * perform a search for something
+ */
+ performSearch : function(query) {
+ // create the required interface elements
+ this.out = $('#search-results');
+ this.title = $('<h2>' + _('Searching') + '</h2>').appendTo(this.out);
+ this.dots = $('<span></span>').appendTo(this.title);
+ this.status = $('<p style="display: none"></p>').appendTo(this.out);
+ this.output = $('<ul class="search"/>').appendTo(this.out);
+
+ $('#search-progress').text(_('Preparing search...'));
+ this.startPulse();
+
+ // index already loaded, the browser was quick!
+ if (this.hasIndex())
+ this.query(query);
+ else
+ this.deferQuery(query);
+ },
+
+ query : function(query) {
+ var stopwords = ["and","then","into","it","as","are","in","if","for","no","there","their","was","is","be","to","that","but","they","not","such","with","by","a","on","these","of","will","this","near","the","or","at"];
+
+ // Stem the searchterms and add them to the correct list
+ var stemmer = new Stemmer();
+ var searchterms = [];
+ var excluded = [];
+ var hlterms = [];
+ var tmp = query.split(/\s+/);
+ var objectterms = [];
+ for (var i = 0; i < tmp.length; i++) {
+ if (tmp[i] != "") {
+ objectterms.push(tmp[i].toLowerCase());
+ }
+
+ if ($u.indexOf(stopwords, tmp[i]) != -1 || tmp[i].match(/^\d+$/) ||
+ tmp[i] == "") {
+ // skip this "word"
+ continue;
+ }
+ // stem the word
+ var word = stemmer.stemWord(tmp[i]).toLowerCase();
+ // select the correct list
+ if (word[0] == '-') {
+ var toAppend = excluded;
+ word = word.substr(1);
+ }
+ else {
+ var toAppend = searchterms;
+ hlterms.push(tmp[i].toLowerCase());
+ }
+ // only add if not already in the list
+ if (!$.contains(toAppend, word))
+ toAppend.push(word);
+ };
+ var highlightstring = '?highlight=' + $.urlencode(hlterms.join(" "));
+
+ // console.debug('SEARCH: searching for:');
+ // console.info('required: ', searchterms);
+ // console.info('excluded: ', excluded);
+
+ // prepare search
+ var filenames = this._index.filenames;
+ var titles = this._index.titles;
+ var terms = this._index.terms;
+ var fileMap = {};
+ var files = null;
+ // different result priorities
+ var importantResults = [];
+ var objectResults = [];
+ var regularResults = [];
+ var unimportantResults = [];
+ $('#search-progress').empty();
+
+ // lookup as object
+ for (var i = 0; i < objectterms.length; i++) {
+ var others = [].concat(objectterms.slice(0,i),
+ objectterms.slice(i+1, objectterms.length))
+ var results = this.performObjectSearch(objectterms[i], others);
+ // Assume first word is most likely to be the object,
+ // other words more likely to be in description.
+ // Therefore put matches for earlier words first.
+ // (Results are eventually used in reverse order).
+ objectResults = results[0].concat(objectResults);
+ importantResults = results[1].concat(importantResults);
+ unimportantResults = results[2].concat(unimportantResults);
+ }
+
+ // perform the search on the required terms
+ for (var i = 0; i < searchterms.length; i++) {
+ var word = searchterms[i];
+ // no match but word was a required one
+ if ((files = terms[word]) == null)
+ break;
+ if (files.length == undefined) {
+ files = [files];
+ }
+ // create the mapping
+ for (var j = 0; j < files.length; j++) {
+ var file = files[j];
+ if (file in fileMap)
+ fileMap[file].push(word);
+ else
+ fileMap[file] = [word];
+ }
+ }
+
+ // now check if the files don't contain excluded terms
+ for (var file in fileMap) {
+ var valid = true;
+
+ // check if all requirements are matched
+ if (fileMap[file].length != searchterms.length)
+ continue;
+
+ // ensure that none of the excluded terms is in the
+ // search result.
+ for (var i = 0; i < excluded.length; i++) {
+ if (terms[excluded[i]] == file ||
+ $.contains(terms[excluded[i]] || [], file)) {
+ valid = false;
+ break;
+ }
+ }
+
+ // if we have still a valid result we can add it
+ // to the result list
+ if (valid)
+ regularResults.push([filenames[file], titles[file], '', null]);
+ }
+
+ // delete unused variables in order to not waste
+ // memory until list is retrieved completely
+ delete filenames, titles, terms;
+
+ // now sort the regular results descending by title
+ regularResults.sort(function(a, b) {
+ var left = a[1].toLowerCase();
+ var right = b[1].toLowerCase();
+ return (left > right) ? -1 : ((left < right) ? 1 : 0);
+ });
+
+ // combine all results
+ var results = unimportantResults.concat(regularResults)
+ .concat(objectResults).concat(importantResults);
+
+ // print the results
+ var resultCount = results.length;
+ function displayNextItem() {
+ // results left, load the summary and display it
+ if (results.length) {
+ var item = results.pop();
+ var listItem = $('<li style="display:none"></li>');
+ if (DOCUMENTATION_OPTIONS.FILE_SUFFIX == '') {
+ // dirhtml builder
+ var dirname = item[0] + '/';
+ if (dirname.match(/\/index\/$/)) {
+ dirname = dirname.substring(0, dirname.length-6);
+ } else if (dirname == 'index/') {
+ dirname = '';
+ }
+ listItem.append($('<a/>').attr('href',
+ DOCUMENTATION_OPTIONS.URL_ROOT + dirname +
+ highlightstring + item[2]).html(item[1]));
+ } else {
+ // normal html builders
+ listItem.append($('<a/>').attr('href',
+ item[0] + DOCUMENTATION_OPTIONS.FILE_SUFFIX +
+ highlightstring + item[2]).html(item[1]));
+ }
+ if (item[3]) {
+ listItem.append($('<span> (' + item[3] + ')</span>'));
+ Search.output.append(listItem);
+ listItem.slideDown(5, function() {
+ displayNextItem();
+ });
+ } else if (DOCUMENTATION_OPTIONS.HAS_SOURCE) {
+ $.get(DOCUMENTATION_OPTIONS.URL_ROOT + '_sources/' +
+ item[0] + '.txt', function(data) {
+ if (data != '') {
+ listItem.append($.makeSearchSummary(data, searchterms, hlterms));
+ Search.output.append(listItem);
+ }
+ listItem.slideDown(5, function() {
+ displayNextItem();
+ });
+ }, "text");
+ } else {
+ // no source available, just display title
+ Search.output.append(listItem);
+ listItem.slideDown(5, function() {
+ displayNextItem();
+ });
+ }
+ }
+ // search finished, update title and status message
+ else {
+ Search.stopPulse();
+ Search.title.text(_('Search Results'));
+ if (!resultCount)
+ Search.status.text(_('Your search did not match any documents. Please make sure that all words are spelled correctly and that you\'ve selected enough categories.'));
+ else
+ Search.status.text(_('Search finished, found %s page(s) matching the search query.').replace('%s', resultCount));
+ Search.status.fadeIn(500);
+ }
+ }
+ displayNextItem();
+ },
+
+ performObjectSearch : function(object, otherterms) {
+ var filenames = this._index.filenames;
+ var objects = this._index.objects;
+ var objnames = this._index.objnames;
+ var titles = this._index.titles;
+
+ var importantResults = [];
+ var objectResults = [];
+ var unimportantResults = [];
+
+ for (var prefix in objects) {
+ for (var name in objects[prefix]) {
+ var fullname = (prefix ? prefix + '.' : '') + name;
+ if (fullname.toLowerCase().indexOf(object) > -1) {
+ var match = objects[prefix][name];
+ var objname = objnames[match[1]][2];
+ var title = titles[match[0]];
+ // If more than one term searched for, we require other words to be
+ // found in the name/title/description
+ if (otherterms.length > 0) {
+ var haystack = (prefix + ' ' + name + ' ' +
+ objname + ' ' + title).toLowerCase();
+ var allfound = true;
+ for (var i = 0; i < otherterms.length; i++) {
+ if (haystack.indexOf(otherterms[i]) == -1) {
+ allfound = false;
+ break;
+ }
+ }
+ if (!allfound) {
+ continue;
+ }
+ }
+ var descr = objname + _(', in ') + title;
+ anchor = match[3];
+ if (anchor == '')
+ anchor = fullname;
+ else if (anchor == '-')
+ anchor = objnames[match[1]][1] + '-' + fullname;
+ result = [filenames[match[0]], fullname, '#'+anchor, descr];
+ switch (match[2]) {
+ case 1: objectResults.push(result); break;
+ case 0: importantResults.push(result); break;
+ case 2: unimportantResults.push(result); break;
+ }
+ }
+ }
+ }
+
+ // sort results descending
+ objectResults.sort(function(a, b) {
+ return (a[1] > b[1]) ? -1 : ((a[1] < b[1]) ? 1 : 0);
+ });
+
+ importantResults.sort(function(a, b) {
+ return (a[1] > b[1]) ? -1 : ((a[1] < b[1]) ? 1 : 0);
+ });
+
+ unimportantResults.sort(function(a, b) {
+ return (a[1] > b[1]) ? -1 : ((a[1] < b[1]) ? 1 : 0);
+ });
+
+ return [importantResults, objectResults, unimportantResults]
+ }
+}
+
+$(document).ready(function() {
+ Search.init();
+});
\ No newline at end of file
diff --git a/doc/rna-seq-example/_static/underscore.js b/doc/rna-seq-example/_static/underscore.js
new file mode 100644
index 0000000..5d89914
--- /dev/null
+++ b/doc/rna-seq-example/_static/underscore.js
@@ -0,0 +1,23 @@
+// Underscore.js 0.5.5
+// (c) 2009 Jeremy Ashkenas, DocumentCloud Inc.
+// Underscore is freely distributable under the terms of the MIT license.
+// Portions of Underscore are inspired by or borrowed from Prototype.js,
+// Oliver Steele's Functional, and John Resig's Micro-Templating.
+// For all details and documentation:
+// http://documentcloud.github.com/underscore/
+(function(){var j=this,n=j._,i=function(a){this._wrapped=a},m=typeof StopIteration!=="undefined"?StopIteration:"__break__",b=j._=function(a){return new i(a)};if(typeof exports!=="undefined")exports._=b;var k=Array.prototype.slice,o=Array.prototype.unshift,p=Object.prototype.toString,q=Object.prototype.hasOwnProperty,r=Object.prototype.propertyIsEnumerable;b.VERSION="0.5.5";b.each=function(a,c,d){try{if(a.forEach)a.forEach(c,d);else if(b.isArray(a)||b.isArguments(a))for(var e=0,f=a.length [...]
+a[e],e,a);else{var g=b.keys(a);f=g.length;for(e=0;e<f;e++)c.call(d,a[g[e]],g[e],a)}}catch(h){if(h!=m)throw h;}return a};b.map=function(a,c,d){if(a&&b.isFunction(a.map))return a.map(c,d);var e=[];b.each(a,function(f,g,h){e.push(c.call(d,f,g,h))});return e};b.reduce=function(a,c,d,e){if(a&&b.isFunction(a.reduce))return a.reduce(b.bind(d,e),c);b.each(a,function(f,g,h){c=d.call(e,c,f,g,h)});return c};b.reduceRight=function(a,c,d,e){if(a&&b.isFunction(a.reduceRight))return a.reduceRight(b.bin [...]
+var f=b.clone(b.toArray(a)).reverse();b.each(f,function(g,h){c=d.call(e,c,g,h,a)});return c};b.detect=function(a,c,d){var e;b.each(a,function(f,g,h){if(c.call(d,f,g,h)){e=f;b.breakLoop()}});return e};b.select=function(a,c,d){if(a&&b.isFunction(a.filter))return a.filter(c,d);var e=[];b.each(a,function(f,g,h){c.call(d,f,g,h)&&e.push(f)});return e};b.reject=function(a,c,d){var e=[];b.each(a,function(f,g,h){!c.call(d,f,g,h)&&e.push(f)});return e};b.all=function(a,c,d){c=c||b.identity;if(a&&b [...]
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+function(a,c){return b.map(a,function(d){return d[c]})};b.max=function(a,c,d){if(!c&&b.isArray(a))return Math.max.apply(Math,a);var e={computed:-Infinity};b.each(a,function(f,g,h){g=c?c.call(d,f,g,h):f;g>=e.computed&&(e={value:f,computed:g})});return e.value};b.min=function(a,c,d){if(!c&&b.isArray(a))return Math.min.apply(Math,a);var e={computed:Infinity};b.each(a,function(f,g,h){g=c?c.call(d,f,g,h):f;g<e.computed&&(e={value:f,computed:g})});return e.value};b.sortBy=function(a,c,d){retur [...]
+function(e,f,g){return{value:e,criteria:c.call(d,e,f,g)}}).sort(function(e,f){e=e.criteria;f=f.criteria;return e<f?-1:e>f?1:0}),"value")};b.sortedIndex=function(a,c,d){d=d||b.identity;for(var e=0,f=a.length;e<f;){var g=e+f>>1;d(a[g])<d(c)?(e=g+1):(f=g)}return e};b.toArray=function(a){if(!a)return[];if(a.toArray)return a.toArray();if(b.isArray(a))return a;if(b.isArguments(a))return k.call(a);return b.values(a)};b.size=function(a){return b.toArray(a).length};b.first=function(a,c,d){return [...]
+0,c):a[0]};b.rest=function(a,c,d){return k.call(a,b.isUndefined(c)||d?1:c)};b.last=function(a){return a[a.length-1]};b.compact=function(a){return b.select(a,function(c){return!!c})};b.flatten=function(a){return b.reduce(a,[],function(c,d){if(b.isArray(d))return c.concat(b.flatten(d));c.push(d);return c})};b.without=function(a){var c=b.rest(arguments);return b.select(a,function(d){return!b.include(c,d)})};b.uniq=function(a,c){return b.reduce(a,[],function(d,e,f){if(0==f||(c===true?b.last( [...]
+e)))d.push(e);return d})};b.intersect=function(a){var c=b.rest(arguments);return b.select(b.uniq(a),function(d){return b.all(c,function(e){return b.indexOf(e,d)>=0})})};b.zip=function(){for(var a=b.toArray(arguments),c=b.max(b.pluck(a,"length")),d=new Array(c),e=0;e<c;e++)d[e]=b.pluck(a,String(e));return d};b.indexOf=function(a,c){if(a.indexOf)return a.indexOf(c);for(var d=0,e=a.length;d<e;d++)if(a[d]===c)return d;return-1};b.lastIndexOf=function(a,c){if(a.lastIndexOf)return a.lastIndexO [...]
+a.length;d--;)if(a[d]===c)return d;return-1};b.range=function(a,c,d){var e=b.toArray(arguments),f=e.length<=1;a=f?0:e[0];c=f?e[0]:e[1];d=e[2]||1;e=Math.ceil((c-a)/d);if(e<=0)return[];e=new Array(e);f=a;for(var g=0;1;f+=d){if((d>0?f-c:c-f)>=0)return e;e[g++]=f}};b.bind=function(a,c){var d=b.rest(arguments,2);return function(){return a.apply(c||j,d.concat(b.toArray(arguments)))}};b.bindAll=function(a){var c=b.rest(arguments);if(c.length==0)c=b.functions(a);b.each(c,function(d){a[d]=b.bind( [...]
+return a};b.delay=function(a,c){var d=b.rest(arguments,2);return setTimeout(function(){return a.apply(a,d)},c)};b.defer=function(a){return b.delay.apply(b,[a,1].concat(b.rest(arguments)))};b.wrap=function(a,c){return function(){var d=[a].concat(b.toArray(arguments));return c.apply(c,d)}};b.compose=function(){var a=b.toArray(arguments);return function(){for(var c=b.toArray(arguments),d=a.length-1;d>=0;d--)c=[a[d].apply(this,c)];return c[0]}};b.keys=function(a){if(b.isArray(a))return b.ran [...]
+var c=[];for(var d in a)q.call(a,d)&&c.push(d);return c};b.values=function(a){return b.map(a,b.identity)};b.functions=function(a){return b.select(b.keys(a),function(c){return b.isFunction(a[c])}).sort()};b.extend=function(a,c){for(var d in c)a[d]=c[d];return a};b.clone=function(a){if(b.isArray(a))return a.slice(0);return b.extend({},a)};b.tap=function(a,c){c(a);return a};b.isEqual=function(a,c){if(a===c)return true;var d=typeof a;if(d!=typeof c)return false;if(a==c)return true;if(!a&&c|| [...]
+if(a.isEqual)return a.isEqual(c);if(b.isDate(a)&&b.isDate(c))return a.getTime()===c.getTime();if(b.isNaN(a)&&b.isNaN(c))return true;if(b.isRegExp(a)&&b.isRegExp(c))return a.source===c.source&&a.global===c.global&&a.ignoreCase===c.ignoreCase&&a.multiline===c.multiline;if(d!=="object")return false;if(a.length&&a.length!==c.length)return false;d=b.keys(a);var e=b.keys(c);if(d.length!=e.length)return false;for(var f in a)if(!b.isEqual(a[f],c[f]))return false;return true};b.isEmpty=function(a [...]
+0};b.isElement=function(a){return!!(a&&a.nodeType==1)};b.isArray=function(a){return!!(a&&a.concat&&a.unshift)};b.isArguments=function(a){return a&&b.isNumber(a.length)&&!b.isArray(a)&&!r.call(a,"length")};b.isFunction=function(a){return!!(a&&a.constructor&&a.call&&a.apply)};b.isString=function(a){return!!(a===""||a&&a.charCodeAt&&a.substr)};b.isNumber=function(a){return p.call(a)==="[object Number]"};b.isDate=function(a){return!!(a&&a.getTimezoneOffset&&a.setUTCFullYear)};b.isRegExp=func [...]
+a.test&&a.exec&&(a.ignoreCase||a.ignoreCase===false))};b.isNaN=function(a){return b.isNumber(a)&&isNaN(a)};b.isNull=function(a){return a===null};b.isUndefined=function(a){return typeof a=="undefined"};b.noConflict=function(){j._=n;return this};b.identity=function(a){return a};b.breakLoop=function(){throw m;};var s=0;b.uniqueId=function(a){var c=s++;return a?a+c:c};b.template=function(a,c){a=new Function("obj","var p=[],print=function(){p.push.apply(p,arguments);};with(obj){p.push('"+a.re [...]
+" ").replace(/'(?=[^%]*%>)/g,"\t").split("'").join("\\'").split("\t").join("'").replace(/<%=(.+?)%>/g,"',$1,'").split("<%").join("');").split("%>").join("p.push('")+"');}return p.join('');");return c?a(c):a};b.forEach=b.each;b.foldl=b.inject=b.reduce;b.foldr=b.reduceRight;b.filter=b.select;b.every=b.all;b.some=b.any;b.head=b.first;b.tail=b.rest;b.methods=b.functions;var l=function(a,c){return c?b(a).chain():a};b.each(b.functions(b),function(a){var c=b[a];i.prototype[a]=function(){var d=b [...]
+o.call(d,this._wrapped);return l(c.apply(b,d),this._chain)}});b.each(["pop","push","reverse","shift","sort","splice","unshift"],function(a){var c=Array.prototype[a];i.prototype[a]=function(){c.apply(this._wrapped,arguments);return l(this._wrapped,this._chain)}});b.each(["concat","join","slice"],function(a){var c=Array.prototype[a];i.prototype[a]=function(){return l(c.apply(this._wrapped,arguments),this._chain)}});i.prototype.chain=function(){this._chain=true;return this};i.prototype.valu [...]
diff --git a/doc/rna-seq-example/_static/up-pressed.png b/doc/rna-seq-example/_static/up-pressed.png
new file mode 100644
index 0000000..8bd587a
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diff --git a/doc/rna-seq-example/_static/up.png b/doc/rna-seq-example/_static/up.png
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diff --git a/doc/rna-seq-example/_static/websupport.js b/doc/rna-seq-example/_static/websupport.js
new file mode 100644
index 0000000..e9bd1b8
--- /dev/null
+++ b/doc/rna-seq-example/_static/websupport.js
@@ -0,0 +1,808 @@
+/*
+ * websupport.js
+ * ~~~~~~~~~~~~~
+ *
+ * sphinx.websupport utilties for all documentation.
+ *
+ * :copyright: Copyright 2007-2011 by the Sphinx team, see AUTHORS.
+ * :license: BSD, see LICENSE for details.
+ *
+ */
+
+(function($) {
+ $.fn.autogrow = function() {
+ return this.each(function() {
+ var textarea = this;
+
+ $.fn.autogrow.resize(textarea);
+
+ $(textarea)
+ .focus(function() {
+ textarea.interval = setInterval(function() {
+ $.fn.autogrow.resize(textarea);
+ }, 500);
+ })
+ .blur(function() {
+ clearInterval(textarea.interval);
+ });
+ });
+ };
+
+ $.fn.autogrow.resize = function(textarea) {
+ var lineHeight = parseInt($(textarea).css('line-height'), 10);
+ var lines = textarea.value.split('\n');
+ var columns = textarea.cols;
+ var lineCount = 0;
+ $.each(lines, function() {
+ lineCount += Math.ceil(this.length / columns) || 1;
+ });
+ var height = lineHeight * (lineCount + 1);
+ $(textarea).css('height', height);
+ };
+})(jQuery);
+
+(function($) {
+ var comp, by;
+
+ function init() {
+ initEvents();
+ initComparator();
+ }
+
+ function initEvents() {
+ $('a.comment-close').live("click", function(event) {
+ event.preventDefault();
+ hide($(this).attr('id').substring(2));
+ });
+ $('a.vote').live("click", function(event) {
+ event.preventDefault();
+ handleVote($(this));
+ });
+ $('a.reply').live("click", function(event) {
+ event.preventDefault();
+ openReply($(this).attr('id').substring(2));
+ });
+ $('a.close-reply').live("click", function(event) {
+ event.preventDefault();
+ closeReply($(this).attr('id').substring(2));
+ });
+ $('a.sort-option').live("click", function(event) {
+ event.preventDefault();
+ handleReSort($(this));
+ });
+ $('a.show-proposal').live("click", function(event) {
+ event.preventDefault();
+ showProposal($(this).attr('id').substring(2));
+ });
+ $('a.hide-proposal').live("click", function(event) {
+ event.preventDefault();
+ hideProposal($(this).attr('id').substring(2));
+ });
+ $('a.show-propose-change').live("click", function(event) {
+ event.preventDefault();
+ showProposeChange($(this).attr('id').substring(2));
+ });
+ $('a.hide-propose-change').live("click", function(event) {
+ event.preventDefault();
+ hideProposeChange($(this).attr('id').substring(2));
+ });
+ $('a.accept-comment').live("click", function(event) {
+ event.preventDefault();
+ acceptComment($(this).attr('id').substring(2));
+ });
+ $('a.delete-comment').live("click", function(event) {
+ event.preventDefault();
+ deleteComment($(this).attr('id').substring(2));
+ });
+ $('a.comment-markup').live("click", function(event) {
+ event.preventDefault();
+ toggleCommentMarkupBox($(this).attr('id').substring(2));
+ });
+ }
+
+ /**
+ * Set comp, which is a comparator function used for sorting and
+ * inserting comments into the list.
+ */
+ function setComparator() {
+ // If the first three letters are "asc", sort in ascending order
+ // and remove the prefix.
+ if (by.substring(0,3) == 'asc') {
+ var i = by.substring(3);
+ comp = function(a, b) { return a[i] - b[i]; };
+ } else {
+ // Otherwise sort in descending order.
+ comp = function(a, b) { return b[by] - a[by]; };
+ }
+
+ // Reset link styles and format the selected sort option.
+ $('a.sel').attr('href', '#').removeClass('sel');
+ $('a.by' + by).removeAttr('href').addClass('sel');
+ }
+
+ /**
+ * Create a comp function. If the user has preferences stored in
+ * the sortBy cookie, use those, otherwise use the default.
+ */
+ function initComparator() {
+ by = 'rating'; // Default to sort by rating.
+ // If the sortBy cookie is set, use that instead.
+ if (document.cookie.length > 0) {
+ var start = document.cookie.indexOf('sortBy=');
+ if (start != -1) {
+ start = start + 7;
+ var end = document.cookie.indexOf(";", start);
+ if (end == -1) {
+ end = document.cookie.length;
+ by = unescape(document.cookie.substring(start, end));
+ }
+ }
+ }
+ setComparator();
+ }
+
+ /**
+ * Show a comment div.
+ */
+ function show(id) {
+ $('#ao' + id).hide();
+ $('#ah' + id).show();
+ var context = $.extend({id: id}, opts);
+ var popup = $(renderTemplate(popupTemplate, context)).hide();
+ popup.find('textarea[name="proposal"]').hide();
+ popup.find('a.by' + by).addClass('sel');
+ var form = popup.find('#cf' + id);
+ form.submit(function(event) {
+ event.preventDefault();
+ addComment(form);
+ });
+ $('#s' + id).after(popup);
+ popup.slideDown('fast', function() {
+ getComments(id);
+ });
+ }
+
+ /**
+ * Hide a comment div.
+ */
+ function hide(id) {
+ $('#ah' + id).hide();
+ $('#ao' + id).show();
+ var div = $('#sc' + id);
+ div.slideUp('fast', function() {
+ div.remove();
+ });
+ }
+
+ /**
+ * Perform an ajax request to get comments for a node
+ * and insert the comments into the comments tree.
+ */
+ function getComments(id) {
+ $.ajax({
+ type: 'GET',
+ url: opts.getCommentsURL,
+ data: {node: id},
+ success: function(data, textStatus, request) {
+ var ul = $('#cl' + id);
+ var speed = 100;
+ $('#cf' + id)
+ .find('textarea[name="proposal"]')
+ .data('source', data.source);
+
+ if (data.comments.length === 0) {
+ ul.html('<li>No comments yet.</li>');
+ ul.data('empty', true);
+ } else {
+ // If there are comments, sort them and put them in the list.
+ var comments = sortComments(data.comments);
+ speed = data.comments.length * 100;
+ appendComments(comments, ul);
+ ul.data('empty', false);
+ }
+ $('#cn' + id).slideUp(speed + 200);
+ ul.slideDown(speed);
+ },
+ error: function(request, textStatus, error) {
+ showError('Oops, there was a problem retrieving the comments.');
+ },
+ dataType: 'json'
+ });
+ }
+
+ /**
+ * Add a comment via ajax and insert the comment into the comment tree.
+ */
+ function addComment(form) {
+ var node_id = form.find('input[name="node"]').val();
+ var parent_id = form.find('input[name="parent"]').val();
+ var text = form.find('textarea[name="comment"]').val();
+ var proposal = form.find('textarea[name="proposal"]').val();
+
+ if (text == '') {
+ showError('Please enter a comment.');
+ return;
+ }
+
+ // Disable the form that is being submitted.
+ form.find('textarea,input').attr('disabled', 'disabled');
+
+ // Send the comment to the server.
+ $.ajax({
+ type: "POST",
+ url: opts.addCommentURL,
+ dataType: 'json',
+ data: {
+ node: node_id,
+ parent: parent_id,
+ text: text,
+ proposal: proposal
+ },
+ success: function(data, textStatus, error) {
+ // Reset the form.
+ if (node_id) {
+ hideProposeChange(node_id);
+ }
+ form.find('textarea')
+ .val('')
+ .add(form.find('input'))
+ .removeAttr('disabled');
+ var ul = $('#cl' + (node_id || parent_id));
+ if (ul.data('empty')) {
+ $(ul).empty();
+ ul.data('empty', false);
+ }
+ insertComment(data.comment);
+ var ao = $('#ao' + node_id);
+ ao.find('img').attr({'src': opts.commentBrightImage});
+ if (node_id) {
+ // if this was a "root" comment, remove the commenting box
+ // (the user can get it back by reopening the comment popup)
+ $('#ca' + node_id).slideUp();
+ }
+ },
+ error: function(request, textStatus, error) {
+ form.find('textarea,input').removeAttr('disabled');
+ showError('Oops, there was a problem adding the comment.');
+ }
+ });
+ }
+
+ /**
+ * Recursively append comments to the main comment list and children
+ * lists, creating the comment tree.
+ */
+ function appendComments(comments, ul) {
+ $.each(comments, function() {
+ var div = createCommentDiv(this);
+ ul.append($(document.createElement('li')).html(div));
+ appendComments(this.children, div.find('ul.comment-children'));
+ // To avoid stagnating data, don't store the comments children in data.
+ this.children = null;
+ div.data('comment', this);
+ });
+ }
+
+ /**
+ * After adding a new comment, it must be inserted in the correct
+ * location in the comment tree.
+ */
+ function insertComment(comment) {
+ var div = createCommentDiv(comment);
+
+ // To avoid stagnating data, don't store the comments children in data.
+ comment.children = null;
+ div.data('comment', comment);
+
+ var ul = $('#cl' + (comment.node || comment.parent));
+ var siblings = getChildren(ul);
+
+ var li = $(document.createElement('li'));
+ li.hide();
+
+ // Determine where in the parents children list to insert this comment.
+ for(i=0; i < siblings.length; i++) {
+ if (comp(comment, siblings[i]) <= 0) {
+ $('#cd' + siblings[i].id)
+ .parent()
+ .before(li.html(div));
+ li.slideDown('fast');
+ return;
+ }
+ }
+
+ // If we get here, this comment rates lower than all the others,
+ // or it is the only comment in the list.
+ ul.append(li.html(div));
+ li.slideDown('fast');
+ }
+
+ function acceptComment(id) {
+ $.ajax({
+ type: 'POST',
+ url: opts.acceptCommentURL,
+ data: {id: id},
+ success: function(data, textStatus, request) {
+ $('#cm' + id).fadeOut('fast');
+ $('#cd' + id).removeClass('moderate');
+ },
+ error: function(request, textStatus, error) {
+ showError('Oops, there was a problem accepting the comment.');
+ }
+ });
+ }
+
+ function deleteComment(id) {
+ $.ajax({
+ type: 'POST',
+ url: opts.deleteCommentURL,
+ data: {id: id},
+ success: function(data, textStatus, request) {
+ var div = $('#cd' + id);
+ if (data == 'delete') {
+ // Moderator mode: remove the comment and all children immediately
+ div.slideUp('fast', function() {
+ div.remove();
+ });
+ return;
+ }
+ // User mode: only mark the comment as deleted
+ div
+ .find('span.user-id:first')
+ .text('[deleted]').end()
+ .find('div.comment-text:first')
+ .text('[deleted]').end()
+ .find('#cm' + id + ', #dc' + id + ', #ac' + id + ', #rc' + id +
+ ', #sp' + id + ', #hp' + id + ', #cr' + id + ', #rl' + id)
+ .remove();
+ var comment = div.data('comment');
+ comment.username = '[deleted]';
+ comment.text = '[deleted]';
+ div.data('comment', comment);
+ },
+ error: function(request, textStatus, error) {
+ showError('Oops, there was a problem deleting the comment.');
+ }
+ });
+ }
+
+ function showProposal(id) {
+ $('#sp' + id).hide();
+ $('#hp' + id).show();
+ $('#pr' + id).slideDown('fast');
+ }
+
+ function hideProposal(id) {
+ $('#hp' + id).hide();
+ $('#sp' + id).show();
+ $('#pr' + id).slideUp('fast');
+ }
+
+ function showProposeChange(id) {
+ $('#pc' + id).hide();
+ $('#hc' + id).show();
+ var textarea = $('#pt' + id);
+ textarea.val(textarea.data('source'));
+ $.fn.autogrow.resize(textarea[0]);
+ textarea.slideDown('fast');
+ }
+
+ function hideProposeChange(id) {
+ $('#hc' + id).hide();
+ $('#pc' + id).show();
+ var textarea = $('#pt' + id);
+ textarea.val('').removeAttr('disabled');
+ textarea.slideUp('fast');
+ }
+
+ function toggleCommentMarkupBox(id) {
+ $('#mb' + id).toggle();
+ }
+
+ /** Handle when the user clicks on a sort by link. */
+ function handleReSort(link) {
+ var classes = link.attr('class').split(/\s+/);
+ for (var i=0; i<classes.length; i++) {
+ if (classes[i] != 'sort-option') {
+ by = classes[i].substring(2);
+ }
+ }
+ setComparator();
+ // Save/update the sortBy cookie.
+ var expiration = new Date();
+ expiration.setDate(expiration.getDate() + 365);
+ document.cookie= 'sortBy=' + escape(by) +
+ ';expires=' + expiration.toUTCString();
+ $('ul.comment-ul').each(function(index, ul) {
+ var comments = getChildren($(ul), true);
+ comments = sortComments(comments);
+ appendComments(comments, $(ul).empty());
+ });
+ }
+
+ /**
+ * Function to process a vote when a user clicks an arrow.
+ */
+ function handleVote(link) {
+ if (!opts.voting) {
+ showError("You'll need to login to vote.");
+ return;
+ }
+
+ var id = link.attr('id');
+ if (!id) {
+ // Didn't click on one of the voting arrows.
+ return;
+ }
+ // If it is an unvote, the new vote value is 0,
+ // Otherwise it's 1 for an upvote, or -1 for a downvote.
+ var value = 0;
+ if (id.charAt(1) != 'u') {
+ value = id.charAt(0) == 'u' ? 1 : -1;
+ }
+ // The data to be sent to the server.
+ var d = {
+ comment_id: id.substring(2),
+ value: value
+ };
+
+ // Swap the vote and unvote links.
+ link.hide();
+ $('#' + id.charAt(0) + (id.charAt(1) == 'u' ? 'v' : 'u') + d.comment_id)
+ .show();
+
+ // The div the comment is displayed in.
+ var div = $('div#cd' + d.comment_id);
+ var data = div.data('comment');
+
+ // If this is not an unvote, and the other vote arrow has
+ // already been pressed, unpress it.
+ if ((d.value !== 0) && (data.vote === d.value * -1)) {
+ $('#' + (d.value == 1 ? 'd' : 'u') + 'u' + d.comment_id).hide();
+ $('#' + (d.value == 1 ? 'd' : 'u') + 'v' + d.comment_id).show();
+ }
+
+ // Update the comments rating in the local data.
+ data.rating += (data.vote === 0) ? d.value : (d.value - data.vote);
+ data.vote = d.value;
+ div.data('comment', data);
+
+ // Change the rating text.
+ div.find('.rating:first')
+ .text(data.rating + ' point' + (data.rating == 1 ? '' : 's'));
+
+ // Send the vote information to the server.
+ $.ajax({
+ type: "POST",
+ url: opts.processVoteURL,
+ data: d,
+ error: function(request, textStatus, error) {
+ showError('Oops, there was a problem casting that vote.');
+ }
+ });
+ }
+
+ /**
+ * Open a reply form used to reply to an existing comment.
+ */
+ function openReply(id) {
+ // Swap out the reply link for the hide link
+ $('#rl' + id).hide();
+ $('#cr' + id).show();
+
+ // Add the reply li to the children ul.
+ var div = $(renderTemplate(replyTemplate, {id: id})).hide();
+ $('#cl' + id)
+ .prepend(div)
+ // Setup the submit handler for the reply form.
+ .find('#rf' + id)
+ .submit(function(event) {
+ event.preventDefault();
+ addComment($('#rf' + id));
+ closeReply(id);
+ })
+ .find('input[type=button]')
+ .click(function() {
+ closeReply(id);
+ });
+ div.slideDown('fast', function() {
+ $('#rf' + id).find('textarea').focus();
+ });
+ }
+
+ /**
+ * Close the reply form opened with openReply.
+ */
+ function closeReply(id) {
+ // Remove the reply div from the DOM.
+ $('#rd' + id).slideUp('fast', function() {
+ $(this).remove();
+ });
+
+ // Swap out the hide link for the reply link
+ $('#cr' + id).hide();
+ $('#rl' + id).show();
+ }
+
+ /**
+ * Recursively sort a tree of comments using the comp comparator.
+ */
+ function sortComments(comments) {
+ comments.sort(comp);
+ $.each(comments, function() {
+ this.children = sortComments(this.children);
+ });
+ return comments;
+ }
+
+ /**
+ * Get the children comments from a ul. If recursive is true,
+ * recursively include childrens' children.
+ */
+ function getChildren(ul, recursive) {
+ var children = [];
+ ul.children().children("[id^='cd']")
+ .each(function() {
+ var comment = $(this).data('comment');
+ if (recursive)
+ comment.children = getChildren($(this).find('#cl' + comment.id), true);
+ children.push(comment);
+ });
+ return children;
+ }
+
+ /** Create a div to display a comment in. */
+ function createCommentDiv(comment) {
+ if (!comment.displayed && !opts.moderator) {
+ return $('<div class="moderate">Thank you! Your comment will show up '
+ + 'once it is has been approved by a moderator.</div>');
+ }
+ // Prettify the comment rating.
+ comment.pretty_rating = comment.rating + ' point' +
+ (comment.rating == 1 ? '' : 's');
+ // Make a class (for displaying not yet moderated comments differently)
+ comment.css_class = comment.displayed ? '' : ' moderate';
+ // Create a div for this comment.
+ var context = $.extend({}, opts, comment);
+ var div = $(renderTemplate(commentTemplate, context));
+
+ // If the user has voted on this comment, highlight the correct arrow.
+ if (comment.vote) {
+ var direction = (comment.vote == 1) ? 'u' : 'd';
+ div.find('#' + direction + 'v' + comment.id).hide();
+ div.find('#' + direction + 'u' + comment.id).show();
+ }
+
+ if (opts.moderator || comment.text != '[deleted]') {
+ div.find('a.reply').show();
+ if (comment.proposal_diff)
+ div.find('#sp' + comment.id).show();
+ if (opts.moderator && !comment.displayed)
+ div.find('#cm' + comment.id).show();
+ if (opts.moderator || (opts.username == comment.username))
+ div.find('#dc' + comment.id).show();
+ }
+ return div;
+ }
+
+ /**
+ * A simple template renderer. Placeholders such as <%id%> are replaced
+ * by context['id'] with items being escaped. Placeholders such as <#id#>
+ * are not escaped.
+ */
+ function renderTemplate(template, context) {
+ var esc = $(document.createElement('div'));
+
+ function handle(ph, escape) {
+ var cur = context;
+ $.each(ph.split('.'), function() {
+ cur = cur[this];
+ });
+ return escape ? esc.text(cur || "").html() : cur;
+ }
+
+ return template.replace(/<([%#])([\w\.]*)\1>/g, function() {
+ return handle(arguments[2], arguments[1] == '%' ? true : false);
+ });
+ }
+
+ /** Flash an error message briefly. */
+ function showError(message) {
+ $(document.createElement('div')).attr({'class': 'popup-error'})
+ .append($(document.createElement('div'))
+ .attr({'class': 'error-message'}).text(message))
+ .appendTo('body')
+ .fadeIn("slow")
+ .delay(2000)
+ .fadeOut("slow");
+ }
+
+ /** Add a link the user uses to open the comments popup. */
+ $.fn.comment = function() {
+ return this.each(function() {
+ var id = $(this).attr('id').substring(1);
+ var count = COMMENT_METADATA[id];
+ var title = count + ' comment' + (count == 1 ? '' : 's');
+ var image = count > 0 ? opts.commentBrightImage : opts.commentImage;
+ var addcls = count == 0 ? ' nocomment' : '';
+ $(this)
+ .append(
+ $(document.createElement('a')).attr({
+ href: '#',
+ 'class': 'sphinx-comment-open' + addcls,
+ id: 'ao' + id
+ })
+ .append($(document.createElement('img')).attr({
+ src: image,
+ alt: 'comment',
+ title: title
+ }))
+ .click(function(event) {
+ event.preventDefault();
+ show($(this).attr('id').substring(2));
+ })
+ )
+ .append(
+ $(document.createElement('a')).attr({
+ href: '#',
+ 'class': 'sphinx-comment-close hidden',
+ id: 'ah' + id
+ })
+ .append($(document.createElement('img')).attr({
+ src: opts.closeCommentImage,
+ alt: 'close',
+ title: 'close'
+ }))
+ .click(function(event) {
+ event.preventDefault();
+ hide($(this).attr('id').substring(2));
+ })
+ );
+ });
+ };
+
+ var opts = {
+ processVoteURL: '/_process_vote',
+ addCommentURL: '/_add_comment',
+ getCommentsURL: '/_get_comments',
+ acceptCommentURL: '/_accept_comment',
+ deleteCommentURL: '/_delete_comment',
+ commentImage: '/static/_static/comment.png',
+ closeCommentImage: '/static/_static/comment-close.png',
+ loadingImage: '/static/_static/ajax-loader.gif',
+ commentBrightImage: '/static/_static/comment-bright.png',
+ upArrow: '/static/_static/up.png',
+ downArrow: '/static/_static/down.png',
+ upArrowPressed: '/static/_static/up-pressed.png',
+ downArrowPressed: '/static/_static/down-pressed.png',
+ voting: false,
+ moderator: false
+ };
+
+ if (typeof COMMENT_OPTIONS != "undefined") {
+ opts = jQuery.extend(opts, COMMENT_OPTIONS);
+ }
+
+ var popupTemplate = '\
+ <div class="sphinx-comments" id="sc<%id%>">\
+ <p class="sort-options">\
+ Sort by:\
+ <a href="#" class="sort-option byrating">best rated</a>\
+ <a href="#" class="sort-option byascage">newest</a>\
+ <a href="#" class="sort-option byage">oldest</a>\
+ </p>\
+ <div class="comment-header">Comments</div>\
+ <div class="comment-loading" id="cn<%id%>">\
+ loading comments... <img src="<%loadingImage%>" alt="" /></div>\
+ <ul id="cl<%id%>" class="comment-ul"></ul>\
+ <div id="ca<%id%>">\
+ <p class="add-a-comment">Add a comment\
+ (<a href="#" class="comment-markup" id="ab<%id%>">markup</a>):</p>\
+ <div class="comment-markup-box" id="mb<%id%>">\
+ reStructured text markup: <i>*emph*</i>, <b>**strong**</b>, \
+ <tt>``code``</tt>, \
+ code blocks: <tt>::</tt> and an indented block after blank line</div>\
+ <form method="post" id="cf<%id%>" class="comment-form" action="">\
+ <textarea name="comment" cols="80"></textarea>\
+ <p class="propose-button">\
+ <a href="#" id="pc<%id%>" class="show-propose-change">\
+ Propose a change ▹\
+ </a>\
+ <a href="#" id="hc<%id%>" class="hide-propose-change">\
+ Propose a change ▿\
+ </a>\
+ </p>\
+ <textarea name="proposal" id="pt<%id%>" cols="80"\
+ spellcheck="false"></textarea>\
+ <input type="submit" value="Add comment" />\
+ <input type="hidden" name="node" value="<%id%>" />\
+ <input type="hidden" name="parent" value="" />\
+ </form>\
+ </div>\
+ </div>';
+
+ var commentTemplate = '\
+ <div id="cd<%id%>" class="sphinx-comment<%css_class%>">\
+ <div class="vote">\
+ <div class="arrow">\
+ <a href="#" id="uv<%id%>" class="vote" title="vote up">\
+ <img src="<%upArrow%>" />\
+ </a>\
+ <a href="#" id="uu<%id%>" class="un vote" title="vote up">\
+ <img src="<%upArrowPressed%>" />\
+ </a>\
+ </div>\
+ <div class="arrow">\
+ <a href="#" id="dv<%id%>" class="vote" title="vote down">\
+ <img src="<%downArrow%>" id="da<%id%>" />\
+ </a>\
+ <a href="#" id="du<%id%>" class="un vote" title="vote down">\
+ <img src="<%downArrowPressed%>" />\
+ </a>\
+ </div>\
+ </div>\
+ <div class="comment-content">\
+ <p class="tagline comment">\
+ <span class="user-id"><%username%></span>\
+ <span class="rating"><%pretty_rating%></span>\
+ <span class="delta"><%time.delta%></span>\
+ </p>\
+ <div class="comment-text comment"><#text#></div>\
+ <p class="comment-opts comment">\
+ <a href="#" class="reply hidden" id="rl<%id%>">reply ▹</a>\
+ <a href="#" class="close-reply" id="cr<%id%>">reply ▿</a>\
+ <a href="#" id="sp<%id%>" class="show-proposal">proposal ▹</a>\
+ <a href="#" id="hp<%id%>" class="hide-proposal">proposal ▿</a>\
+ <a href="#" id="dc<%id%>" class="delete-comment hidden">delete</a>\
+ <span id="cm<%id%>" class="moderation hidden">\
+ <a href="#" id="ac<%id%>" class="accept-comment">accept</a>\
+ </span>\
+ </p>\
+ <pre class="proposal" id="pr<%id%>">\
+<#proposal_diff#>\
+ </pre>\
+ <ul class="comment-children" id="cl<%id%>"></ul>\
+ </div>\
+ <div class="clearleft"></div>\
+ </div>\
+ </div>';
+
+ var replyTemplate = '\
+ <li>\
+ <div class="reply-div" id="rd<%id%>">\
+ <form id="rf<%id%>">\
+ <textarea name="comment" cols="80"></textarea>\
+ <input type="submit" value="Add reply" />\
+ <input type="button" value="Cancel" />\
+ <input type="hidden" name="parent" value="<%id%>" />\
+ <input type="hidden" name="node" value="" />\
+ </form>\
+ </div>\
+ </li>';
+
+ $(document).ready(function() {
+ init();
+ });
+})(jQuery);
+
+$(document).ready(function() {
+ // add comment anchors for all paragraphs that are commentable
+ $('.sphinx-has-comment').comment();
+
+ // highlight search words in search results
+ $("div.context").each(function() {
+ var params = $.getQueryParameters();
+ var terms = (params.q) ? params.q[0].split(/\s+/) : [];
+ var result = $(this);
+ $.each(terms, function() {
+ result.highlightText(this.toLowerCase(), 'highlighted');
+ });
+ });
+
+ // directly open comment window if requested
+ var anchor = document.location.hash;
+ if (anchor.substring(0, 9) == '#comment-') {
+ $('#ao' + anchor.substring(9)).click();
+ document.location.hash = '#s' + anchor.substring(9);
+ }
+});
diff --git a/doc/rna-seq-example/counts_boxplot.png b/doc/rna-seq-example/counts_boxplot.png
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diff --git a/doc/rna-seq-example/lincRNA.png b/doc/rna-seq-example/lincRNA.png
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diff --git a/doc/rna-seq-example/lincRNA_boxplot.png b/doc/rna-seq-example/lincRNA_boxplot.png
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diff --git a/doc/rna-seq-example/miRNA.png b/doc/rna-seq-example/miRNA.png
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index 0000000..1441b95
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diff --git a/doc/rna-seq-example/miRNA_boxplot.png b/doc/rna-seq-example/miRNA_boxplot.png
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index 0000000..e4cf9b2
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diff --git a/doc/rna-seq-example/misc_RNA.png b/doc/rna-seq-example/misc_RNA.png
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index 0000000..cfde5a9
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diff --git a/doc/rna-seq-example/misc_RNA_boxplot.png b/doc/rna-seq-example/misc_RNA_boxplot.png
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index 0000000..382c9b1
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diff --git a/doc/rna-seq-example/mitocondrial.png b/doc/rna-seq-example/mitocondrial.png
new file mode 100644
index 0000000..8c64db6
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diff --git a/doc/rna-seq-example/mitocondrial_boxplot.png b/doc/rna-seq-example/mitocondrial_boxplot.png
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index 0000000..f4ff434
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diff --git a/doc/rna-seq-example/processed_transcript.png b/doc/rna-seq-example/processed_transcript.png
new file mode 100644
index 0000000..55930d2
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diff --git a/doc/rna-seq-example/processed_transcript_boxplot.png b/doc/rna-seq-example/processed_transcript_boxplot.png
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index 0000000..4058861
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diff --git a/doc/rna-seq-example/protein_coding.png b/doc/rna-seq-example/protein_coding.png
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index 0000000..bd9342d
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diff --git a/doc/rna-seq-example/protein_coding_boxplot.png b/doc/rna-seq-example/protein_coding_boxplot.png
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index 0000000..aa4088f
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diff --git a/doc/rna-seq-example/pseudogene.png b/doc/rna-seq-example/pseudogene.png
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index 0000000..ce8f150
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diff --git a/doc/rna-seq-example/pseudogene_boxplot.png b/doc/rna-seq-example/pseudogene_boxplot.png
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index 0000000..14ebe23
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diff --git a/doc/rna-seq-example/qualimapReport.html b/doc/rna-seq-example/qualimapReport.html
new file mode 100644
index 0000000..7757efa
--- /dev/null
+++ b/doc/rna-seq-example/qualimapReport.html
@@ -0,0 +1,436 @@
+<!DOCTYPE HTML>
+<html>
+ <head>
+ <link rel="stylesheet" href="_static/agogo.css" type="text/css" />
+ <link rel="stylesheet" href="_static/report.css" type="text/css" />
+ <title>Qualimap report: Genomic analysis</title>
+
+ </head>
+<body>
+ <div class="header-wrapper">
+ <div class="header">
+ <p class="logo"><a href="http://qualimap.bioinfo.cipf.es/">
+ <img class="logo" src="_static/qualimap_logo_small.png" alt="Logo"/>
+ </a></p>
+<div class="headertitle"><a href="">Qualimap Report</a></div>
+ </div>
+</div>
+
+<div class="content-wrapper">
+<div class="content">
+<div class="document">
+<div class="documentwrapper">
+<div class="bodywrapper">
+<div class="body">
+<div class=section>
+<h2>Input data and parameters<a class="headerlink" name="input" title="Permalink to this headline"> </a></h2>
+<div class=summary>
+
+
+<div class=table-summary>
+<h3>Liver</h3>
+<table class="summary hovertable">
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Path: </td>
+<td class=column2>/home/fgarcia/Downloads/liver.counts</td>
+</tr>
+</table>
+</div>
+
+
+<div class=table-summary>
+<h3>Liver</h3>
+<table class="summary hovertable">
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Path: </td>
+<td class=column2>/home/fgarcia/Downloads/kidney.counts</td>
+</tr>
+</table>
+</div>
+
+
+<div class=table-summary>
+<h3>Options</h3>
+<table class="summary hovertable">
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Threshold: </td>
+<td class=column2>5</td>
+</tr>
+<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
+<td class=column1>Species info: </td>
+<td class=column2>/home/fgarcia/qualimapLatestBuild/qualimap-build-26-03-12/./species/human.61.genes.biotypes.txt</td>
+</tr>
+</table>
+</div>
+
+</div>
+</div> <!-- summary section -->
+
+
+
+<div class=section>
+
+<h2>snRNA_boxplot.png<a class="headerlink" name="snRNA_boxplot.png" title="Permalink to this headline"> </a></h2>
+
+<div><img width=100% src="snRNA_boxplot.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>snoRNA_boxplot.png<a class="headerlink" name="snoRNA_boxplot.png" title="Permalink to this headline"> </a></h2>
+
+<div><img width=100% src="snoRNA_boxplot.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>unknown.png<a class="headerlink" name="unknown.png" title="Permalink to this headline"> </a></h2>
+
+<div><img width=100% src="unknown.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>miRNA.png<a class="headerlink" name="miRNA.png" title="Permalink to this headline"> </a></h2>
+
+<div><img width=100% src="miRNA.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>misc_RNA_boxplot.png<a class="headerlink" name="misc_RNA_boxplot.png" title="Permalink to this headline"> </a></h2>
+
+<div><img width=100% src="misc_RNA_boxplot.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>scRNA_pseudogene_boxplot.png<a class="headerlink" name="scRNA_pseudogene_boxplot.png" title="Permalink to this headline"> </a></h2>
+
+<div><img width=100% src="scRNA_pseudogene_boxplot.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>tRNA_pseudogene.png<a class="headerlink" name="tRNA_pseudogene.png" title="Permalink to this headline"> </a></h2>
+
+<div><img width=100% src="tRNA_pseudogene.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>pseudogene.png<a class="headerlink" name="pseudogene.png" title="Permalink to this headline"> </a></h2>
+
+<div><img width=100% src="pseudogene.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>scRNA_pseudogene.png<a class="headerlink" name="scRNA_pseudogene.png" title="Permalink to this headline"> </a></h2>
+
+<div><img width=100% src="scRNA_pseudogene.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>counts_boxplot.png<a class="headerlink" name="counts_boxplot.png" title="Permalink to this headline"> </a></h2>
+
+<div><img width=100% src="counts_boxplot.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>protein_coding.png<a class="headerlink" name="protein_coding.png" title="Permalink to this headline"> </a></h2>
+
+<div><img width=100% src="protein_coding.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>protein_coding_boxplot.png<a class="headerlink" name="protein_coding_boxplot.png" title="Permalink to this headline"> </a></h2>
+
+<div><img width=100% src="protein_coding_boxplot.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>IG.png<a class="headerlink" name="IG.png" title="Permalink to this headline"> </a></h2>
+
+<div><img width=100% src="IG.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>mitocondrial_boxplot.png<a class="headerlink" name="mitocondrial_boxplot.png" title="Permalink to this headline"> </a></h2>
+
+<div><img width=100% src="mitocondrial_boxplot.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>misc_RNA.png<a class="headerlink" name="misc_RNA.png" title="Permalink to this headline"> </a></h2>
+
+<div><img width=100% src="misc_RNA.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>TR_boxplot.png<a class="headerlink" name="TR_boxplot.png" title="Permalink to this headline"> </a></h2>
+
+<div><img width=100% src="TR_boxplot.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>miRNA_boxplot.png<a class="headerlink" name="miRNA_boxplot.png" title="Permalink to this headline"> </a></h2>
+
+<div><img width=100% src="miRNA_boxplot.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>GlobalSaturation.png<a class="headerlink" name="GlobalSaturation.png" title="Permalink to this headline"> </a></h2>
+
+<div><img width=100% src="GlobalSaturation.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>snRNA.png<a class="headerlink" name="snRNA.png" title="Permalink to this headline"> </a></h2>
+
+<div><img width=100% src="snRNA.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>processed_transcript_boxplot.png<a class="headerlink" name="processed_transcript_boxplot.png" title="Permalink to this headline"> </a></h2>
+
+<div><img width=100% src="processed_transcript_boxplot.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>TR.png<a class="headerlink" name="TR.png" title="Permalink to this headline"> </a></h2>
+
+<div><img width=100% src="TR.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>lincRNA_boxplot.png<a class="headerlink" name="lincRNA_boxplot.png" title="Permalink to this headline"> </a></h2>
+
+<div><img width=100% src="lincRNA_boxplot.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>IG_boxplot.png<a class="headerlink" name="IG_boxplot.png" title="Permalink to this headline"> </a></h2>
+
+<div><img width=100% src="IG_boxplot.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>processed_transcript.png<a class="headerlink" name="processed_transcript.png" title="Permalink to this headline"> </a></h2>
+
+<div><img width=100% src="processed_transcript.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>mitocondrial.png<a class="headerlink" name="mitocondrial.png" title="Permalink to this headline"> </a></h2>
+
+<div><img width=100% src="mitocondrial.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>lincRNA.png<a class="headerlink" name="lincRNA.png" title="Permalink to this headline"> </a></h2>
+
+<div><img width=100% src="lincRNA.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>rRNA.png<a class="headerlink" name="rRNA.png" title="Permalink to this headline"> </a></h2>
+
+<div><img width=100% src="rRNA.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>rRNA_boxplot.png<a class="headerlink" name="rRNA_boxplot.png" title="Permalink to this headline"> </a></h2>
+
+<div><img width=100% src="rRNA_boxplot.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>tRNA_pseudogene_boxplot.png<a class="headerlink" name="tRNA_pseudogene_boxplot.png" title="Permalink to this headline"> </a></h2>
+
+<div><img width=100% src="tRNA_pseudogene_boxplot.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>pseudogene_boxplot.png<a class="headerlink" name="pseudogene_boxplot.png" title="Permalink to this headline"> </a></h2>
+
+<div><img width=100% src="pseudogene_boxplot.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>DetectionPerGroup.png<a class="headerlink" name="DetectionPerGroup.png" title="Permalink to this headline"> </a></h2>
+
+<div><img width=100% src="DetectionPerGroup.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>unknown_boxplot.png<a class="headerlink" name="unknown_boxplot.png" title="Permalink to this headline"> </a></h2>
+
+<div><img width=100% src="unknown_boxplot.png"></div>
+
+</div><!-- graph section -->
+
+
+<div class=section>
+
+<h2>snoRNA.png<a class="headerlink" name="snoRNA.png" title="Permalink to this headline"> </a></h2>
+
+<div><img width=100% src="snoRNA.png"></div>
+
+</div><!-- graph section -->
+
+
+</div>
+
+</div>
+
+</div>
+
+</div>
+
+
+<div class="sidebar">
+<h3>Contents</h3>
+<li class="toctree-l1"><a class="reference internal" href="#input">Input data & parameters</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#snRNA_boxplot.png">snRNA_boxplot.png</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#snoRNA_boxplot.png">snoRNA_boxplot.png</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#unknown.png">unknown.png</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#miRNA.png">miRNA.png</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#misc_RNA_boxplot.png">misc_RNA_boxplot.png</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#scRNA_pseudogene_boxplot.png">scRNA_pseudogene_boxplot.png</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#tRNA_pseudogene.png">tRNA_pseudogene.png</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#pseudogene.png">pseudogene.png</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#scRNA_pseudogene.png">scRNA_pseudogene.png</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#counts_boxplot.png">counts_boxplot.png</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#protein_coding.png">protein_coding.png</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#protein_coding_boxplot.png">protein_coding_boxplot.png</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#IG.png">IG.png</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#mitocondrial_boxplot.png">mitocondrial_boxplot.png</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#misc_RNA.png">misc_RNA.png</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#TR_boxplot.png">TR_boxplot.png</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#miRNA_boxplot.png">miRNA_boxplot.png</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#GlobalSaturation.png">GlobalSaturation.png</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#snRNA.png">snRNA.png</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#processed_transcript_boxplot.png">processed_transcript_boxplot.png</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#TR.png">TR.png</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#lincRNA_boxplot.png">lincRNA_boxplot.png</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#IG_boxplot.png">IG_boxplot.png</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#processed_transcript.png">processed_transcript.png</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#mitocondrial.png">mitocondrial.png</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#lincRNA.png">lincRNA.png</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#rRNA.png">rRNA.png</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#rRNA_boxplot.png">rRNA_boxplot.png</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#tRNA_pseudogene_boxplot.png">tRNA_pseudogene_boxplot.png</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#pseudogene_boxplot.png">pseudogene_boxplot.png</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#DetectionPerGroup.png">DetectionPerGroup.png</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#unknown_boxplot.png">unknown_boxplot.png</a></li>
+<li class="toctree-l1"><a class="reference internal" href="#snoRNA.png">snoRNA.png</a></li>
+</div> <!-- sidebar -->
+
+<div class="clearer"></div>
+</div>
+
+</div>
+
+
+<div class="footer-wrapper">
+<div class="footer">
+<div class="left">
+<div class="footer">
+2012/03/28 11:58:36
+</div>
+</div>
+<div class="right">
+<div class="footer">
+Generated by QualiMap
+</div
+</div>
+<div class="clearer"></div>
+</div> <!-- footer -->
+</div>
+</body>
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diff --git a/doc/samples.rst b/doc/samples.rst
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+++ b/doc/samples.rst
@@ -0,0 +1,141 @@
+.. _samples:
+
+Examples
+========
+
+Sample Data
+-----------
+
+.. _bam-samples:
+
+Alignments
+**********
+
+- `ERR089819.bam <http://qualimap.bioinfo.cipf.es/samples/alignments/ERR089819.bam>`_ (2.6 GB)
+ Whole genome sequencing data of C. elegans from the following `study <http://trace.ncbi.nlm.nih.gov/Traces/sra/?study=ERP000975>`_.
+
+- `HG00096.chrom20.bam <http://qualimap.bioinfo.cipf.es/samples/alignments/HG00096.chrom20.bam>`_ (278 MB)
+ Sequencing of the chromosome 20 from a H. sapiens sample from `1000 Genomes project <http://www.1000genomes.org/>`_. The header of the BAM file was changed in order to contain only chromosome 20. Original file can be found `here <ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/data/HG00096/alignment/HG00096.chrom20.ILLUMINA.bwa.GBR.low_coverage.20101123.bam>`_.
+
+- `kidney.bam <http://qualimap.bioinfo.cipf.es/samples/counts/kidney.bam>`_ (386 MB) and `liver.bam <http://qualimap.bioinfo.cipf.es/samples/counts/liver.bam>`_ (412 MB)
+ Human RNA-seq sequencing data from from the paper of `Marioni JC et al <http://genome.cshlp.org/content/18/9/1509.abstract>`_
+
+Annotations
+***********
+
+.. _annotation-files:
+
+- `human.64.gtf <http://qualimap.bioinfo.cipf.es/samples/annotations/human.64.gtf>`_
+ Human genome annotations from Ensembl database (v. 64).
+- `transcripts.human.64.bed <http://qualimap.bioinfo.cipf.es/samples/annotations/transcripts.human.64.bed>`_
+ Human transcripts in BED format from Ensembl database (v. 64).
+
+.. `Plasmodium-falciparum-3D7.gff <http://qualimap.bioinfo.cipf.es/samples/annotations/Plasmodium-falciparum-3D7.gff>`_
+ Gene Annotations of Plasmodium falciparum 3D7 clone , from `Wellcome Trust Sanger Institue <http://www.sanger.ac.uk/resources/downloads/protozoa/plasmodium-falciparum.html>`_.
+
+.. _multibamqc-samples:
+
+Multisample BAM QC
+******************
+
+- `gh2ax_chip_seq.zip <http://kokonech.github.io/qualimap/samples/gh2ax_chip_seq.zip>`_
+
+ Example dataset from an unpublished ChiP-seq experiment with 4 condtions, each having 3 replicates (12 sampels in total). The archive contains BAM QC results for each sample and input configuration for command line version of Multisample BAM QC.
+
+
+.. _counts-samples:
+
+Counts QC
+*********
+
+- `mouse_counts_ensembl.txt <http://kokonech.github.io/qualimap/samples/mouse_counts_ensembl.txt>`_
+ Mouse counts data from a `study <http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE54853>`_ investigating effects of D-Glucosamine:
+
+- `GlcN_countsqc_input.txt <http://kokonech.github.io/qualimap/samples/GlcN_countsqc_input.txt>`_
+ Command line input configuration for the counts data above.
+
+
+- `kidney.counts <http://qualimap.bioinfo.cipf.es/samples/counts/kidney.counts>`_ and `liver.counts <http://qualimap.bioinfo.cipf.es/samples/counts/liver.counts>`_
+ Counts data from the paper by `Marioni JC et al <http://genome.cshlp.org/content/18/9/1509.abstract>`_.
+
+- `marioini_countsqc_input.txt <http://kokonech.github.io/qualimap/samples/marioni_countsqc_input.txt>`_
+ Command line input configuration for the counts data above.
+
+
+.. _clustering-samples:
+
+Clustering
+**********
+
+- `hmeDIP.bam <http://qualimap.bioinfo.cipf.es/samples/clustering/hmeDIP.bam>`_ (988M)
+ MeDIP-seq of human embryonic stem cells from the study of `Stroud H et al <http://genomebiology.com/content/12/6/R54>`_.
+
+- `input.bam <http://qualimap.bioinfo.cipf.es/samples/clustering/input.bam>`_ (1.8G)
+ Input data of the same study
+
+Sample Output
+-------------
+
+BAM QC
+******
+
+Analysis of the WG-seq data (HG00096.chrom20.bam): `QualiMap HTML report <http://rawgit.com/kokonech/kokonech.github.io/master/qualimap/HG00096.chr20_bamqc/qualimapReport.html>`_.
+
+Analysis of the WG-seq data (ERR089819.bam): `QualiMap PDF report <http://rawgit.com/kokonech/kokonech.github.io/master/qualimap/ERR089819_report.pdf>`_.
+
+
+RNA-seq QC
+**********
+
+Analysis of RNA-seq data (kidney.bam, human.64.gtf): `QualiMap HTML report <http://rawgit.com/kokonech/kokonech.github.io/master/qualimap/kidney_rnaseqqc/qualimapReport.html>`_.
+
+
+Multisample BAM QC
+******************
+
+Multisample analysis of 12 gH2AX ChiP-seq alignments: `Qualimap HTML report <http://rawgit.com/kokonech/kokonech.github.io/master/qualimap/gh2ax_multibamqc/multisampleBamQcReport.html>`_.
+
+
+Counts QC
+*********
+
+.. _counts-example-output:
+
+Counts QC HTML reports computed from RNA-seq experiment analyzing influence of D-Glucosamine on mice. The analysis was performed for 6 samples in 2 conditions - GlcN positive and negative (mouse_counts_ensembl.txt):
+
+- `Global report <http://kokonech.github.io/qualimap/glcn_mice_counts/GlobalReport.html>`_
+
+- `Comparison of conditions <http://kokonech.github.io/qualimap/glcn_mice_counts/ComparisonReport.html>`_
+
+- `Sample 01 (GlcN negative) <http://kokonech.github.io/qualimap/glcn_mice_counts/nGlcn01Report.html>`_
+
+- `Sample 02 (GlcN negative) <http://kokonech.github.io/qualimap/glcn_mice_counts/nGlcn02Report.html>`_
+
+- `Sample 03 (GlcN negative) <http://kokonech.github.io/qualimap/glcn_mice_counts/nGlcn03Report.html>`_
+
+- `Sample 04 (GlcN positive) <http://kokonech.github.io/qualimap/glcn_mice_counts/pGlcn01Report.html>`_
+
+- `Sample 05 (GlcN positive) <http://kokonech.github.io/qualimap/glcn_mice_counts/pGlcn02Report.html>`_
+
+- `Sample 06 (GlcN positive) <http://kokonech.github.io/qualimap/glcn_mice_counts/pGlcn03Report.html>`_
+
+Counts QC HTML reports from human RNA-seq data from study by `Marioni JC et al <http://genome.cshlp.org/content/18/9/1509.abstract>`_ (kidney.counts, liver.counts):
+
+- `Global report <http://kokonech.github.io/qualimap/marioni_counts/GlobalReport.html>`_
+
+- `Comparison of conditions <http://kokonech.github.io/qualimap/marioni_counts/ComparisonReport.html>`_
+
+- `Sample 01 (Kidney) <http://kokonech.github.io/qualimap/marioni_counts/KidneyReport.html>`_
+
+- `Sample 02 (Liver) <http://kokonech.github.io/qualimap/marioni_counts/LiverReport.html>`_
+
+
+
+Clustering
+**********
+
+Analysis of MeDIP-seq data: `QualiMap HTML report <http://qualimap.bioinfo.cipf.es/samples/clustering_result/qualimapReport.html>`_.
+
+
+
+
diff --git a/doc/tools.rst b/doc/tools.rst
new file mode 100644
index 0000000..303e28b
--- /dev/null
+++ b/doc/tools.rst
@@ -0,0 +1,208 @@
+.. _tools:
+
+
+Tools
+=====
+
+.. _compute-counts:
+
+Compute counts
+--------------
+
+* Given a BAM file and an annotation (`GTF file <http://genome.ucsc.edu/FAQ/FAQformat.html#format4>`_), this tool calculates how many reads are mapped to each region of interest.
+
+
+* The user can decide:
+
+ - At which level wants to perform the counting (genes, transcripts...).
+
+ - What to do whith reads mapped to multiple locations.
+
+ - Paired-end reads status and strand-specifity.
+
+ - When a transcriptome GTF file is provided the tool allows to calculate 5' and 3' prime coverage bias.
+
+To access the tool use :menuselection:`Tools --> Compute counts`.
+
+
+.. _example-compute-counts:
+
+Example
+^^^^^^^
+
+- Input data:
+
+ - BAM file: `liver.bam <http://qualimap.bioinfo.cipf.es/samples/counts/liver.bam>`_. RNA-seq of liver tissue from `Marioni JC et al <http://genome.cshlp.org/content/18/9/1509.abstract>`_
+
+ - GTF file: `human.64.gtf <http://qualimap.bioinfo.cipf.es/samples/annotations/human.64.gtf>`_ . Human annotation from Ensembl (v. 64)
+
+ - Parameters:
+
+ - Feature ID: gene_id (to count at the level of genes)
+ - Feature type: exon (to ignore other features like start/end codons)
+ - Paired-end reads counts computation and strand-specificity
+ - Multimapped reads: uniquely-mapped-reads (to ignore not unique alignments)
+
+- Output:
+
+ - `liver.counts <http://qualimap.bioinfo.cipf.es/samples/counts/liver.counts>`_. Two-column tab-delimited text file, with the feature IDs in the first column and the number of counts in the second column.
+
+
+Input
+^^^^^
+
+:guilabel:`BAM file`
+ Path to the BAM alignment file.
+:guilabel:`Annotation file`
+ Path to the GTF or BED file containing regions of interest.
+
+:guilabel:`Protocol`
+
+ Controls when to consider reads and features to be overlapping:
+
+ :dfn:`non-strand-specific`
+ Reads overlap features if they share genomic regions regardless of the strand.
+ :dfn:`forward-stranded`
+ For single-end reads, the read and the feature must have the same strand to be overlapping.
+ For paired-end reads, the first read of the pair must be mapped to the same strand as the feature, while the second read must be mapped to the opposite strand.
+
+ :dfn:`reverse-strand`
+ For single-end reads, the read and the feature must have the opposite strand.
+ For paired-end reads, the first read of pair must be mapped to the opposite strand of the feature, while the second read of the pair must be on the same strand as the feature.
+
+:guilabel:`Feature ID`
+ The user can select the attribute of the GTF file to be used as the feature ID. Regions with the same ID will be aggregated as part of the same feature. The application preload the first 1000 lines of the file so a list with possible feature IDs is conveniently provided.
+
+:guilabel:`Feature type`
+ The user can select the feature type (value of the third column of the GTF) considered for counting. Other types will be ignored. The application preload the first 1000 lines of the file so a list with possible feature IDs is conveniently provided.
+
+:guilabel:`Paired-end reads`
+ This option allows to activate counting of pairs of reads instead of single reads
+
+:guilabel:`Alignment sorted by name`
+ For correct analysis of paired-end reads alignment should be sorted by name. If this operation is already performed, sorting can be skipped.
+
+:guilabel:`Output`
+ Path to the ouput file.
+
+:guilabel:`Save computation summary`
+ This option controls whether to save overall computation statistics. If selected, the statistics will be saved in a file named `$INPUT_BAM`.counts
+
+
+.. _multimapped-reads-count:
+
+:guilabel:`Multi-mapped reads`
+ This option controls what to do whith reads mapped to multiple location:
+
+
+ :dfn:`uniquely-mapped-reads`
+ Reads mapped to multiple locations will be ignored.
+
+
+ :dfn:`proportional`
+ Multi-mapped reads are detected based on "NH" tag from SAM format. Each read is weighted according to the number of mapped locations. For example, a read mapped to 4 different locations will add 0.25 to the counts of each location. After analysis is finished the value will converted to intger value.
+
+:guilabel:`Calculate 5' and 3' coverage bias`
+ If a **GTF file** is provided, the user has the possibility of computing **5' - 3' bias**. The application automatically constructs the 5' and 3' UTR (100 bp) from the gene definitions of the GTF file and determines the coverage rate of the 1000 most highly expressed transcripts in the UTR regions. This information is then stored in the *computation summary* file, together with the statistics of the counting procedure.
+
+.. note:: This option requires a standard gene model definition. The UTRs are computed for the first and last exons of each transcript. Therefore, `exon` is the feature of interest (third field of the GTF) and `gene_id`, `transcript_id` should be attributes (ninth field of the GTF).
+
+
+Output
+^^^^^^
+
+A two-column tab-delimited text file, with the feature IDs in the first column and the number of counts in the second column, and overall calculation stats.
+
+The calculation stats include:
+
+ :dfn:`Feature counts`
+ Number of reads assigned to various features
+
+ :dfn:`No feature`
+ Number of reads not aligned to any feature
+
+ :dfn:`Not unique alignment`
+ Number of reads with non-unique alignment
+
+ :dfn:`Ambiguous`
+ Number of reads that align to features ambigously
+
+The following stats are calculate only if option `Calulate 5' and 3' bias` was set:
+
+ :dfn:`Median 5' bias`
+ For 1000 most expressed genes the ratio between coverage of 100 leftmost bases and mean coverage is calcualted and median value is provided.
+
+ :dfn:`Median 3' bias`
+ For 1000 most expressed gene the ratio between coverage of 100 rightmost bases and mean coverage is calculated and median value is provided.
+
+ :dfn:`Median 5' to 3`
+ For 1000 most expressed genes the ratio between coverag of 100 leftmost and 100 rightmost bases is calculated and median value is provided.
+
+
+.. _clustering:
+
+Clustering
+----------
+
+* Qualimap provides the possibility of clustering genomic features according to their surrounding coverage profiles. This is particulary interesting in epigenomic studies (e.g. methylation). The user can import a set of features (e.g. TSSs or CpG Islands) together with the BAM file. Then the application preprocess the data and clusters the profiles using the Repitools package (`Statham et al <http://bioinformatics.oxfordjournals.org/content/26/13/1662.abstract>`_). The obtained groups of [...]
+
+* Summary of the process:
+
+ - filter out the non-uniquely-mapped reads
+ - compute the smoothed coverages values of the samples at the desired locations
+ - apply k-means on the smoothed coverage values for the desired values of k
+
+
+* To perform this analysis the user needs to provide at least two BAM files -- one for the sample (enriched) and other for the control (input) -- and a list of features as BED file.
+
+* Clustering analysis can be accesed using the menu item :menuselection:`File --> Tools --> Clustering`.
+
+.. note:: Clustering coverage profiles is not a straightforward task and it may be necessary to perform a number of empirical filter steps. In order to correctly interpret the approach the results we encourage the users to read Repitools User Manual.
+
+
+Input Parameters
+^^^^^^^^^^^^^^^^
+
+:guilabel:`Experiment ID`
+ The experiment name
+
+:guilabel:`Alignment data`
+ Here you can provide your replicates to analyze. Each replicate includes sample file and a control file. For example, in an epigenomics experiment, the sample file could be the MeDIP-seq data and the control the non-enriched data (the so-called INPUT data). Thus, for each replicate the following information has to be provided:
+
+ :guilabel:`Replicate name`
+ Name of the replicate
+ :guilabel:`Sample file`
+ Path to sample BAM file
+ :guilabel:`Control file`
+ Path to control BAM file
+
+ To add a replicate click :guilabel:`Add` button. To remove a replicate select it and click :guilabel:`Remove` button. You can modify replicate by using :guilabel:`Edit` button.
+
+:guilabel:`Regions of interest`
+ Path to an annotation file in `BED <http://genome.ucsc.edu/FAQ/FAQformat.html#format1>`_ or `GFF <http://genome.ucsc.edu/FAQ/FAQformat.html#format3>`_ format, which contains regions of interest.
+
+
+:guilabel:`Location`
+ Relative location to analyze
+:guilabel:`Left offset`
+ Offset in bp upstream the selected regions
+:guilabel:`Right offset`
+ Offset in bp downstream the selected regions
+:guilabel:`Bin size`
+ Can be thought as the resolution of the plot. Bins of the desired size will be computed and the information falling on each bin will be aggregated
+:guilabel:`Number of clusters`
+ Number of groups that you the user wants to divide the data. Several values can be used by separating them with commas
+:guilabel:`Fragment length`
+ Length of the fragments that were initially sequenced. All reads will be enlarged to this length.
+:guilabel:`Visualization type`
+ You can visualize cluster using heatmaps or line-based graphs.
+
+Output
+^^^^^^
+
+After the analysis is performed, the regions of interest are clustered in groups based on the coverage pattern. The output graph shows the coverage pattern for each cluster either as a heatmap or a line graph. There can be multiple graphs based on the number of clusters provided as input. The name of each graph consists of the experiment name and the number of clusters.
+
+It is possible to export list of features beloning to the particular cluster. To do this use main menu item :menuselection:`File --> Export gene list` or context menu item :menuselection:`Export gene list`. After activating the item a dialog will appear where you can choose some specific cluster. One can either copy the list of features belonging to this cluster in the clipboard or export it to a text file.
+
+
+
diff --git a/doc/workflow.rst b/doc/workflow.rst
new file mode 100644
index 0000000..44a3ea5
--- /dev/null
+++ b/doc/workflow.rst
@@ -0,0 +1,64 @@
+.. _workflow:
+
+Workflow
+========
+
+This chapter describes how to perform QC analysis of alignment data with graphical user interface of Qualimap. To run analysis with command line interface please refer to the :ref:`corresponding chapter <command-line>`.
+
+Starting a new analysis
+-----------------------
+
+- To start new analysis activate main menu item :menuselection:`File --> New Analysis` and select the desired type of analysis. Read more about different types of analysis :ref:`here <analysis-types>`.
+
+.. image:: images/start_analysis.png
+ :width: 500pt
+ :align: center
+
+
+- After the corresponding item is selected a dialog will appear that allows customizing analysis options (input files, algorithm parameters, etc.).
+
+.. image:: images/genomic.png
+ :width: 500pt
+ :align: center
+
+
+- To run the analysis click the :guilabel:`Start analysis` button.
+
+- During the computation a status message and a graphic bar will indicate the progress of the computation.
+
+Viewing the results of the analysis
+-----------------------------------
+
+- After the selected analysis is finished the results are shown as an interactive report in the Qualimap main window. Several reports can be opened at the same time in different tabs.
+
+.. image:: images/output.png
+ :width: 500pt
+ :align: center
+
+- In the left part of the report window one can find a list containing available result items. Clicking on an item will automatically show the corresponding information report or graph. Some report items are common for different types of analysis.
+
+- For example, the :guilabel:`Summary` section provides a short summary of performed quality control checks, while the :guilabel:`Input` section lists all the input parameters. Further information about each specific result is provided :ref:`here <analysis-types>`.
+
+.. _export:
+
+Exporting results
+-----------------
+
+- The resulting report along with raw statistics data can be saved to HTML page or PDF document.
+
+- To export results to HTML use a main menu item :menuselection:`File --> Export to HTML`. In the dialog window one can select the output folder. After clicking :guilabel:`OK` button the web-page, containing analysis results along with raw statistics data will be saved to the specified directory.
+
+- Similarly one can save the report to a PDF document by using a main menu item :menuselection:`File --> Export to PDF`.
+
+- Note that for plots in :ref:`BAM QC <bamqc>` and :ref:`Counts QC <countsqc>` it is also possible to export the underlying raw data using the context menu, with appears by clicking the right mouse button in the corresponding plot. In addition, when the report is exported to HTML, the raw data for all plots can be found in the output folder.
+
+
+Using tools
+-----------
+
+- Qualimap is desgined to provide NGS-related tools that can be used aside from the quality control analysis. Currently two tools are available (more are planned to be added in the future):
+
+ 1. :ref:`Compute Counts <compute-counts>` for counting how many reads are mapped to each region of interest at the desired level (genes, transcripts, etc.)
+
+ 2. :ref:`Clustering <clustering>` for obtaining groups of genomic features that share similar coverage profiles
+
diff --git a/pom.xml b/pom.xml
new file mode 100644
index 0000000..8d81ee1
--- /dev/null
+++ b/pom.xml
@@ -0,0 +1,203 @@
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+
+ <modelVersion>4.0.0</modelVersion>
+ <groupId>org.bioinfo.ngs</groupId>
+ <artifactId>qualimap</artifactId>
+ <version>2.1.3-dev</version>
+ <name>qualimap</name>
+
+ <properties>
+ <maven.build.timestamp.format>yyyy-MM-dd HH:mm</maven.build.timestamp.format>
+ <buildTime>${maven.build.timestamp}</buildTime>
+ </properties>
+
+ <dependencies>
+ <dependency>
+ <groupId>com.oracle</groupId>
+ <artifactId>javafx</artifactId>
+ <version>2.2</version>
+ <systemPath>${java.home}/lib/jfxrt.jar</systemPath>
+ <scope>system</scope>
+ </dependency>
+ <dependency>
+ <groupId>junit</groupId>
+ <artifactId>junit</artifactId>
+ <version>4.4</version>
+ <scope>test</scope>
+ </dependency>
+ <dependency>
+ <groupId>org.bioinfo</groupId>
+ <artifactId>bioinfo-formats</artifactId>
+ <version>0.2.0</version>
+ <scope>compile</scope>
+ </dependency>
+ <dependency>
+ <groupId>org.bioinfo</groupId>
+ <artifactId>bioinfo-ngs</artifactId>
+ <version>0.1.0</version>
+ <scope>compile</scope>
+ </dependency>
+ <dependency>
+ <groupId>org.bioinfo</groupId>
+ <artifactId>bioinfo-commons</artifactId>
+ <version>0.10.1</version>
+ <type>jar</type>
+ <scope>compile</scope>
+ </dependency>
+ <dependency>
+ <groupId>org.bioinfo</groupId>
+ <artifactId>bioinfo-math</artifactId>
+ <version>0.3.0</version>
+ </dependency>
+ <dependency>
+ <groupId>org.bioinfo</groupId>
+ <artifactId>bioinfo-graphics</artifactId>
+ <version>0.4.0</version>
+ <scope>compile</scope>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.picard</groupId>
+ <artifactId>picard</artifactId>
+ <version>1.70</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.samtools</groupId>
+ <artifactId>samtools</artifactId>
+ <version>1.70</version>
+ <scope>compile</scope>
+ </dependency>
+ <dependency>
+ <groupId>com.miglayout</groupId>
+ <artifactId>miglayout</artifactId>
+ <version>3.7.4</version>
+ </dependency>
+ <dependency>
+ <groupId>org.ejml</groupId>
+ <artifactId>ejml</artifactId>
+ <version>0.24</version>
+ </dependency>
+
+ </dependencies>
+
+ <repositories>
+
+ <repository>
+ <id>org.bioinfo</id>
+ <name>Bioinfo Library</name>
+ <url>http://repos.bioinfo.cipf.es/maven2/</url>
+ </repository>
+
+
+ </repositories>
+
+ <pluginRepositories>
+
+ <pluginRepository>
+ <id>mc-release</id>
+ <name>Local Maven repository of releases</name>
+ <url>http://mc-repo.googlecode.com/svn/maven2/releases</url>
+ <snapshots>
+ <enabled>false</enabled>
+ </snapshots>
+ <releases>
+ <enabled>true</enabled>
+ </releases>
+ </pluginRepository>
+ </pluginRepositories>
+
+ <build>
+
+ <finalName>${project.artifactId}</finalName>
+ <sourceDirectory>src/main/java</sourceDirectory>
+ <testSourceDirectory>src/test/java</testSourceDirectory>
+
+ <resources>
+ <resource>
+ <directory>src/main/resources</directory>
+ <filtering>true</filtering>
+ <includes>
+ <include>app.properties</include>
+ </includes>
+ </resource>
+ <resource>
+ <directory>src/main/resources</directory>
+ <filtering>false</filtering>
+ <excludes>
+ <exclude>app.properties</exclude>
+ </excludes>
+ </resource>
+ </resources>
+
+ <plugins>
+ <plugin>
+ <artifactId>maven-surefire-plugin</artifactId>
+ <version>2.10</version>
+ <configuration>
+ <skipTests>true</skipTests>
+ </configuration>
+ </plugin>
+
+ <plugin>
+ <artifactId>maven-compiler-plugin</artifactId>
+ <configuration>
+ <source>1.6</source>
+ <target>1.6</target>
+ </configuration>
+ </plugin>
+ <plugin>
+ <artifactId>maven-dependency-plugin</artifactId>
+ <executions>
+ <execution>
+ <phase>install</phase>
+ <goals>
+ <goal>copy-dependencies</goal>
+ </goals>
+ <configuration>
+ <outputDirectory>${project.build.directory}/install/lib</outputDirectory>
+ </configuration>
+ </execution>
+ </executions>
+ </plugin>
+
+ <plugin>
+ <groupId>com.mycila.maven-license-plugin</groupId>
+ <artifactId>maven-license-plugin</artifactId>
+ <configuration>
+ <header>src/etc/header.txt</header>
+ <includes>
+ <include>src/main/java/**</include>
+ <include>src/test/java/**</include>
+ </includes>
+ </configuration>
+ </plugin>
+
+ <plugin>
+ <artifactId>maven-antrun-plugin</artifactId>
+ <executions>
+ <execution>
+ <phase>install</phase>
+ <configuration>
+ <tasks>
+ <copy todir="${project.build.directory}/install">
+ <fileset dir="cli"></fileset>
+ </copy>
+ <copy todir="${project.build.directory}/install" file="LICENSE"></copy>
+ <chmod file="${project.build.directory}/install/qualimap"
+ perm="755" />
+ <copy file="${project.build.directory}/qualimap.jar" todir="${project.build.directory}/install" />
+ </tasks>
+ </configuration>
+ <goals>
+ <goal>run</goal>
+ </goals>
+ </execution>
+ </executions>
+ </plugin>
+
+ </plugins>
+
+ </build>
+
+
+</project>
diff --git a/src/etc/header.txt b/src/etc/header.txt
new file mode 100644
index 0000000..8e121ce
--- /dev/null
+++ b/src/etc/header.txt
@@ -0,0 +1,19 @@
+QualiMap: evaluation of next generation sequencing alignment data
+Copyright (C) ${year} Garcia-Alcalde et al.
+http://qualimap.org
+
+This program is free software; you can redistribute it and/or
+modify it under the terms of the GNU General Public License
+as published by the Free Software Foundation; either version 2
+of the License, or (at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program; if not, write to the Free Software
+Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+MA 02110-1301, USA.
+
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/beans/AnalysisResultManager.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/beans/AnalysisResultManager.java
new file mode 100644
index 0000000..36a2d31
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/beans/AnalysisResultManager.java
@@ -0,0 +1,88 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.beans;
+
+import javafx.util.Pair;
+import org.bioinfo.commons.io.utils.FileUtils;
+import org.bioinfo.ngs.qc.qualimap.common.AnalysisType;
+import org.bioinfo.ngs.qc.qualimap.common.UniqueID;
+import org.bioinfo.ngs.qc.qualimap.gui.frames.HomeFrame;
+
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
+
+/**
+ * Created by kokonech
+ * Date: 7/13/13
+ * Time: 3:34 PM
+ */
+public class AnalysisResultManager {
+
+ AnalysisType typeAnalysis;
+ String outputFolder;
+ List<StatsReporter> reporters;
+ Pair<String,String> resultReport;
+
+ public AnalysisResultManager(AnalysisType analysisType) {
+ this.typeAnalysis = analysisType;
+ this.outputFolder = "";
+ reporters = new ArrayList<StatsReporter>();
+ }
+
+ public AnalysisType getTypeAnalysis() {
+ return typeAnalysis;
+ }
+
+ public String getOutputFolder() {
+ return outputFolder;
+ }
+
+ public void addReporter(StatsReporter reporter) {
+ reporters.add(reporter);
+ }
+
+ public List<StatsReporter> getReporters() {
+ return reporters;
+ }
+
+ public StringBuilder createDirectory(){
+ boolean created = false;
+ StringBuilder folderName = null;
+ StringBuilder folderPath = new StringBuilder(HomeFrame.outputpath);
+ StringBuilder outputDirPath = null;
+
+ while(!created){
+ try {
+ folderName = new StringBuilder(""+ UniqueID.get() + "/");
+ outputDirPath = new StringBuilder(folderPath.toString() + folderName.toString());
+ FileUtils.checkDirectory(outputDirPath.toString());
+ } catch (IOException e) {
+ FileUtils.createDirectory(outputDirPath.toString(), true);
+ outputFolder = folderName.toString();
+ created = true;
+ }
+ }
+
+ return outputDirPath;
+ }
+
+}
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/beans/BamDetailedGenomeWindow.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/beans/BamDetailedGenomeWindow.java
new file mode 100644
index 0000000..c975995
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/beans/BamDetailedGenomeWindow.java
@@ -0,0 +1,165 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.beans;
+
+
+//TODO: BamDetailedGenomeWindow has to be removed, all processing can be done in BamGenomeWindow
+
+
+public class BamDetailedGenomeWindow extends BamGenomeWindow {
+
+ // reference sequence
+ private byte[] reference;
+
+ // coverageData
+ private int[] coverageAcrossReference;
+
+ // quality
+ private long[] mappingQualityAcrossReference;
+
+ // required for calculation of mean and std of coverage
+ private long sumCoverageSquared;
+ private long sumCoverage;
+
+
+ public BamDetailedGenomeWindow(String name, long start, long end, byte[] reference){
+
+ super(name,start,end,reference);
+
+ if(reference!=null){
+ this.reference = reference;
+ }
+
+ // init arrays
+ coverageAcrossReference = new int[(int)this.windowSize];
+ mappingQualityAcrossReference = new long[(int)this.windowSize];
+// sequencingQualityAcrossReference = new int[this.windowSize];
+// aContentAcrossReference = new long[(int)this.windowSize];
+// cContentAcrossReference = new long[(int)this.windowSize];
+// gContentAcrossReference = new long[(int)this.windowSize];
+// tContentAcrossReference = new long[(int)this.windowSize];
+// nContentAcrossReference = new long[(int)this.windowSize];
+// gcContentAcrossReference = new double[(int)this.windowSize];
+// atContentAcrossReference = new double[(int)this.windowSize];
+
+ }
+
+ @Override
+ protected void acumBase(long relative){
+ super.acumBase(relative);
+ coverageAcrossReference[(int)relative] = coverageAcrossReference[(int)relative]+1;
+ }
+
+ @Override
+ protected void acumProperlyPairedBase(long relative){
+ super.acumProperlyPairedBase(relative);
+ //properlyPairedCoverageAcrossReference[(int)relative] = properlyPairedCoverageAcrossReference[(int)relative] + 1;
+ }
+
+ @Override
+ protected void acumMappingQuality(long relative, int mappingQuality){
+ super.acumMappingQuality(relative,mappingQuality);
+ // quality
+ mappingQualityAcrossReference[(int)relative] = mappingQualityAcrossReference[(int)relative]+mappingQuality;
+ }
+
+ @Override
+ public void computeDescriptors() throws CloneNotSupportedException{
+
+ super.computeDescriptors();
+
+ // normalize vectors
+
+ sumCoverage = 0;
+
+ for(int i=0; i<coverageAcrossReference.length; i++){
+
+ long coverageAtPosition = coverageAcrossReference[i];
+
+ if(coverageAtPosition > 0){
+
+ // quality
+ mappingQualityAcrossReference[i] = mappingQualityAcrossReference[i] / coverageAtPosition;
+ // insert size
+ // System.err.println(properlyPairedCoverageAcrossReference[i]);
+ // insertSizeAcrossReference[i] = insertSizeAcrossReference[i]/(double)properlyPairedCoverageAcrossReference[i];
+
+ sumCoverageSquared += coverageAtPosition*coverageAtPosition;
+ sumCoverage += coverageAtPosition;
+ //numberOfProperlyPairedMappedBases++;
+
+ } else {
+ // make it invalid for histogram
+ mappingQualityAcrossReference[i] = -1;
+ }
+
+ }
+
+ // compute std coverageData
+
+ long meanCoverage = sumCoverage / coverageAcrossReference.length;
+ stdCoverage = Math.sqrt( (double) sumCoverageSquared / coverageAcrossReference.length - meanCoverage*meanCoverage);
+
+ }
+
+ @Override
+ public void addReadAlignmentData(SingleReadData readData) {
+ super.addReadAlignmentData(readData);
+ for (int pos : readData.coverageData) {
+ coverageAcrossReference[pos]++;
+ }
+
+ for (SingleReadData.Cell cell : readData.mappingQualityData) {
+ int pos = cell.getPosition();
+ int val = cell.getValue();
+ mappingQualityAcrossReference[pos] += val;
+ super.acumMappingQuality += val;
+ }
+
+ }
+
+ /**
+ * @return the coverageAcrossReference
+ */
+ public int[] getCoverageAcrossReference() {
+ return coverageAcrossReference;
+ }
+
+ public long getSumCoverageSquared() {
+ return sumCoverageSquared;
+ }
+
+ public long getSumCoverage() {
+ return sumCoverage;
+ }
+
+ /**
+ * @return the mappingQualityAcrossReference
+ */
+ public long[] getMappingQualityAcrossReference() {
+ return mappingQualityAcrossReference;
+ }
+
+
+
+
+
+}
\ No newline at end of file
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/beans/BamGenomeWindow.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/beans/BamGenomeWindow.java
new file mode 100644
index 0000000..e4dcac2
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/beans/BamGenomeWindow.java
@@ -0,0 +1,497 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.beans;
+
+import java.util.BitSet;
+
+public class BamGenomeWindow {
+ protected String name;
+
+ // window params
+ protected long start;
+ protected long end;
+ protected long windowSize;
+
+ // general
+ protected long numberOfMappedBases;
+ protected long numberOfSequencedBases;
+ protected long numberOfAlignedBases;
+
+ // gff-like
+ protected boolean selectedRegionsAvailable;
+ protected BitSet selectedRegions;
+
+ /*
+ *
+ * Reference params
+ *
+ */
+ protected boolean referenceAvailable;
+
+ // A content
+ protected long numberOfAsInReference;
+ protected double aRelativeContentInReference;
+
+ // C content
+ protected long numberOfCsInReference;
+ protected double cRelativeContentInReference;
+
+ // T content
+ protected long numberOfTsInReference;
+ protected double tRelativeContentInReference;
+
+ // G content
+ protected long numberOfGsInReference;
+ protected double gRelativeContentInReference;
+
+ // N content
+ protected long numberOfNsInReference;
+ protected double nRelativeContentInReference;
+
+ // GC content
+ protected long numberOfGcsInReference;
+ protected double gcRelativeContentInReference;
+
+ // AT content
+ protected long numberOfAtsInReference;
+ protected double atRelativeContentInReference;
+
+ /*
+ *
+ * Sample params
+ *
+ */
+
+ // coverageData
+ protected double meanCoverage;
+ protected double stdCoverage;
+
+ // quality
+ protected double acumMappingQuality;
+ protected double meanMappingQuality;
+
+ // A content
+ protected long numberOfAs;
+ protected double meanAContent;
+ protected double meanARelativeContent;
+
+ // C content
+ protected long numberOfCs;
+ protected double meanCContent;
+ protected double meanCRelativeContent;
+
+ // G content
+ protected long numberOfTs;
+ protected double meanGContent;
+ protected double meanGRelativeContent;
+
+ // T content
+ protected long numberOfGs;
+ protected double meanTContent;
+ protected double meanTRelativeContent;
+
+ // N content
+ protected long numberOfNs;
+ protected double meanNContent;
+ protected double meanNRelativeContent;
+
+ // GC content
+ protected double meanGcContent;
+ protected double meanGcRelativeContent;
+
+ protected int correctInsertSizes;
+ protected double acumInsertSize;
+ protected double meanInsertSize;
+ protected long effectiveWindowLength;
+
+ public BamGenomeWindow(String name, long start, long end, byte[] reference){
+ this.name = name;
+
+ // windows params
+ this.start = start;
+ this.end = end;
+ this.windowSize = (end - start + 1);
+
+ // process reference
+ if(reference!=null){
+ processReference(reference);
+ }
+
+ // init counters
+ numberOfMappedBases = 0;
+ numberOfSequencedBases = 0;
+ numberOfAlignedBases = 0;
+
+ }
+
+ public void processReference(byte[] reference){
+ char nucleotide;
+ for(long i=0; i<reference.length; i++){
+ nucleotide = (char)reference[(int)i];
+ if(nucleotide=='A'){
+ numberOfAsInReference++;
+ }
+ else if(nucleotide=='C'){
+ numberOfCsInReference++;
+ }
+ else if(nucleotide=='T'){
+ numberOfTsInReference++;
+ }
+ else if(nucleotide=='G'){
+ numberOfGsInReference++;
+ }
+ else if(nucleotide=='N'){
+ numberOfNsInReference++;
+ }
+ }
+ numberOfGcsInReference = numberOfGsInReference + numberOfCsInReference;
+ numberOfAtsInReference = numberOfAsInReference + numberOfTsInReference;
+
+ // relative contents
+ aRelativeContentInReference = ((double)numberOfAsInReference/(double)windowSize)*100.0;
+ cRelativeContentInReference = ((double)numberOfCsInReference/(double)windowSize)*100.0;
+ tRelativeContentInReference = ((double)numberOfTsInReference/(double)windowSize)*100.0;
+ gRelativeContentInReference = ((double)numberOfGsInReference/(double)windowSize)*100.0;
+ nRelativeContentInReference = ((double)numberOfNsInReference/(double)windowSize)*100.0;
+ gcRelativeContentInReference = ((double)numberOfGcsInReference/(double)windowSize)*100.0;
+ atRelativeContentInReference = ((double)numberOfAtsInReference/(double)windowSize)*100.0;
+
+ referenceAvailable = true;
+ }
+
+
+ protected void acumBase(long relative){
+ numberOfSequencedBases++;
+ numberOfMappedBases++;
+ }
+
+ protected void acumProperlyPairedBase(long relative){
+
+ }
+
+ protected void acumMappingQuality(long relative, int mappingQuality){
+ acumMappingQuality+=mappingQuality;
+ }
+
+ public void acumInsertSize(long insertSize){
+ if(insertSize > 0 /*& insertSize<5000*/){
+ correctInsertSizes++;
+ acumInsertSize += Math.abs(insertSize);
+ }
+ }
+
+ public void computeDescriptors() throws CloneNotSupportedException{
+
+ // org.bioinfo.ntools.process acums
+
+ effectiveWindowLength = windowSize;
+ if ( selectedRegionsAvailable ) {
+ effectiveWindowLength = selectedRegions.cardinality();
+ }
+
+ if (effectiveWindowLength != 0) {
+ meanCoverage = (double) numberOfMappedBases / effectiveWindowLength;
+ } else {
+ meanCoverage = 0;
+ }
+
+
+ if (correctInsertSizes > 0) {
+ meanInsertSize = acumInsertSize/(double)correctInsertSizes;
+ }
+
+ // ACTG absolute content
+ if(meanCoverage > 0){
+
+ meanMappingQuality = acumMappingQuality/(double)numberOfMappedBases;
+
+ //meanARelativeContent = numberOfAs / numberOfMappedBases * 100.0
+
+ meanAContent = (double)numberOfAs/ meanCoverage;
+ meanCContent = (double)numberOfCs/ meanCoverage;
+ meanTContent = (double)numberOfTs/ meanCoverage;
+ meanGContent = (double)numberOfGs/ meanCoverage;
+ meanNContent = (double)numberOfNs/ meanCoverage;
+ meanGcContent = meanCContent + meanGContent; //(double)(numberOfGs+numberOfCs)/(double)meanCoverage;
+ //
+ // meanAtContent = meanAContent + meanTContent; //(double)(numberOfAs+numberOfTs)/(double)meanCoverage;
+ // ACTG relative content
+ double acumMeanContent = meanAContent + meanCContent + meanTContent + meanGContent + meanNContent;
+ meanARelativeContent = ( meanAContent / acumMeanContent)*100.0;
+ meanCRelativeContent = ( meanCContent / acumMeanContent)*100.0;
+ meanTRelativeContent = ( meanTContent / acumMeanContent)*100.0;
+ meanGRelativeContent = ( meanGContent / acumMeanContent)*100.0;
+ meanNRelativeContent = ( meanNContent / acumMeanContent)*100.0;
+ meanGcRelativeContent = meanCRelativeContent + meanGRelativeContent;
+// meanAtRelativeContent = meanARelativeContent + meanTRelativeContent;
+ }
+
+ }
+
+ /**
+ * @return the name
+ */
+ public String getName() {
+ return name;
+ }
+
+ /**
+ * @return the start
+ */
+ public long getStart() {
+ return start;
+ }
+
+ /**
+ * @return the end
+ */
+ public long getEnd() {
+ return end;
+ }
+
+ /**
+ * @return the windowSize
+ */
+ public long getWindowSize() {
+ return windowSize;
+ }
+
+ /**
+
+ /**
+ * @return the numberOfMappedBases
+ */
+ public long getNumberOfMappedBases() {
+ return numberOfMappedBases;
+ }
+
+ /**
+ * @return the numberOfSequencedBases
+ */
+ public long getNumberOfSequencedBases() {
+ return numberOfSequencedBases;
+ }
+
+ /**
+ * @return the numberOfAlignedBases
+ */
+ public long getNumberOfAlignedBases() {
+ return numberOfAlignedBases;
+ }
+
+ /**
+ * @param selectedRegionsAvailable the selectedRegionsAvailable to set
+ */
+ public void setSelectedRegionsAvailable(boolean selectedRegionsAvailable) {
+ this.selectedRegionsAvailable = selectedRegionsAvailable;
+ }
+
+ /**
+ * @return the selectedRegions
+ */
+ public BitSet getSelectedRegions() {
+ return selectedRegions;
+ }
+
+ /**
+ * @param selectedRegions the selectedRegions to set
+ */
+ public void setSelectedRegions(BitSet selectedRegions) {
+ this.selectedRegions = selectedRegions;
+ }
+
+ /**
+ * @return the meanCoverage
+ */
+ public double getMeanCoverage() {
+ return meanCoverage;
+ }
+
+ /**
+ * @return the stdCoverage
+ */
+ public double getStdCoverage() {
+ return stdCoverage;
+ }
+
+ /**
+ * @return the meanMappingQuality
+ */
+ public double getMeanMappingQuality() {
+ return meanMappingQuality;
+ }
+
+ /**
+ * @return the numberOfAs
+ */
+ public long getNumberOfAs() {
+ return numberOfAs;
+ }
+
+ /**
+ * @return the meanAContent
+ */
+ public double getMeanAContent() {
+ return meanAContent;
+ }
+
+ /**
+ * @return the meanARelativeContent
+ */
+ public double getMeanARelativeContent() {
+ return meanARelativeContent;
+ }
+
+ /**
+ * @return the numberOfCs
+ */
+ public long getNumberOfCs() {
+ return numberOfCs;
+ }
+
+ /**
+ * @return the meanCContent
+ */
+ public double getMeanCContent() {
+ return meanCContent;
+ }
+
+ /**
+ * @return the meanCRelativeContent
+ */
+ public double getMeanCRelativeContent() {
+ return meanCRelativeContent;
+ }
+
+
+ /**
+ * @return the numberOfTs
+ */
+ public long getNumberOfTs() {
+ return numberOfTs;
+ }
+
+ /**
+ * @return the meanGContent
+ */
+ public double getMeanGContent() {
+ return meanGContent;
+ }
+
+ /**
+ * @return the meanGRelativeContent
+ */
+ public double getMeanGRelativeContent() {
+ return meanGRelativeContent;
+ }
+
+ /**
+ * @return the numberOfGs
+ */
+ public long getNumberOfGs() {
+ return numberOfGs;
+ }
+
+
+ /**
+ * @return the meanTContent
+ */
+ public double getMeanTContent() {
+ return meanTContent;
+ }
+
+
+ /**
+ * @return the meanTRelativeContent
+ */
+ public double getMeanTRelativeContent() {
+ return meanTRelativeContent;
+ }
+
+
+ /**
+ * @return the numberOfNs
+ */
+ public long getNumberOfNs() {
+ return numberOfNs;
+ }
+
+
+ /**
+ * @return the meanNContent
+ */
+ public double getMeanNContent() {
+ return meanNContent;
+ }
+
+
+ /**
+ * @return the meanNRelativeContent
+ */
+ public double getMeanNRelativeContent() {
+ return meanNRelativeContent;
+ }
+
+
+ /**
+ * @return the meanGcContent
+ */
+ public double getMeanGcContent() {
+ return meanGcContent;
+ }
+
+
+ /**
+ * @return the meanGcRelativeContent
+ */
+ public double getMeanGcRelativeContent() {
+ return meanGcRelativeContent;
+ }
+
+
+ /**
+ * @return the meanInsertSize
+ */
+ public double getMeanInsertSize() {
+ return meanInsertSize;
+ }
+
+ public void inverseRegions() {
+ selectedRegions.flip(0, selectedRegions.size());
+ }
+
+ public void addReadAlignmentData(SingleReadData readData) {
+
+ numberOfMappedBases += readData.numberOfMappedBases;
+ numberOfSequencedBases += readData.numberOfSequencedBases;
+
+ numberOfAs += readData.numberOfAs;
+ numberOfCs += readData.numberOfCs;
+ numberOfGs += readData.numberOfGs;
+ numberOfTs += readData.numberOfTs;
+
+
+ }
+
+ public long getEffectiveWindowLength() {
+ return effectiveWindowLength;
+ }
+}
\ No newline at end of file
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/beans/BamQCBarChart.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/beans/BamQCBarChart.java
new file mode 100644
index 0000000..687df2e
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/beans/BamQCBarChart.java
@@ -0,0 +1,204 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.beans;
+
+import org.jfree.chart.ChartFactory;
+import org.jfree.chart.JFreeChart;
+import org.jfree.chart.plot.CategoryPlot;
+import org.jfree.chart.plot.PlotOrientation;
+import org.jfree.chart.renderer.category.BarPainter;
+import org.jfree.chart.renderer.category.BarRenderer;
+import org.jfree.chart.renderer.category.CategoryItemRenderer;
+import org.jfree.chart.title.TextTitle;
+import org.jfree.data.category.DefaultCategoryDataset;
+import org.jfree.ui.RectangleEdge;
+import org.jfree.ui.RectangleInsets;
+
+import java.awt.*;
+import java.awt.geom.RectangularShape;
+import java.io.BufferedWriter;
+import java.io.IOException;
+import java.util.Arrays;
+import java.util.Collection;
+
+/**
+ * Created by kokonech
+ * Date: 6/27/12
+ * Time: 12:00 PM
+ */
+public class BamQCBarChart extends ChartRawDataWriter {
+
+
+ String xLabel, yLabel, title, subTitle;
+ Collection<CategoryItem> series;
+ JFreeChart chart;
+
+
+ static class CustomBarPainter implements BarPainter {
+
+ private static Color DEFAULT_BORDER_BAR_COLOR = new Color(50,50,50);
+
+
+ @Override
+ public void paintBar(Graphics2D g, BarRenderer barRenderer, int i, int i1, RectangularShape rectangularShape, RectangleEdge rectangleEdge) {
+ // create shape
+ RectangularShape myshape = (RectangularShape) rectangularShape.clone();
+
+ // fill
+ g.setPaint(barRenderer.getItemPaint(i, i1));
+ g.fill(myshape);
+
+ // border
+ g.setColor(DEFAULT_BORDER_BAR_COLOR);
+ g.setStroke(new BasicStroke(1.5f));
+ g.draw(myshape);
+ }
+
+ @Override
+ public void paintBarShadow(Graphics2D graphics2D, BarRenderer barRenderer, int i, int i1, RectangularShape rectangularShape, RectangleEdge rectangleEdge, boolean b) {
+ // NOTHING TO DO
+ }
+ }
+
+ static class CustomBarRenderer extends BarRenderer {
+
+ /** The colors. */
+ private Paint[] colors;
+
+ /**
+ * Creates a new renderer.
+ *
+ * @param colors the colors.
+ */
+ public CustomBarRenderer(final Paint[] colors) {
+ this.colors = colors;
+ BarPainter barPainter = new CustomBarPainter();
+ setBarPainter(barPainter);
+ }
+
+ /**
+ * Returns the paint for an item. Overrides the default behaviour inherited from
+ * AbstractSeriesRenderer.
+ *
+ * @param row the series.
+ * @param column the category.
+ *
+ * @return The item color.
+ */
+ public Paint getItemPaint(final int row, final int column) {
+ return this.colors[column % this.colors.length];
+ }
+ }
+
+ public BamQCBarChart(String title, String subTitle, String xLabel, String yLabel,
+ Collection<CategoryItem> series) {
+ this.title = title;
+ this.subTitle = subTitle;
+ this.xLabel = xLabel;
+ this.yLabel = yLabel;
+ this.series = series;
+
+ }
+
+
+
+ public void render() throws IOException {
+
+ // create the dataset...
+ final DefaultCategoryDataset dataset = new DefaultCategoryDataset();
+
+ for (CategoryItem item : series) {
+ dataset.addValue(item.getValue(), "data", item.getName());
+ }
+
+ chart = ChartFactory.createBarChart(
+ title, // chart title
+ xLabel, // domain axis label
+ yLabel, // range axis label
+ dataset, // data
+ PlotOrientation.VERTICAL,
+ true, // include legend
+ true, // tooltips?
+ false // URLs?
+ );
+
+ // title
+ TextTitle textTitle = new TextTitle(title);
+ textTitle.setFont(new Font(Font.SANS_SERIF,Font.BOLD,18));
+ textTitle.setPaint(Color.darkGray);
+ chart.setTitle(textTitle);
+
+ // subtitle
+ TextTitle sub = new TextTitle(subTitle);
+ Font subFont = new Font(Font.SANS_SERIF,Font.PLAIN,12);
+ sub.setFont(subFont);
+ sub.setPadding(5, 5, 15, 5);
+ sub.setPaint(Color.darkGray);
+ chart.setSubtitles(Arrays.asList(sub));
+
+ // other params
+ chart.setPadding(new RectangleInsets(30,20,30,20));
+
+ CategoryPlot plot = chart.getCategoryPlot();
+ // axis style
+ Font axisFont = new Font(Font.SANS_SERIF,Font.PLAIN,11);
+ plot.getDomainAxis().setLabelFont(axisFont);
+ plot.getRangeAxis().setLabelFont(axisFont);
+ Font tickFont = new Font(Font.SANS_SERIF,Font.PLAIN,10);
+ plot.getDomainAxis().setTickLabelFont(tickFont);
+ plot.getRangeAxis().setTickLabelFont(tickFont);
+
+ //plot.getDomainAxis().setCategoryLabelPositions(CategoryLabelPositions.DOWN_90);
+ plot.getDomainAxis().setMaximumCategoryLabelWidthRatio(100.0f);
+
+ final CategoryItemRenderer renderer = new CustomBarRenderer(
+ new Paint[] {new Color(255,20,20,150), new Color(20,20,255,150), new Color(20,255,20,150),
+ new Color(20,20,20,150), new Color(20,255,255,150), new Color(255,180,20,150) }
+ );
+
+
+ plot.setRenderer(renderer);
+
+
+ // grid
+ plot.setBackgroundPaint(Color.WHITE);
+ chart.setBackgroundPaint(new Color(230,230,230));
+ plot.setDomainGridlinePaint(new Color(214,139,74));
+ plot.setRangeGridlinePaint(new Color(214,139,74));
+
+
+ }
+
+ @Override
+ void exportData(BufferedWriter dataWriter) throws IOException {
+ dataWriter.write("#" + xLabel + "\t" + yLabel + "\n");
+
+ for (CategoryItem item : series) {
+ dataWriter.write(item.getName() + "\t" + Integer.toString(item.getValue()) + "\n");
+ }
+
+
+ }
+
+ public JFreeChart getChart() {
+ return chart;
+ }
+}
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/beans/BamQCChart.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/beans/BamQCChart.java
new file mode 100644
index 0000000..9e47b4e
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/beans/BamQCChart.java
@@ -0,0 +1,446 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.beans;
+
+import java.awt.*;
+import java.io.BufferedWriter;
+import java.io.IOException;
+import java.io.Serializable;
+import java.util.*;
+import java.util.List;
+
+import org.jfree.chart.ChartFactory;
+import org.jfree.chart.JFreeChart;
+import org.jfree.chart.LegendItem;
+import org.jfree.chart.LegendItemCollection;
+import org.jfree.chart.LegendItemSource;
+import org.jfree.chart.annotations.XYBoxAnnotation;
+import org.jfree.chart.annotations.XYTextAnnotation;
+import org.jfree.chart.axis.NumberAxis;
+import org.jfree.chart.axis.NumberTickUnit;
+import org.jfree.chart.labels.XYToolTipGenerator;
+import org.jfree.chart.plot.PlotOrientation;
+import org.jfree.chart.renderer.xy.*;
+import org.jfree.chart.title.LegendTitle;
+import org.jfree.chart.title.TextTitle;
+import org.jfree.data.xy.*;
+import org.jfree.ui.*;
+
+public class BamQCChart extends ChartRawDataWriter implements Serializable {
+
+ private String title;
+ private String subTitle;
+ private String xLabel;
+ private String yLabel;
+
+ // series
+ private List<String> names;
+ private List<XYVector> series;
+ private List<Color> colors;
+ private List<Stroke> strokes;
+ private List<AbstractXYItemRenderer> renderers;
+ private XYToolTipGenerator toolTipGenerator;
+ private int numberOfSeries;
+ private int seriesToExportIndex;
+ private double chromNameYPos;
+ private Map<Double,String> chrNames;
+
+ // other params
+ private boolean aPercentageChart;
+ private boolean rangeAxisIntegerTicks;
+ private boolean domainAxisIntegerTicks;
+ private boolean adjustDomainAxisLimits;
+ private boolean showLegend;
+
+ // chart
+ private JFreeChart chart;
+ private double domainAxisTickUnitSize;
+
+
+ public BamQCChart(String title,String subTitle, String xLabel, String yLabel){
+ // init org.bioinfo.ntools.main params
+ this.title = title;
+ this.subTitle = subTitle;
+ this.xLabel = xLabel;
+ this.yLabel = yLabel;
+
+ // init series
+ names = new ArrayList<String>();
+ series = new ArrayList<XYVector>();
+ colors = new ArrayList<Color>();
+ strokes = new ArrayList<Stroke>();
+ renderers = new ArrayList<AbstractXYItemRenderer>();
+ numberOfSeries = 0;
+
+ // other params
+ adjustDomainAxisLimits = true;
+ domainAxisTickUnitSize = 0;
+ seriesToExportIndex = -1;
+ showLegend = true;
+ chromNameYPos = 0;
+ chrNames = null;
+
+ }
+
+ // line rendered series
+ public void addSeries(String name, XYVector series, Color color){
+ addSeries(name,series,color,new BasicStroke(1.5f), true);
+ }
+
+ public void addSeries(String name, XYVector series, Color color, Stroke stroke, boolean visibleInLegend,
+ List<XYBoxAnnotation> annotations){
+ XYLineAndShapeRenderer renderer = new XYLineAndShapeRenderer();
+ for (XYBoxAnnotation ann : annotations) {
+ renderer.addAnnotation(ann, Layer.BACKGROUND);
+ }
+ renderer.setSeriesShapesVisible(0, false);
+ renderer.setSeriesVisibleInLegend(0, visibleInLegend);
+ addSeries(name,series,color,stroke,renderer);
+ }
+
+ public void addSeries(String name, XYVector series, Color color, Stroke stroke, boolean visibleInLegend){
+ XYLineAndShapeRenderer renderer = new XYLineAndShapeRenderer();
+ renderer.setSeriesShapesVisible(0, false);
+ renderer.setSeriesVisibleInLegend(0, visibleInLegend);
+ addSeries(name,series,color,stroke,renderer);
+ }
+
+ // point rendered series
+ /*public void addPointRenderedSeries(String name, XYVector series, Color color){
+ XYLineAndShapeRenderer renderer = new XYLineAndShapeRenderer();
+ //renderer.setSeriesLinesVisible(0, false);
+ //renderer.setSeriesVisibleInLegend(0, true);
+ addSeries(name,series,color,new BasicStroke(10f), renderer);
+ }*/
+
+ // bar rendered series
+ public void addBarRenderedSeries(String name, XYVector series, Color color){
+ addBarRenderedSeries(name,series,color,new BasicStroke(1.5f));
+ }
+
+
+ public void addBarRenderedSeries(String name, XYVector series, Color color, Stroke stroke){
+ XYBarRenderer renderer = new XYBarRenderer();
+ BamXYBarPainter barPainter = new BamXYBarPainter(color);
+ renderer.setBarPainter(barPainter);
+ addSeries(name, series, color, stroke, renderer);
+ }
+
+
+ // interval rendered series
+ public void addIntervalRenderedSeries(String name, XYVector series, Color lineColor, Color deviationColor, float alpha){
+ addIntervalRenderedSeries(name,series,lineColor,deviationColor,alpha,new BasicStroke(1.5f));
+ }
+
+
+ public void addIntervalRenderedSeries(String name, XYVector series, Color lineColor, Color deviationColor, float alpha, Stroke stroke){
+ DeviationRenderer renderer = new DeviationRenderer(true,false);
+ renderer.setSeriesFillPaint(0,deviationColor);
+ renderer.setAlpha(alpha);
+ addSeries(name, series, lineColor, stroke, renderer);
+ }
+
+
+ public void addSeries(String name, XYVector series, Color color, Stroke stroke, AbstractXYItemRenderer renderer){
+ this.names.add(name);
+ this.series.add(series);
+ this.colors.add(color);
+ this.strokes.add(stroke);
+ this.renderers.add(renderer);
+ numberOfSeries++;
+ }
+
+ void setToolTipGenerator(XYToolTipGenerator toolTipGenerator) {
+ this.toolTipGenerator = toolTipGenerator;
+ }
+
+ public void setAdjustDomainAxisLimits(boolean adjustDomainAxisLimits) {
+ this.adjustDomainAxisLimits = adjustDomainAxisLimits;
+ }
+
+ public void render(){
+ // init chart
+ chart = ChartFactory.createXYLineChart(title,xLabel,yLabel, null, PlotOrientation.VERTICAL, true, true, false);
+
+ // title
+ TextTitle textTitle = new TextTitle(title);
+ textTitle.setFont(new Font(Font.SANS_SERIF,Font.BOLD,18));
+ textTitle.setPaint(Color.darkGray);
+ chart.setTitle(textTitle);
+
+ // subtitle
+ TextTitle sub = new TextTitle(subTitle);
+ Font subFont = new Font(Font.SANS_SERIF,Font.PLAIN,12);
+ sub.setFont(subFont);
+ sub.setPadding(5, 5, 15, 5);
+ sub.setPaint(Color.darkGray);
+ chart.setSubtitles(Arrays.asList(sub));
+
+ // other params
+ chart.setPadding(new RectangleInsets(30,20,30,20));
+
+ // axis style
+ Font axisFont = new Font(Font.SANS_SERIF,Font.PLAIN,11);
+ chart.getXYPlot().getDomainAxis().setLabelFont(axisFont);
+ chart.getXYPlot().getRangeAxis().setLabelFont(axisFont);
+ Font tickFont = new Font(Font.SANS_SERIF,Font.PLAIN,10);
+ chart.getXYPlot().getDomainAxis().setTickLabelFont(tickFont);
+ chart.getXYPlot().getRangeAxis().setTickLabelFont(tickFont);
+
+ if(aPercentageChart) {
+ chart.getXYPlot().getRangeAxis().setAutoRange(false);
+ chart.getXYPlot().getRangeAxis().setRange(0, 100);
+ }
+
+ if(domainAxisIntegerTicks){
+ NumberAxis numberaxis = (NumberAxis)chart.getXYPlot().getDomainAxis();
+ numberaxis.setAutoRangeIncludesZero(false);
+ numberaxis.setStandardTickUnits(NumberAxis.createIntegerTickUnits());
+
+ }
+
+ if (domainAxisTickUnitSize != 0) {
+ NumberAxis numberaxis = (NumberAxis)chart.getXYPlot().getDomainAxis();
+ numberaxis.setTickLabelFont(new Font(Font.SANS_SERIF,Font.PLAIN,8));
+ numberaxis.setTickUnit( new NumberTickUnit(domainAxisTickUnitSize));
+ }
+
+
+ if(rangeAxisIntegerTicks){
+ NumberAxis numberaxis = (NumberAxis)chart.getXYPlot().getRangeAxis();
+ numberaxis.setAutoRangeIncludesZero(false);
+ numberaxis.setStandardTickUnits(NumberAxis.createIntegerTickUnits());
+ }
+
+ // grid
+ chart.getXYPlot().setBackgroundPaint(Color.WHITE);
+ chart.setBackgroundPaint(new Color(230,230,230));
+ chart.getXYPlot().setDomainGridlinePaint(new Color(214,139,74));
+ chart.getXYPlot().setRangeGridlinePaint(new Color(214,139,74));
+ chart.getXYPlot().setDomainMinorGridlinesVisible(true);
+ chart.getXYPlot().setDomainMinorGridlinePaint(Color.red);
+
+
+ if (numberOfSeries == 0) {
+ chart.getXYPlot().setDomainGridlinesVisible(false);
+ chart.getXYPlot().setRangeGridlinesVisible(false);
+ chart.getXYPlot().getDomainAxis().setVisible(false); // X
+ chart.getXYPlot().getRangeAxis().setVisible(false); // Y
+ double middleX = chart.getXYPlot().getRangeAxis().getRange().getLength() / 2;
+ double middleY = chart.getXYPlot().getDomainAxis().getRange().getLength() / 2;
+ final XYTextAnnotation annotation = new XYTextAnnotation("No data available.", middleX, middleY);
+ annotation.setFont(new Font("SansSerif", Font.BOLD, 12));
+ chart.getXYPlot().addAnnotation(annotation);
+ return;
+ }
+
+
+ // prepare legend
+ LegendItemSource lis = new LegendItemSource() {
+ LegendItemCollection lic = new LegendItemCollection();
+ public LegendItemCollection getLegendItems() {
+ return lic;
+ }
+ };
+
+ double minDomainAxis = Double.MAX_VALUE;
+ double maxDomainAxis = Double.NEGATIVE_INFINITY;
+ double minNumberOfPoints = Double.MAX_VALUE;
+ double minDomainAxisSeries, maxDomainAxisSeries, numberOfSeriesPoints;
+ boolean anyBarRendered = false;
+
+ // prepare series
+ for (int i=0; i<numberOfSeries; i++){
+ minDomainAxisSeries = series.get(i).get(0).getX();
+ maxDomainAxisSeries = series.get(i).get(series.get(i).getSize()-1).getX();
+ numberOfSeriesPoints = series.get(i).getSize();
+
+ if(minDomainAxisSeries<minDomainAxis) minDomainAxis = minDomainAxisSeries;
+ if(maxDomainAxisSeries>maxDomainAxis) maxDomainAxis = maxDomainAxisSeries;
+ if(numberOfSeriesPoints<minNumberOfPoints) minNumberOfPoints = numberOfSeriesPoints;
+
+ if(renderers.get(i) instanceof DeviationRenderer){
+ YIntervalSeries currentIntervalSeries = new YIntervalSeries(names.get(i));
+
+ // add points
+ XYIntervalItem item;
+ for(int j=0; j<series.get(i).getSize(); j++){
+ item = (XYIntervalItem) series.get(i).get(j);
+ currentIntervalSeries.add(item.getX(),item.getY(),item.getyDownDeviation(),item.getyUpDeviation());
+ }
+
+ // add series
+ YIntervalSeriesCollection data = new YIntervalSeriesCollection();
+ data.addSeries(currentIntervalSeries);
+ chart.getXYPlot().setDataset(i,data);
+ } else {
+ if(renderers.get(i) instanceof XYBarRenderer) anyBarRendered = true;
+ // init series
+ XYSeries currentSeries = new XYSeries(names.get(i));
+
+ // add points
+ for(int j=0; j<series.get(i).getSize(); j++){
+ XYItem item = series.get(i).get(j);
+ currentSeries.add(item.getX(),item.getY());
+ }
+
+
+
+ // add series
+ chart.getXYPlot().setDataset(i, new XYSeriesCollection(currentSeries));
+ }
+
+
+ boolean addChrNames = chrNames != null;
+ if (addChrNames) {
+ for (Map.Entry<Double,String> entry : chrNames.entrySet()) {
+ final XYTextAnnotation annotation = new XYTextAnnotation(
+ entry.getValue(), entry.getKey(), chromNameYPos );
+ annotation.setRotationAngle(- Math.PI / 2.0);
+ chart.getXYPlot().addAnnotation(annotation);
+ }
+ }
+
+
+ // set stroke
+ renderers.get(i).setSeriesStroke(0, strokes.get(i));
+
+ // set color
+ renderers.get(i).setSeriesPaint(0, colors.get(i));
+
+ // set tooltip generator
+ renderers.get(i).setBaseToolTipGenerator(toolTipGenerator);
+
+ // add renderer
+ chart.getXYPlot().setRenderer(i,renderers.get(i));
+
+ // add legend item
+ LegendItem legendItem = new LegendItem(names.get(i));
+ legendItem.setLabelFont(new Font(Font.SANS_SERIF,Font.PLAIN,11));
+ legendItem.setLabelPaint(Color.darkGray);
+ legendItem.setFillPaint(colors.get(i));
+ lis.getLegendItems().add(legendItem);
+ }
+
+ // finalize legend
+ if (showLegend) {
+ chart.addLegend(new LegendTitle(lis));
+ chart.getLegend().setMargin(2,0,-7,10);
+ chart.getLegend().setVerticalAlignment(VerticalAlignment.TOP);
+ chart.getLegend().setHorizontalAlignment(HorizontalAlignment.RIGHT);
+ chart.getLegend().setLegendItemGraphicPadding(new RectangleInsets(5,5,5,5));
+ }
+
+ // adjust axis limits
+ double abit = 0;
+ if(anyBarRendered) abit = ((maxDomainAxis-minDomainAxis)/minNumberOfPoints)/2.0;
+
+ if(adjustDomainAxisLimits){
+ chart.getXYPlot().getDomainAxis().setRange(minDomainAxis-abit,maxDomainAxis+abit);
+ }
+ }
+
+ /**
+ * @return the chart
+ */
+ public JFreeChart getChart() {
+ return chart;
+ }
+
+
+ /**
+ * @param aPercentageChart the aPercentageChart to set
+ */
+ public void setPercentageChart(boolean aPercentageChart) {
+ this.aPercentageChart = aPercentageChart;
+ }
+
+ /**
+ * @param domainAxisIntegerTicks the domainAxisIntegerTicks to set
+ */
+ public void setDomainAxisIntegerTicks(boolean domainAxisIntegerTicks) {
+ this.domainAxisIntegerTicks = domainAxisIntegerTicks;
+ }
+
+ public void setDomainAxisTickUnitSize(double domainAxisTickUnitSize) {
+ this.domainAxisTickUnitSize = domainAxisTickUnitSize;
+ }
+
+ public void setSeriesToExportIndex(int seriesToExportIndex) {
+ this.seriesToExportIndex = seriesToExportIndex;
+ }
+
+ @Override
+ void exportData(BufferedWriter dataWriter) throws IOException {
+
+ dataWriter.write("#" + xLabel);
+
+ if (seriesToExportIndex != -1 && names.size() > seriesToExportIndex && series.size() > seriesToExportIndex ) {
+ //export only single series
+ dataWriter.write("\t" + names.get(seriesToExportIndex) + "\n");
+ XYVector s = series.get(seriesToExportIndex);
+ int len = s.getSize();
+ for (int i = 0; i < len; ++i) {
+ dataWriter.write(s.get(i).getX() + "\t" + s.get(i).getY() + "\n");
+ }
+
+
+ } else {
+
+ //Export whole data set
+
+ for (String name : names) {
+ dataWriter.write("\t" + name);
+ }
+ dataWriter.write("\n");
+
+ int len = series.get(0).getSize();
+ double[] xData = series.get(0).getXVector();
+
+ for (int i = 0; i < len; ++i) {
+ dataWriter.write(Double.toString(xData[i]));
+ for (XYVector data : series) {
+ if (data.getSize() > i) {
+ dataWriter.write("\t" + data.get(i).getY());
+ }
+ }
+ dataWriter.write("\n");
+ }
+
+ }
+
+ }
+
+ public void setShowLegend(boolean showLegend) {
+ this.showLegend = showLegend;
+ }
+
+
+ public void setTitle(String title) {
+ this.title = title;
+ }
+
+ public void writeChromsomeNames(double yPos, Map<Double,String> names) {
+ chromNameYPos = yPos;
+ chrNames = names;
+
+ }
+}
\ No newline at end of file
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/beans/BamQCHistogramChart.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/beans/BamQCHistogramChart.java
new file mode 100644
index 0000000..b6707b1
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/beans/BamQCHistogramChart.java
@@ -0,0 +1,184 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.beans;
+
+import org.jfree.chart.ChartFactory;
+import org.jfree.chart.JFreeChart;
+import org.jfree.chart.axis.NumberAxis;
+import org.jfree.chart.axis.NumberTickUnit;
+import org.jfree.chart.plot.PlotOrientation;
+import org.jfree.chart.plot.XYPlot;
+import org.jfree.chart.renderer.xy.XYBarRenderer;
+import org.jfree.chart.title.TextTitle;
+import org.jfree.data.xy.XYSeries;
+import org.jfree.data.xy.XYSeriesCollection;
+import org.jfree.ui.RectangleInsets;
+
+import java.awt.*;
+import java.io.BufferedWriter;
+import java.io.IOException;
+import java.util.Arrays;
+import java.util.Map;
+
+/**
+ * Created by kokonech
+ * Date: 3/23/12
+ * Time: 10:10 AM
+ */
+public class BamQCHistogramChart extends ChartRawDataWriter {
+
+ private String title;
+ private String subTitle;
+ private String xLabel;
+ private String yLabel;
+
+ // histogram series
+ XYVector data;
+ Map<Double,String> barNames;
+
+ // chart
+ private JFreeChart chart;
+
+ public BamQCHistogramChart(String title,String subTitle, String xLabel, String yLabel,
+ XYVector data, Map<Double,String> barNames){
+
+ // main params
+ this.title = title;
+ this.subTitle = subTitle;
+ this.xLabel = xLabel;
+ this.yLabel = yLabel;
+ this.data = data;
+ this.barNames = barNames;
+
+ }
+
+ public JFreeChart getChart() {
+ return chart;
+ }
+
+
+ static class CustomTickUnit extends NumberTickUnit {
+
+ double maxValue;
+ Map<Double,String> tickLabels;
+ public CustomTickUnit(double size, double maxValue, Map<Double,String> tickLabels) {
+ super(size);
+ this.maxValue = maxValue;
+ this.tickLabels = tickLabels;
+
+ }
+
+ public String valueToString(double val) {
+ if (val >= 0 && val <= maxValue){
+ if (Math.floor(val) == val) {
+ if (tickLabels.containsKey(val)) {
+ //System.out.println("Val is " + val);
+ return tickLabels.get(val);
+ }
+ }
+ }
+ return "";
+ }
+
+ }
+
+ public void render() throws IOException {
+
+ // init chart
+ chart = ChartFactory.createHistogram(title, xLabel, yLabel, null, PlotOrientation.VERTICAL, true, true, false);
+
+
+ // title
+ TextTitle textTitle = new TextTitle(title);
+ textTitle.setFont(new Font(Font.SANS_SERIF,Font.BOLD,18));
+ textTitle.setPaint(Color.darkGray);
+ chart.setTitle(textTitle);
+
+ // subtitle
+ TextTitle sub = new TextTitle(subTitle);
+ Font subFont = new Font(Font.SANS_SERIF,Font.PLAIN,12);
+ sub.setFont(subFont);
+ sub.setPadding(5, 5, 15, 5);
+ sub.setPaint(Color.darkGray);
+ chart.setSubtitles(Arrays.asList(sub));
+
+ // other params
+ chart.setPadding(new RectangleInsets(30,20,30,20));
+
+ XYPlot plot = chart.getXYPlot();
+ // axis style
+ Font axisFont = new Font(Font.SANS_SERIF,Font.PLAIN,11);
+ plot.getDomainAxis().setLabelFont(axisFont);
+ plot.getRangeAxis().setLabelFont(axisFont);
+ Font tickFont = new Font(Font.SANS_SERIF,Font.PLAIN,10);
+ plot.getDomainAxis().setTickLabelFont(tickFont);
+ plot.getRangeAxis().setTickLabelFont(tickFont);
+
+ // grid
+ plot.setBackgroundPaint(Color.WHITE);
+ chart.setBackgroundPaint(new Color(230,230,230));
+ plot.setDomainGridlinePaint(new Color(214,139,74));
+ plot.setRangeGridlinePaint(new Color(214,139,74));
+
+ XYSeries series = new XYSeries("Coverage");
+
+ double[] covs = data.getXVector();
+ double[] freqs = data.getYVector();
+ int len = covs.length;
+
+ for (int i = 0; i < len; ++i) {
+ series.add(covs[i], freqs[i]);
+ }
+
+ // mean dataset
+ chart.getXYPlot().setDataset(0, new XYSeriesCollection(series));
+
+ NumberAxis domainAxis = (NumberAxis) chart.getXYPlot().getDomainAxis();
+ //domainAxis.setTickLabelsVisible(false);
+ domainAxis.setTickMarksVisible(false);
+ double maxCov = covs[len - 1];
+ domainAxis.setTickUnit( new CustomTickUnit(0.5,maxCov,barNames));
+ domainAxis.setVerticalTickLabels(true);
+
+ // mean renderer
+ XYBarRenderer renderer = new XYBarRenderer();
+ BamXYBarPainter barPainter = new BamXYBarPainter();
+ renderer.setBarPainter(barPainter);
+ plot.setRenderer(renderer);
+
+ }
+
+
+ @Override
+ void exportData(BufferedWriter dataWriter) throws IOException{
+ dataWriter.write(xLabel + "\t" + yLabel + "\n");
+ int datalen = data.getSize();
+ double[] covs = data.getXVector();
+ double[] freqs = data.getYVector();
+ for (int i = 0; i < datalen; ++i) {
+ dataWriter.write(freqs[i] + "\t" + covs[i] + "\n");
+ }
+
+ }
+
+
+
+}
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/beans/BamQCPieChart.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/beans/BamQCPieChart.java
new file mode 100644
index 0000000..1c33f6b
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/beans/BamQCPieChart.java
@@ -0,0 +1,126 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.beans;
+
+import org.bioinfo.commons.utils.StringUtils;
+import org.jfree.chart.*;
+import org.jfree.chart.labels.PieSectionLabelGenerator;
+import org.jfree.chart.plot.PiePlot;
+import org.jfree.chart.title.TextTitle;
+import org.jfree.data.general.PieDataset;
+import org.jfree.ui.RectangleInsets;
+
+import java.awt.*;
+import java.text.AttributedString;
+import java.util.Arrays;
+
+/**
+ * Created by kokonech
+ * Date: 8/18/14
+ * Time: 4:04 PM
+ */
+public class BamQCPieChart {
+ String chartTitle, subTitle;
+ JFreeChart chart;
+ PieDataset pieDataset;
+
+ static class CustomLabelGenerator implements PieSectionLabelGenerator {
+
+
+ @Override
+ public String generateSectionLabel(final PieDataset dataset, final Comparable key) {
+ String result = null;
+ if (dataset != null) {
+ String formattedVal = StringUtils.decimalFormat(dataset.getValue(key).doubleValue(), "###.##") + "%";
+ result = key.toString() + " - " + formattedVal;
+ }
+ return result;
+ }
+
+ @Override
+ public AttributedString generateAttributedSectionLabel(PieDataset dataset, Comparable key) {
+ return null;
+ }
+
+ }
+
+
+ public BamQCPieChart(String chartTitle, String subTitle, PieDataset pieDataset ) {
+ this.chartTitle = chartTitle;
+ this.subTitle = subTitle;
+ this.pieDataset = pieDataset;
+ }
+
+
+ public void render() {
+
+ // create the chart...
+ chart = ChartFactory.createPieChart(
+ chartTitle, // chart title
+ pieDataset, // data
+ true, // include legend
+ true, // tooltips
+ false // urls
+ );
+
+ // title
+ TextTitle textTitle = new TextTitle(chartTitle);
+ textTitle.setFont(new Font(Font.SANS_SERIF,Font.BOLD,18));
+ textTitle.setPaint(Color.darkGray);
+ chart.setTitle(textTitle);
+
+ // subtitle
+ TextTitle sub = new TextTitle(subTitle);
+ Font subFont = new Font(Font.SANS_SERIF,Font.PLAIN,12);
+ sub.setFont(subFont);
+ sub.setPadding(5, 5, 15, 5);
+ sub.setPaint(Color.darkGray);
+ chart.setSubtitles(Arrays.asList(sub));
+
+ //background
+ chart.setBackgroundPaint(new Color(230,230,230));
+
+ // other params
+ chart.setPadding(new RectangleInsets(30,20,30,20));
+
+ //final StandardLegend legend = (StandardLegend) chart.getLegend();
+ //legend.setDisplaySeriesShapes(true);
+
+ PiePlot piePlot = (PiePlot) chart.getPlot();
+ piePlot.setNoDataMessage("No data available");
+ //piePlot.setCircular(false);
+ piePlot.setLabelGap(0.02);
+ piePlot.setLabelGenerator( new CustomLabelGenerator() );
+
+
+
+ // grid
+ piePlot.setBackgroundPaint(Color.white);
+
+
+
+ }
+
+ public JFreeChart getJFreeChart() {
+ return chart;
+ }
+
+}
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/beans/BamQCPointChart.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/beans/BamQCPointChart.java
new file mode 100644
index 0000000..cd0952c
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/beans/BamQCPointChart.java
@@ -0,0 +1,168 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.beans;
+
+import org.jfree.chart.*;
+import org.jfree.chart.axis.NumberAxis;
+import org.jfree.chart.plot.PlotOrientation;
+import org.jfree.chart.plot.XYPlot;
+import org.jfree.chart.renderer.xy.XYLineAndShapeRenderer;
+import org.jfree.chart.title.LegendTitle;
+import org.jfree.chart.title.TextTitle;
+import org.jfree.data.xy.XYSeries;
+import org.jfree.data.xy.XYSeriesCollection;
+import org.jfree.ui.HorizontalAlignment;
+import org.jfree.ui.RectangleInsets;
+import org.jfree.ui.VerticalAlignment;
+
+import java.awt.*;
+import java.awt.geom.Ellipse2D;
+import java.util.*;
+import java.util.List;
+
+/**
+ * Created by kokonech
+ * Date: 7/16/14
+ * Time: 3:08 PM
+ */
+public class BamQCPointChart {
+
+
+ String chartTitle, subTitle, xLabel, yLabel;
+ JFreeChart chart;
+ XYSeriesCollection dataset;
+ List<Color> colors;
+ List<String> names;
+
+ public BamQCPointChart(String title, String subTitle, String xLabel, String yLabel) {
+ this.chartTitle = title;
+ this.subTitle = subTitle;
+ this.xLabel = xLabel;
+ this.yLabel = yLabel;
+ dataset = new XYSeriesCollection();
+ colors = new ArrayList<Color>();
+ names = new ArrayList<String>();
+
+ }
+
+ public void addPoint(String sampleName, double x, double y, Color c) {
+ XYSeries series = new XYSeries(sampleName);
+ series.add(x, y);
+ dataset.addSeries(series);
+ colors.add(c);
+ names.add(sampleName);
+
+ }
+
+ public void render() {
+ // create the chart...
+ chart = ChartFactory.createXYLineChart(
+ chartTitle, // chart title
+ xLabel, // x axis label
+ yLabel, // y axis label
+ dataset, // data
+ PlotOrientation.VERTICAL,
+ true, // include legend
+ true, // tooltips
+ false // urls
+ );
+
+ // title
+ TextTitle textTitle = new TextTitle(chartTitle);
+ textTitle.setFont(new Font(Font.SANS_SERIF,Font.BOLD,18));
+ textTitle.setPaint(Color.darkGray);
+ chart.setTitle(textTitle);
+
+ // subtitle
+ TextTitle sub = new TextTitle(subTitle);
+ Font subFont = new Font(Font.SANS_SERIF,Font.PLAIN,12);
+ sub.setFont(subFont);
+ sub.setPadding(5, 5, 15, 5);
+ sub.setPaint(Color.darkGray);
+ chart.setSubtitles(Arrays.asList(sub));
+
+ //background
+ chart.setBackgroundPaint(new Color(230,230,230));
+
+
+ // other params
+ chart.setPadding(new RectangleInsets(30,20,30,20));
+
+ //final StandardLegend legend = (StandardLegend) chart.getLegend();
+ //legend.setDisplaySeriesShapes(true);
+
+ final XYPlot plot = chart.getXYPlot();
+
+ // grid
+ plot.setBackgroundPaint(Color.white);
+ plot.setDomainGridlinePaint(new Color(214, 139, 74));
+ plot.setRangeGridlinePaint(new Color(214, 139, 74));
+ plot.setDomainMinorGridlinesVisible(true);
+ plot.setDomainMinorGridlinePaint(Color.red);
+
+
+ // prepare legend
+ LegendItemSource lis = new LegendItemSource() {
+ LegendItemCollection lic = new LegendItemCollection();
+ public LegendItemCollection getLegendItems() {
+ return lic;
+ }
+ };
+
+ final XYLineAndShapeRenderer renderer = new XYLineAndShapeRenderer();
+ plot.setRenderer(renderer);
+
+ for (int i = 0; i < plot.getSeriesCount(); ++i) {
+ LegendItem legendItem = new LegendItem(names.get(i));
+ legendItem.setLabelFont(new Font(Font.SANS_SERIF,Font.PLAIN,11));
+ legendItem.setLabelPaint(Color.darkGray);
+ legendItem.setFillPaint(colors.get(i));
+ lis.getLegendItems().add(legendItem);
+
+ double size = 10.0;
+ double delta = size / 2;
+ renderer.setSeriesShape(i, new Ellipse2D.Double(-delta, -delta, size, size));
+ renderer.setSeriesPaint(i, colors.get(i));
+
+ }
+
+ chart.addLegend(new LegendTitle(lis));
+ chart.getLegend().setMargin(2,0,-7,10);
+ chart.getLegend().setVerticalAlignment(VerticalAlignment.TOP);
+ chart.getLegend().setHorizontalAlignment(HorizontalAlignment.RIGHT);
+ chart.getLegend().setLegendItemGraphicPadding(new RectangleInsets(5,5,5,5));
+
+
+ // change the auto tick unit selection to integer units only...
+ final NumberAxis rangeAxis = (NumberAxis) plot.getRangeAxis();
+ rangeAxis.setStandardTickUnits(NumberAxis.createIntegerTickUnits());
+
+
+
+
+ }
+
+
+ public JFreeChart getChart() {
+ return chart;
+ }
+
+}
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/beans/BamQCRegionReporter.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/beans/BamQCRegionReporter.java
new file mode 100644
index 0000000..44e050a
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/beans/BamQCRegionReporter.java
@@ -0,0 +1,1246 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.beans;
+
+import java.awt.*;
+import java.io.*;
+import java.text.DecimalFormat;
+import java.text.NumberFormat;
+import java.util.*;
+import java.util.List;
+
+import org.apache.commons.lang.ArrayUtils;
+import org.apache.commons.math.stat.StatUtils;
+import org.bioinfo.commons.utils.ListUtils;
+import org.bioinfo.commons.utils.StringUtils;
+import org.bioinfo.ngs.qc.qualimap.beans.BamStats.ChromosomeInfo;
+import org.bioinfo.ngs.qc.qualimap.common.Constants;
+import org.bioinfo.ngs.qc.qualimap.gui.utils.StatsKeeper;
+import org.bioinfo.ngs.qc.qualimap.gui.utils.StringUtilsSwing;
+import org.bioinfo.ngs.qc.qualimap.process.BamStatsAnalysis;
+import org.jfree.chart.JFreeChart;
+import org.jfree.chart.annotations.XYBoxAnnotation;
+import org.jfree.chart.axis.*;
+import org.jfree.chart.labels.CustomXYToolTipGenerator;
+import org.jfree.chart.labels.XYToolTipGenerator;
+import org.jfree.chart.plot.*;
+import org.jfree.ui.RectangleInsets;
+
+public class BamQCRegionReporter extends StatsReporter implements Serializable {
+
+
+
+ public double getPercentSingletons() {
+ return percentageSingletons;
+ }
+
+ public double getPercentageBothMatesPaired() {
+ return ((numPairedReads - numSingletons) * 100.0) / (double) numReads ;
+ }
+
+ public double getPercentageClippedReads() {
+ return (numClippedReads * 100.0) / (double) numReads;
+ }
+
+ public double getPercentageOverlappingPairs() {
+ // pair has 2 reads
+ return (numOverlappingReadPairs * 200.0 / (double) numReads);
+ }
+
+ public double getPercentageBothMatesPairedInRegions() {
+ return ((numPairedReadsInRegions - numSingletonsInRegions) * 100.0) / (double) numReads ;
+ }
+
+ public double getPercentageDublicateReadsMarked() {
+ return (numDuplicatedReadsMarked * 100.0) / (double) numReads ;
+ }
+
+ public double getPercentageDublicateReadsEstimated() {
+ return (numDuplicatedReadsEstimated * 100.0) / (double) numReads ;
+ }
+
+ public void setGenomeGCContentName(String genomeName) {
+ this.genomeGCContentName = genomeName;
+ }
+
+ private boolean paintChromosomeLimits;
+
+ private Long referenceSize, aNumber, cNumber, gNumber,
+ tNumber, nNumber, numReads, numMappedReads,
+ /*numMappedBases, numSequencedBases, numAlignedBases,*/
+ numBasesInsideRegions;
+
+ private Double aPercent, cPercent, gPercent, tPercent, nPercent,
+ gcPercent, percentMappedReads, meanMappingQuality, meanInsertSize,
+ stdInsertSize, meanCoverage, stdCoverage, adaptedMeanCoverage;
+
+ private int p25InsertSize, medianInsertSize, p75InsertSize;
+
+ int readMinSize, readMaxSize;
+ int numClippedReads;
+ double readsWithInsertionPercentage, readsWithDeletionPercentage;
+ double readMeanSize;
+
+ private long numPairedReads, numberOfMappedFirstOfPair, numberOfMappedSecondOfPair;
+ private double percantagePairedReads, percentageOfMappedFirstOfPair, percentageOfMappedSecondOfPair;
+ private long numSingletons;
+ private double percentageSingletons;
+ private long numCorrectStrandReads;
+ private long numDuplicatedReadsMarked, numDuplicatedReadsEstimated;
+
+ boolean includeIntersectingPairs;
+ private long numOverlappingReadPairs;
+
+ private long numMappedReadsInRegions, numPairedReadsInRegions;
+ private double percentageMappedReadsInRegions;
+
+ private long numMappedFirstOfPairInRegions, numMappedSecondOfPairInRegions;
+ private double percentageOfMappedFirstOfPairInRegions, percentageOfMappedSecondOfPairInRegions;
+ private long numSingletonsInRegions;
+ private double percentageSingletonsInRegions, percentageCorrectStrandReads;
+
+ private double duplicationRate;
+
+ private int numInsertions, numDeletions;
+ private long numMismatches;
+ private double homopolymerIndelFraction;
+ private double alignmentErrorRate;
+
+ private Map<String,String> warnings;
+ String genomeGCContentName;
+ int numSelectedRegions;
+
+ static NumberFormat decimailFormatter = DecimalFormat.getInstance(Locale.US);
+
+ public BamQCRegionReporter(boolean gffIsAvailable, boolean inside) {
+ if (gffIsAvailable) {
+ if (inside) {
+ namePostfix = " (inside of regions)";
+ } else {
+ namePostfix = " (outside of regions)";
+ fileName = "qualimapReportOutsideRegions";
+ }
+ } else {
+ namePostfix = "";
+ }
+ genomeGCContentName = "";
+
+ decimailFormatter.setMaximumFractionDigits(2);
+
+ }
+
+
+ public void writeReport(BamStats bamStats, String outdir) throws IOException{
+ // init report
+ String reportFile = outdir + "/" + bamStats.getName() + "_results.txt";
+ PrintWriter report = new PrintWriter(new File(reportFile));
+
+ // header
+ report.println("BamQC report");
+ report.println("-----------------------------------");
+ report.println("");
+
+ // input
+ report.println(">>>>>>> Input");
+ report.println("");
+ report.println(" bam file = " + bamStats.getSourceFile());
+ report.println(" outfile = " + reportFile);
+ report.println("");
+ report.println("");
+
+ // globals
+ report.println(">>>>>>> Reference");
+ report.println("");
+ report.println(" number of bases = " + formatLong(bamStats.getReferenceSize()) + " bp");
+ report.println(" number of contigs = " + bamStats.getNumberOfReferenceContigs());
+ report.println("");
+ report.println("");
+
+ // globals
+ report.println(">>>>>>> Globals");
+ report.println("");
+ report.println(" number of windows = " + bamStats.getNumberOfWindows());
+ report.println("");
+ report.println(" number of reads = " + formatLong(bamStats.getNumberOfReads()));
+ report.println(" number of mapped reads = " + formatLong(bamStats.getNumberOfMappedReads()) +
+ " (" + formatPercentage(bamStats.getPercentageOfMappedReads())+ ")");
+ report.println("");
+
+ if (bamStats.getNumberOfPairedReads() > 0) {
+ report.println(" number of mapped paired reads (first in pair) = "
+ + formatLong(bamStats.getNumberOfMappedFirstOfPair()) );
+ report.println(" number of mapped paired reads (second in pair) = "
+ + formatLong(bamStats.getNumberOfMappedSecondOfPair()) );
+ report.println(" number of mapped paired reads (both in pair) = "
+ + formatLong(bamStats.getNumberOfPairedReads() - bamStats.getNumberOfSingletons()) );
+ report.println(" number of mapped paired reads (singletons) = "
+ + formatLong(bamStats.getNumberOfSingletons()) );
+ if (bamStats.getNumOverlappingReadPairs() > 0) {
+ report.println(" number of overlapping read pairs = "
+ + formatLong(bamStats.getNumOverlappingReadPairs()) );
+ }
+ report.println("");
+ }
+
+ report.println(" number of mapped bases = " + formatLong(bamStats.getNumberOfMappedBases()) + " bp");
+ report.println(" number of sequenced bases = " + formatLong(bamStats.getNumberOfSequencedBases()) + " bp");
+ report.println(" number of aligned bases = " + formatLong(bamStats.getNumberOfAlignedBases()) + " bp");
+ if (bamStats.getNumDetectedDuplicatedReads() > 0) {
+ report.println(" number of duplicated reads (marked) = " + formatLong(bamStats.getNumDetectedDuplicatedReads()) );
+ } else {
+ report.println(" number of duplicated reads (estimated) = " + formatLong(bamStats.getNumDuplicatedReadsEstimated()) );
+ report.println(" duplication rate = " + formatPercentage(bamStats.getDuplicationRate()) );
+ }
+
+ if (bamStats.getNumberOfMappedReads() == 0) {
+ report.close();
+ return;
+ }
+
+
+ report.println("");
+ report.println("");
+
+ // insert size
+ report.println(">>>>>>> Insert size");
+ report.println("");
+ report.println(" mean insert size = " + formatDecimal(bamStats.getMeanInsertSize()) );
+ report.println(" std insert size = " + formatDecimal(bamStats.getStdInsertSize()) );
+ report.println(" median insert size = " + bamStats.getMedianInsertSize());
+ report.println("");
+ report.println("");
+
+ // mapping quality
+ report.println(">>>>>>> Mapping quality");
+ report.println("");
+ report.println(" mean mapping quality = " + formatDecimal(bamStats.getMeanMappingQualityPerWindow()));
+ report.println("");
+ report.println("");
+
+ // actg content
+ report.println(">>>>>>> ACTG content");
+ report.println("");
+ report.println(" number of A's = " + formatLong(bamStats.getNumberOfAs()) + " bp (" +
+ formatPercentage(bamStats.getMeanARelativeContent()) + ")");
+ report.println(" number of C's = " + formatLong(bamStats.getNumberOfCs()) + " bp (" +
+ formatPercentage(bamStats.getMeanCRelativeContent()) + ")");
+ report.println(" number of T's = " + formatLong(bamStats.getNumberOfTs()) + " bp (" +
+ formatPercentage(bamStats.getMeanTRelativeContent()) + ")");
+ report.println(" number of G's = " + formatLong(bamStats.getNumberOfGs()) + " bp (" +
+ formatPercentage(bamStats.getMeanGRelativeContent()) + ")");
+ report.println(" number of N's = " + formatLong(bamStats.getNumberOfNs()) + " bp (" +
+ formatPercentage(bamStats.getMeanNRelativeContent()) + ")");
+ report.println("");
+ report.println(" GC percentage = " + formatPercentage(bamStats.getMeanGcRelativeContent()));
+ // report.println(" AT percentage = " + formatPercentage(bamStats.getMeanAtRelativeContent()));
+ report.println("");
+ report.println("");
+
+
+ // Mismatches and indels
+
+ report.println(">>>>>>> Mismatches and indels");
+ report.println("");
+ report.println(" general error rate = " + formatDecimal(bamStats.getErrorRate()) ) ;
+ report.println(" number of mismatches = " + formatLong(bamStats.getNumMismatches()) ) ;
+
+ long numIndels= bamStats.getNumIndels();
+ if (numIndels > 0) {
+ report.println(" number of insertions = " + formatLong(bamStats.getNumInsertions()) );
+ report.println(" mapped reads with insertion percentage = " +
+ formatPercentage(bamStats.getReadsWithInsertionPercentage()));
+ report.println(" number of deletions = " + formatLong(bamStats.getNumDeletions()) );
+ report.println(" mapped reads with deletion percentage = " +
+ formatPercentage(bamStats.getReadsWithDeletionPercentage()));
+ report.println(" homopolymer indels = " + formatPercentage(bamStats.getHomopolymerIndelFraction() * 100.0));
+ }
+
+ report.println("");
+ report.println("");
+
+
+ // coverageData
+ report.println(">>>>>>> Coverage");
+ report.println("");
+ report.println(" mean coverageData = " + formatDecimal(bamStats.getMeanCoverage()) + "X");
+ report.println(" std coverageData = " + formatDecimal(bamStats.getStdCoverage()) + "X");
+ if (bamStats.getNumOverlappingReadPairs() > 0) {
+ report.println(" paired-end adapted mean coverage = "
+ + formatDecimal(bamStats.getAdaptedMeanCoverage()) + "X" );
+ }
+
+ report.println("");
+ for(int i=0; i<bamStats.getCoverageQuotes().getSize(); i++){
+ report.println(" There is a " +
+ StringUtils.decimalFormat(bamStats.getCoverageQuotes().get(i).getY(),"#0.##") +
+ "% of reference with a coverageData >= " + (int)bamStats.getCoverageQuotes().get(i).getX()
+ + "X");
+ }
+ report.println("");
+ report.println("");
+
+
+ // coverage per chromosome data
+ report.println(">>>>>>> Coverage per contig");
+ report.println("");
+ ChromosomeInfo[] chromosomeStats = bamStats.getChromosomeStats();
+ for (ChromosomeInfo chromosomeInfo : chromosomeStats) {
+ report.println("\t" + chromosomeInfo.getName() + "\t" +
+ chromosomeInfo.getLength() + "\t" + chromosomeInfo.getNumBases() + "\t" +
+ chromosomeInfo.getCovMean() + "\t" + chromosomeInfo.getCovStd());
+ }
+ report.println("");
+ report.println("");
+
+ report.close();
+ }
+
+ private XYToolTipGenerator createTooltipGenerator(List<Double> windowReferences, GenomeLocator locator ) {
+
+ if (locator == null) {
+ return null;
+ }
+
+ List<String> toolTips = new ArrayList<String>();
+
+ for (double pos : windowReferences) {
+ ContigRecord rec = locator.getContigCoordinates((long) pos);
+ long start = rec.getStart();
+ long relativePos = (long)pos - start + 1;
+ toolTips.add(rec.getName() + ", relative position: " + relativePos);
+ }
+
+ CustomXYToolTipGenerator generator = new CustomXYToolTipGenerator();
+ generator.addToolTipSeries(toolTips);
+
+ return generator;
+
+ }
+
+ /**
+ * Function to load the data variables obtained from the input file/s
+ * @param bamStats data read in the input file
+ */
+ public void loadReportData(BamStats bamStats) {
+
+ this.referenceSize = bamStats.getReferenceSize();
+
+ /*if(bamStats.isReferenceAvailable()) {
+ this.referenceFileName = bamStats.getReferenceFile();
+ this.aReferenceNumber = bamStats.getNumberOfAsInReference();
+ this.aReferencePercent = bamStats.getMeanARelativeContentPerWindowInReference();
+ this.cReferenceNumber = bamStats.getNumberOfCsInReference();
+ this.cReferencePercent = bamStats.getMeanCRelativeContentPerWindowInReference();
+ this.tReferenceNumber = bamStats.getNumberOfTsInReference();
+ this.tReferencePercent = bamStats.getMeanTRelativeContentPerWindowInReference();
+ this.gReferenceNumber = bamStats.getNumberOfGsInReference();
+ this.gReferencePercent = bamStats.getMeanGRelativeContentPerWindowInReference();
+ this.nReferenceNumber = bamStats.getNumberOfNsInReference();
+ this.nReferencePercent = bamStats.getMeanNRelativeContentPerWindowInReference();
+ this.gcPercent = bamStats.getMeanGcRelativeContentPerWindowInReference();
+ }*/
+
+ // globals
+ this.numReads = bamStats.getNumberOfReads();
+ this.numMappedReads = bamStats.getNumberOfMappedReads();
+ this.percentMappedReads = bamStats.getPercentageOfMappedReads();
+ /*this.numMappedBases = bamStats.getNumberOfMappedBases();
+ this.numSequencedBases = bamStats.getNumberOfSequencedBases();
+ this.numAlignedBases = bamStats.getNumberOfAlignedBases();*/
+ this.duplicationRate = bamStats.getDuplicationRate();
+ this.numDuplicatedReadsMarked = bamStats.getNumDetectedDuplicatedReads();
+ this.numDuplicatedReadsEstimated = bamStats.getNumDuplicatedReadsEstimated();
+
+
+ // paired reads
+ this.numPairedReads = bamStats.getNumberOfPairedReads();
+ this.percantagePairedReads = bamStats.getPercentageOfPairedReads();
+ this.numSingletons = bamStats.getNumberOfSingletons();
+ this.percentageSingletons = bamStats.getPercentageOfSingletons();
+ this.numberOfMappedFirstOfPair = bamStats.getNumberOfMappedFirstOfPair();
+ this.percentageOfMappedFirstOfPair = ( (double) numberOfMappedFirstOfPair / numReads) * 100.0;
+ this.numberOfMappedSecondOfPair = bamStats.getNumberOfMappedSecondOfPair();
+ this.percentageOfMappedSecondOfPair = ( (double) numberOfMappedSecondOfPair / numReads ) * 100.0;
+
+ this.includeIntersectingPairs = bamStats.reportOverlappingReadPairs();
+ this.numOverlappingReadPairs = bamStats.getNumOverlappingReadPairs();
+
+ // read properties
+ this.numClippedReads = bamStats.getNumClippedReads();
+ this.readsWithInsertionPercentage = bamStats.getReadsWithInsertionPercentage();
+ this.readsWithDeletionPercentage = bamStats.getReadsWithDeletionPercentage();
+
+
+ // regions related
+ this.numSelectedRegions = bamStats.getNumSelectedRegions();
+ this.numBasesInsideRegions = bamStats.getInRegionReferenceSize();
+ this.numMappedReadsInRegions = bamStats.getNumberOfMappedReadsInRegions();
+ this.numPairedReadsInRegions = bamStats.getNumberOfPairedReadsInRegions();
+ this.percentageMappedReadsInRegions = bamStats.getPercentageOfInsideMappedReads();
+ this.numMappedFirstOfPairInRegions = bamStats.getNumberOfMappedFirstOfPairInRegions();
+ this.percentageOfMappedFirstOfPairInRegions =
+ ( (double) numMappedFirstOfPairInRegions / numReads) * 100.0;
+ this.numMappedSecondOfPairInRegions = bamStats.getNumberOfMappedSecondOfPairInRegions();
+ this.percentageOfMappedSecondOfPairInRegions =
+ ( (double) numMappedSecondOfPairInRegions / numReads) * 100.0;
+ this.numSingletonsInRegions = bamStats.getNumberOfSingletonsInRegions();
+ this.percentageSingletonsInRegions = ( (double) numSingletonsInRegions / numReads ) * 100.0;
+ this.numCorrectStrandReads = bamStats.getNumCorrectStrandReads();
+ this.percentageCorrectStrandReads = ((double) numCorrectStrandReads / numReads ) * 100.0;
+
+ // mapping quality
+ this.meanMappingQuality = bamStats.getMeanMappingQualityPerWindow();
+
+ // insert size
+ this.meanInsertSize = bamStats.getMeanInsertSize();
+ this.p25InsertSize = bamStats.getP25InsertSize();
+ this.medianInsertSize = bamStats.getMedianInsertSize();
+ this.p75InsertSize = bamStats.getP75InsertSize();
+ this.stdInsertSize = bamStats.getStdInsertSize();
+
+ // actg content
+ this.aNumber = bamStats.getNumberOfAs();
+ this.aPercent = bamStats.getMeanARelativeContent();
+ this.cNumber = bamStats.getNumberOfCs();
+ this.cPercent = bamStats.getMeanCRelativeContent();
+ this.tNumber = bamStats.getNumberOfTs();
+ this.tPercent = bamStats.getMeanTRelativeContent();
+ this.gNumber = bamStats.getNumberOfGs();
+ this.gPercent = bamStats.getMeanGRelativeContent();
+ this.nNumber = bamStats.getNumberOfNs();
+ this.nPercent = bamStats.getMeanNRelativeContent();
+ this.gcPercent = bamStats.getMeanGcRelativeContent();
+
+ // coverageData
+ this.meanCoverage = bamStats.getMeanCoverage();
+ this.stdCoverage = bamStats.getStdCoverage();
+ this.adaptedMeanCoverage = bamStats.getAdaptedMeanCoverage();
+
+ // read sizes
+ readMaxSize = bamStats.getReadMaxSize();
+ readMinSize = bamStats.getReadMinSize();
+ readMeanSize = bamStats.getReadMeanSize();
+
+ // indels
+ numInsertions = bamStats.getNumInsertions();
+ numDeletions = bamStats.getNumDeletions();
+ homopolymerIndelFraction = bamStats.getHomopolymerIndelFraction();
+ numMismatches = bamStats.getNumMismatches();
+ alignmentErrorRate = bamStats.getErrorRate();
+
+ warnings = bamStats.getWarnings();
+
+ prepareSummaryStatsKeeper();
+
+ prepareChromosomeStatsKeeper(bamStats.getChromosomeStats());
+
+
+
+ }
+
+ /**
+ * Create all the charts from the input file/s and save each of them into a bufferedImage
+ * @param bamStats BamStats class that contains the information of the graphics titles
+ * @param locator Genomic locator
+ * @param isPairedData Paired data identifier
+ * @throws IOException Error during computation
+ */
+ public void computeChartsBuffers(BamStats bamStats, GenomeLocator locator, boolean isPairedData) throws IOException{
+
+ // define a stroke
+ Stroke stroke = new BasicStroke(1.5f, BasicStroke.CAP_ROUND, BasicStroke.JOIN_ROUND, 1.0f, new float[] {4.0f, 8.0f}, 0.0f);
+
+ if (charts == null) {
+ charts = new ArrayList<QChart>();
+ }
+
+ if (bamStats.getNumberOfMappedBases() == 0) {
+ return;
+ }
+
+
+ // some variables
+ double maxValue = 50;
+ String subTitle = new File(bamStats.getSourceFile()).getName() + namePostfix;
+
+ // compute window centers
+ List<Double> windowReferences = new ArrayList<Double>(bamStats.getNumberOfWindows());
+
+ for(int i=0; i<bamStats.getNumberOfWindows(); i++){
+ windowReferences.add((double)(bamStats.getWindowStart(i)+bamStats.getWindowEnd(i))/2.0);
+ }
+ double lastReference = windowReferences.get(windowReferences.size()-1);
+
+ // max coverageData+std
+ double maxCoverage = 0;
+ for(int i=0; i<bamStats.getCoverageAcrossReference().size(); i++){
+ if (bamStats.getCoverageAcrossReference().get(i)+bamStats.getStdCoverageAcrossReference().get(i)>maxCoverage) {
+ maxCoverage = bamStats.getCoverageAcrossReference().get(i)+bamStats.getStdCoverageAcrossReference().get(i);
+ }
+ }
+
+ double maxInsertSize = 0;
+ if (isPairedData && maxCoverage > 0) {
+ for (int i = 0; i < bamStats.getInsertSizeAcrossReference().size(); i++) {
+ double iSize = bamStats.getInsertSizeAcrossReference().get(i);
+ if (iSize > maxInsertSize) {
+ maxInsertSize = iSize;
+ }
+ }
+ }
+
+ // compute chromosome limits
+ Color chromosomeColor = new Color(40,40,40,150);
+ XYVector chromosomeCoverageLimits = null;
+ XYVector chromosomePercentageLimits = null;
+ XYVector chromosomeBytedLimits = null;
+ XYVector chromosomeInsertSizeLimits = null;
+ List<XYBoxAnnotation> chromosomeAnnotations = null;
+ Map<Double,String> chromosomeNames = null;
+
+ if(paintChromosomeLimits && locator!=null){
+ int numberOfChromosomes = locator.getContigs().size();
+ chromosomeCoverageLimits = new XYVector();
+ chromosomePercentageLimits = new XYVector();
+ chromosomeBytedLimits = new XYVector();
+ chromosomeInsertSizeLimits = new XYVector();
+ chromosomeAnnotations = new ArrayList<XYBoxAnnotation>();
+ chromosomeNames = new HashMap<Double, String>();
+ for(int i=0; i<numberOfChromosomes; i++){
+ long chrStart = locator.getContigs().get(i).getPosition();
+ long chrSize = locator.getContigs().get(i).getSize();
+ long chrEnd = locator.getContigs().get(i).getEnd();
+ String chrName = locator.getContigs().get(i).getName();
+
+ XYBoxAnnotation xyBoxAnnotation = new XYBoxAnnotation( (double) chrStart, 0.0,
+ (double)( chrStart + chrSize), maxCoverage, null, null);
+ xyBoxAnnotation.setToolTipText(chrName);
+ chromosomeAnnotations.add(xyBoxAnnotation);
+
+ // chromosome names on boundaries
+ chromosomeNames.put( (double) chrStart + ((double)chrSize)*0.8, chrName);
+
+ //QUESTION: why are there are three of them???
+
+ // coverageData
+ chromosomeCoverageLimits.addItem(new XYItem(chrEnd,0));
+ chromosomeCoverageLimits.addItem(new XYItem(chrEnd,maxCoverage));
+ chromosomeCoverageLimits.addItem(new XYItem(chrEnd,0));
+ // percentage
+ chromosomePercentageLimits.addItem(new XYItem(chrEnd,0));
+ chromosomePercentageLimits.addItem(new XYItem(chrEnd,100));
+ chromosomePercentageLimits.addItem(new XYItem(chrEnd,0));
+ // byte
+ chromosomeBytedLimits.addItem(new XYItem(chrEnd,0));
+ chromosomeBytedLimits.addItem(new XYItem(chrEnd,255));
+ chromosomeBytedLimits.addItem(new XYItem(chrEnd,0));
+ // insert size
+ chromosomeInsertSizeLimits.addItem(new XYItem(chrEnd,0));
+ chromosomeInsertSizeLimits.addItem(new XYItem(chrEnd,maxInsertSize));
+ chromosomeInsertSizeLimits.addItem(new XYItem(chrEnd,0));
+
+
+ }
+ }
+
+ ///////////////// Coverage and GC-content across reference ////////////////////////////////
+
+ // coverageData
+ BamQCChart coverageChart = new BamQCChart(Constants.PLOT_TITLE_COVERAGE_ACROSS_REFERENCE,
+ subTitle, "Position (bp)", "Coverage (X)");
+ XYToolTipGenerator toolTipGenerator = createTooltipGenerator(windowReferences, locator);
+ coverageChart.setToolTipGenerator(toolTipGenerator);
+ coverageChart.setSeriesToExportIndex(0);
+ coverageChart.addIntervalRenderedSeries("Coverage",new XYVector(windowReferences,
+ bamStats.getCoverageAcrossReference(), bamStats.getStdCoverageAcrossReference()),
+ new Color(250,50,50,150), new Color(50,50,250), 0.2f);
+
+ //Preparing "smart" zoom for coverage across region
+ Double[] coverageData = ListUtils.toArray(bamStats.getCoverageAcrossReference());
+ double upperCoverageBound = 2*StatUtils.percentile(ArrayUtils.toPrimitive(coverageData), 90);
+ if (upperCoverageBound == 0) {
+ // possible in rare cases when the coverage is very low coverage
+ upperCoverageBound = maxCoverage*0.9;
+ }
+
+
+ if( paintChromosomeLimits && locator!=null ) {
+ coverageChart.addSeries("chromosomes", chromosomeCoverageLimits, chromosomeColor, stroke,
+ false, chromosomeAnnotations);
+ coverageChart.writeChromsomeNames(0.9*upperCoverageBound, chromosomeNames);
+ }
+ coverageChart.render();
+
+ coverageChart.getChart().getXYPlot().getRangeAxis().setRange(0, upperCoverageBound);
+
+ // gc content
+ BamQCChart gcContentChart = new BamQCChart("GC/AT relative content", subTitle,
+ "absolute position (bp)", "GC (%)");
+ gcContentChart.setToolTipGenerator(toolTipGenerator);
+ gcContentChart.setPercentageChart(true);
+ gcContentChart.addSeries("GC content(%)", new XYVector(windowReferences,bamStats.getGcRelativeContentAcrossReference()), new Color(50,50,50,150));
+ gcContentChart.addSeries("mean GC content", new XYVector(Arrays.asList(0.0,lastReference), Arrays.asList(bamStats.getMeanGcRelativeContentPerWindow(),bamStats.getMeanGcRelativeContentPerWindow())),new Color(255,0,0,180),stroke,true);
+ if(paintChromosomeLimits && locator!=null) {
+ gcContentChart.addSeries("chromosomes",chromosomePercentageLimits,chromosomeColor,stroke,
+ false, chromosomeAnnotations);
+ }
+ gcContentChart.render();
+
+
+ // combined plot
+ CombinedDomainXYPlot plot = new CombinedDomainXYPlot(new NumberAxis("Position (bp)"));
+ plot.getDomainAxis().setTickLabelsVisible(false);
+ plot.getDomainAxis().setTickMarksVisible(false);
+ plot.add(coverageChart.getChart().getXYPlot(),5);
+ plot.setGap(0);
+ plot.add(gcContentChart.getChart().getXYPlot(),1);
+ plot.setOrientation(PlotOrientation.VERTICAL);
+ JFreeChart combinedChart = new JFreeChart("Coverage across reference",plot);
+ combinedChart.setPadding(new RectangleInsets(30,20,30,20));
+ combinedChart.addSubtitle(coverageChart.getChart().getSubtitle(0));
+ charts.add(new QChart(bamStats.getName() + "_coverage_across_reference.png", combinedChart, coverageChart) );
+
+
+
+ ////////////////////////////// Balanced coverage histogram ////////////////////////////////
+
+ BamQCHistogramChart coverageHistogram = new BamQCHistogramChart(Constants.PLOT_TITLE_COVERAGE_HISTOGRAM,
+ subTitle, "Coverage (X)", "Number of genomic locations",
+ bamStats.getBalancedCoverageHistogram(), bamStats.getBalancedCoverageBarNames());
+
+ coverageHistogram.render();
+
+ XYVectorDataWriter coverageHistDataWriter = new XYVectorDataWriter(bamStats.getCoverageHistogram(),
+ "Coverage", "Number of genomic locations");
+ charts.add( new QChart(bamStats.getName() + "_coverage_histogram.png",
+ coverageHistogram.getChart(), coverageHistDataWriter) );
+
+
+ /////////////////////////////// Coverage Histogram 0-50x //////////////////////////////////
+
+ double minCoverage = bamStats.getCoverageHistogram().get(0).getX();
+ if (minCoverage < 40) {
+ // This histogram only makes sense for low coverage samples
+ BamQCXYHistogramChart coverageRangedHistogram =
+ new BamQCXYHistogramChart(Constants.PLOT_TITLE_COVERAGE_HISTOGRAM_0_50,
+ subTitle, "Coverage (X)", "Number of genomic locations");
+ coverageRangedHistogram.addHistogram("coverageData", bamStats.getCoverageHistogram(), Color.blue);
+ coverageRangedHistogram.setNumberOfBins(50);
+ coverageRangedHistogram.zoom(maxValue);
+ coverageRangedHistogram.setDomainAxisIntegerTicks(true);
+ coverageRangedHistogram.setDomainAxisTickUnitSize(1.0);
+ coverageRangedHistogram.render();
+
+ charts.add( new QChart(bamStats.getName() + "_coverage_0to" + (int)maxValue + "_histogram.png",
+ coverageRangedHistogram.getChart() ) );
+ }
+
+
+ //////////////////////////////// Genome Fraction Coverage /////////////////////////////////
+ BamQCChart coverageQuota = new BamQCChart(Constants.PLOT_TITLE_GENOME_FRACTION_COVERAGE, subTitle,
+ "Coverage (X)", "Fraction of reference (%)");
+ coverageQuota.setPercentageChart(true);
+ coverageQuota.addBarRenderedSeries("Coverage", bamStats.getCoverageQuotes(), new Color(255,20,20,150));
+ coverageQuota.setDomainAxisIntegerTicks(true);
+ coverageQuota.setDomainAxisTickUnitSize(1.0);
+ coverageQuota.render();
+ charts.add( new QChart(bamStats.getName() + "_coverage_quotes.png", coverageQuota.getChart(),
+ coverageQuota) );
+
+ /////////////////////////////// Duplication Rate Histogram ///////////////////////////////
+ BamQCXYHistogramChart uniqueReadStartsHistogram =
+ new BamQCXYHistogramChart(Constants.PLOT_TITLE_DUPLICATION_RATE_HISTOGRAM,
+ subTitle, "Duplication rate", "Number of loci");
+ uniqueReadStartsHistogram.addHistogram("Coverage", bamStats.getUniqueReadStartsHistogram(), Color.GREEN);
+ uniqueReadStartsHistogram.setDomainAxisIntegerTicks(true);
+ uniqueReadStartsHistogram.setDomainAxisTickUnitSize(1.0);
+ uniqueReadStartsHistogram.render();
+
+ charts.add(new QChart( bamStats.getName() + "_uniq_read_starts_histogram.png",
+ uniqueReadStartsHistogram.getChart(), uniqueReadStartsHistogram ) );
+
+
+
+ ////////////////////////////// Reads nucleotide content ////////////////////////////////////
+ if (bamStats.getReadMaxSize() > 0) {
+ BamQCChart readsContentChart = new BamQCChart(Constants.PLOT_TITLE_READS_NUCLEOTIDE_CONTENT,
+ subTitle, " Position (bp)", " Nucleotide Content (%) ");
+ readsContentChart.addSeries("A", bamStats.getReadsAsHistogram(), new Color(255, 0,0,255));
+ readsContentChart.addSeries("C", bamStats.getReadsCsHistogram(), new Color(0, 0,255,255));
+ readsContentChart.addSeries("G", bamStats.getReadsGsHistogram(), new Color(0, 255,0,255));
+ readsContentChart.addSeries("T", bamStats.getReadsTsHistogram(), new Color(0, 0, 0,255));
+ readsContentChart.addSeries("N", bamStats.getReadsNsHistogram(), new Color(0, 255, 255, 255));
+ readsContentChart.setAdjustDomainAxisLimits(false);
+ readsContentChart.setDomainAxisIntegerTicks(true);
+ readsContentChart.setPercentageChart(true);
+ readsContentChart.render();
+ charts.add(new QChart(bamStats.getName() + "_reads_content_per_read_position.png",
+ readsContentChart.getChart(), readsContentChart));
+ }
+
+
+ /////////////////////////////// Reads GC Content histogram ///////////////////////////////////
+
+ BamQCChart gcContentHistChart = new BamQCChart(Constants.PLOT_TITLE_READS_GC_CONTENT, subTitle,
+ "GC Content (%)", "Fraction of reads");
+ gcContentHistChart.addSeries("Sample", bamStats.getGcContentHistogram(), new Color(20, 10, 255, 255));
+ if (!genomeGCContentName.isEmpty()) {
+ XYVector gcContentHist = getGenomeGcContentHistogram();
+ if (gcContentHist.getSize() != 0) {
+ gcContentHistChart.addSeries(genomeGCContentName, gcContentHist, new Color(255, 10, 20, 255));
+ }
+ }
+ gcContentHistChart.setDomainAxisIntegerTicks(true);
+ gcContentHistChart.setAdjustDomainAxisLimits(false);
+ gcContentHistChart.setPercentageChart(false);
+ gcContentHistChart.render();
+ charts.add(new QChart(bamStats.getName() + "_gc_content_per_window.png", gcContentHistChart.getChart(),
+ gcContentHistChart ));
+
+ ///////////////// Clipping profile ///////////////
+
+
+ if (bamStats.clippingIsPresent()) {
+ BamQCChart clippingProfile = new BamQCChart(Constants.PLOT_TITLE_READS_CLIPPING_PROFILE,
+ subTitle, "Read position (bp)", " Clipped bases (%)");
+ clippingProfile.addSeries("Clipping profile", bamStats.getReadsClippingProfileHistogram(), new Color(255, 0, 0, 255));
+ clippingProfile.setAdjustDomainAxisLimits(false);
+ clippingProfile.setDomainAxisIntegerTicks(true);
+ clippingProfile.setPercentageChart(true);
+ clippingProfile.setShowLegend(false);
+ clippingProfile.render();
+ charts.add(new QChart(bamStats.getName() + "_reads_clipping_profile.png",
+ clippingProfile.getChart(), clippingProfile));
+
+ }
+
+ ///////////////// Homopolymer indels ///////////////
+
+ if (bamStats.getNumIndels() > 0 ) {
+ BamQCBarChart homopolymerIndels = new BamQCBarChart( Constants.PLOT_TITLE_HOMOPOLYMER_INDELS,
+ subTitle, "Type of indel", "Number of indels", bamStats.getHomopolymerIndels() );
+ homopolymerIndels.render();
+ charts.add( new QChart(bamStats.getName() + "_homopolymer_indels", homopolymerIndels.getChart(), homopolymerIndels ));
+ }
+
+
+ ///////////////// mapping quality charts ///////////////
+
+ // mapping quality across reference
+ BamQCChart mappingQuality = new BamQCChart(Constants.PLOT_TITLE_MAPPING_QUALITY_ACROSS_REFERENCE,
+ subTitle, "Position (bp)", "Mapping quality");
+ mappingQuality.addSeries("mapping quality",new XYVector(windowReferences, bamStats.getMappingQualityAcrossReference()), new Color(250,50,50,150));
+ mappingQuality.setSeriesToExportIndex(0);
+ if( paintChromosomeLimits && locator!=null ) {
+ mappingQuality.addSeries("chromosomes", chromosomeBytedLimits, chromosomeColor, stroke,
+ false, chromosomeAnnotations);
+ mappingQuality.writeChromsomeNames(220, chromosomeNames);
+
+ }
+ mappingQuality.render();
+ mappingQuality.getChart().getXYPlot().getRangeAxis().setRange(0,255);
+ charts.add(new QChart(bamStats.getName() + "_mapping_quality_across_reference.png",
+ mappingQuality.getChart(), mappingQuality ) );
+
+
+ // mapping quality histogram
+ BamQCXYHistogramChart mappingQualityHistogram =
+ new BamQCXYHistogramChart(Constants.PLOT_TITLE_MAPPING_QUALITY_HISTOGRAM,
+ subTitle, "Mapping quality", "Number of genomic locations");
+ mappingQualityHistogram.addHistogram("mapping quality", bamStats.getMappingQualityHistogram(), Color.blue);
+ mappingQualityHistogram.setNumberOfBins(50);
+ mappingQualityHistogram.render();
+ charts.add(new QChart( bamStats.getName() + "_mapping_quality_histogram.png",
+ mappingQualityHistogram.getChart(), mappingQualityHistogram ) );
+
+
+ // Insert size
+
+ if(isPairedData){
+ // insert size across reference
+ BamQCChart insertSize = new BamQCChart(Constants.PLOT_TITLE_INSERT_SIZE_ACROSS_REFERENCE,
+ subTitle, "Position (bp)", "Insert size (bp)");
+ insertSize.addSeries("insert size",new XYVector(windowReferences, bamStats.getInsertSizeAcrossReference()), new Color(15,170,90,150));
+ if(paintChromosomeLimits && locator!=null) {
+ insertSize.addSeries("chromosomes",chromosomeInsertSizeLimits,chromosomeColor,stroke,
+ false,chromosomeAnnotations);
+ insertSize.writeChromsomeNames(maxInsertSize*0.9, chromosomeNames);
+
+ }
+ insertSize.render();
+ insertSize.getChart().getXYPlot().getRangeAxis().setRange(0,maxInsertSize);
+
+ charts.add(new QChart( bamStats.getName() + "_insert_size_across_reference.png",
+ insertSize.getChart(), insertSize ));
+
+ // mapping quality histogram
+ BamQCXYHistogramChart insertSizeHistogram =
+ new BamQCXYHistogramChart(Constants.PLOT_TITLE_INSERT_SIZE_HISTOGRAM,
+ subTitle, "Insert size (bp)", "Number of reads");
+ insertSizeHistogram.addHistogram("insert size", bamStats.getInsertSizeHistogram(), new Color(15,170,90,150));
+ insertSizeHistogram.setNumberOfBins(50);
+ insertSizeHistogram.setRangeAxisIntegerTicks(true);
+ insertSizeHistogram.render();
+ charts.add(new QChart(bamStats.getName() + "_insert_size_histogram.png",
+ insertSizeHistogram.getChart(), insertSizeHistogram));
+ }
+ }
+
+ private String formatLong(long decimal){
+ return decimailFormatter.format(decimal);
+ }
+
+ private String formatDecimal(double decimal){
+ return decimailFormatter.format(decimal);
+ }
+
+ private String formatPercentage(double percentage){
+ return decimailFormatter.format(percentage) + "%";
+ }
+
+
+
+
+ /**
+ * @param paintChromosomeLimits the paintChromosomeLimits to set
+ */
+ public void setPaintChromosomeLimits(boolean paintChromosomeLimits) {
+ this.paintChromosomeLimits = paintChromosomeLimits;
+ }
+
+ public Long getaNumber() {
+ return aNumber;
+ }
+
+ public Long getcNumber() {
+ return cNumber;
+ }
+
+ public Long getgNumber() {
+ return gNumber;
+ }
+
+ public Long gettNumber() {
+ return tNumber;
+ }
+
+ public Long getnNumber() {
+ return nNumber;
+ }
+
+ public Double getaPercent() {
+ return aPercent;
+ }
+
+ public Double getcPercent() {
+ return cPercent;
+ }
+
+ public Double getgPercent() {
+ return gPercent;
+ }
+
+ public Double gettPercent() {
+ return tPercent;
+ }
+
+ public Double getnPercent() {
+ return nPercent;
+ }
+
+ public Double getGcPercent() {
+ return gcPercent;
+ }
+
+ public Double getPercentMappedReads() {
+ return percentMappedReads;
+ }
+
+ public List<StatsKeeper.Section> getInputDataSections() {
+ return inputDataKeeper.getSections();
+ }
+
+ private void prepareSummaryStatsKeeper() {
+ StringUtilsSwing sdf = new StringUtilsSwing();
+ String postfix = getNamePostfix();
+
+ if (warnings != null && !warnings.isEmpty()) {
+ StatsKeeper.Section warningsSection = new StatsKeeper.Section("Warnings");
+ for (Map.Entry<String,String> entry : warnings.entrySet()) {
+ warningsSection.addRow(entry.getKey(), entry.getValue());
+ }
+ summaryStatsKeeper.addSection(warningsSection);
+ }
+
+ StatsKeeper.Section globals = new StatsKeeper.Section("Globals");
+
+ globals.addRow("Reference size", sdf.formatLong(referenceSize));
+
+ globals.addRow("Number of reads", sdf.formatLong(numReads));
+
+ globals.addRow("Mapped reads", sdf.formatLong(numMappedReads)
+ + " / " + sdf.formatPercentage(getPercentMappedReads()));
+
+ globals.addRow("Unmapped reads",
+ sdf.formatLong(numReads - numMappedReads) + " / "
+ + sdf.formatPercentage(100.0 - getPercentMappedReads()));
+
+ globals.addRow("Mapped paired reads",
+ sdf.formatLong(numPairedReads) + " / "
+ + sdf.formatPercentage(percantagePairedReads) );
+ if (numPairedReads > 0) {
+
+ globals.addRow("Mapped reads, first in pair",
+ sdf.formatLong(numberOfMappedFirstOfPair) + " / " +
+ sdf.formatPercentage(percentageOfMappedFirstOfPair));
+
+ globals.addRow("Mapped reads, second in pair",
+ sdf.formatLong(numberOfMappedSecondOfPair) + " / " +
+ sdf.formatPercentage(percentageOfMappedSecondOfPair));
+
+ globals.addRow("Mapped reads, both in pair",
+ sdf.formatLong(numPairedReads - numSingletons) + " / "
+ + sdf.formatPercentage((getPercentageBothMatesPaired())));
+
+ globals.addRow("Mapped reads, singletons",
+ sdf.formatLong(numSingletons) + " / "
+ + sdf.formatPercentage(getPercentSingletons()));
+
+
+ }
+
+ globals.addRow("Read min/max/mean length",
+ sdf.formatLong(readMinSize) + " / "
+ + sdf.formatLong(readMaxSize) + " / "
+ + sdf.formatDecimal(readMeanSize));
+
+ if (numSelectedRegions == 0) {
+
+ globals.addRow("Clipped reads",
+ sdf.formatInteger(numClippedReads) + " / " +
+ sdf.formatPercentage(getPercentageClippedReads()));
+ if (includeIntersectingPairs) {
+ globals.addRow("Overlapping read pairs",
+ sdf.formatLong(numOverlappingReadPairs) + " / " +
+ sdf.formatPercentage(getPercentageOverlappingPairs()));
+ }
+
+ if (numDuplicatedReadsMarked > 0) {
+ globals.addRow("Duplicated reads (flagged)", sdf.formatLong(numDuplicatedReadsMarked) + " / " +
+ sdf.formatPercentage(getPercentageDublicateReadsMarked()));
+ } else {
+ globals.addRow("Duplicated reads (estimated)",
+ sdf.formatLong(numDuplicatedReadsEstimated) + " / " +
+ sdf.formatPercentage(getPercentageDublicateReadsEstimated()));
+ globals.addRow("Duplication rate", sdf.formatPercentage(duplicationRate));
+ }
+
+ }
+
+ summaryStatsKeeper.addSection(globals);
+
+ if (numSelectedRegions > 0) {
+
+ StatsKeeper.Section globalsInRegions = new StatsKeeper.Section("Globals" + postfix);
+ globalsInRegions.addRow("Regions size/percentage of reference",
+ sdf.formatLong((numBasesInsideRegions))
+ + " / " + sdf.formatPercentage(getSelectedRegionsPercentage()));
+
+
+ globalsInRegions.addRow("Mapped reads",
+ sdf.formatLong(numMappedReadsInRegions)
+ + " / " + sdf.formatPercentage(percentageMappedReadsInRegions));
+ if (numPairedReads > 0) {
+ globalsInRegions.addRow("Mapped reads, only first in pair",
+ sdf.formatLong(numMappedFirstOfPairInRegions) + " / " +
+ sdf.formatPercentage(percentageOfMappedFirstOfPairInRegions));
+
+ globalsInRegions.addRow("Mapped reads, only second in pair",
+ sdf.formatLong(numMappedSecondOfPairInRegions) + " / " +
+ sdf.formatPercentage(percentageOfMappedSecondOfPairInRegions));
+ globalsInRegions.addRow("Mapped reads, both in pair",
+ sdf.formatLong(numPairedReadsInRegions - numSingletonsInRegions) + " / "
+ + sdf.formatPercentage((getPercentageBothMatesPairedInRegions())));
+ globalsInRegions.addRow("Mapped reads, singletons",
+ sdf.formatLong(numSingletonsInRegions) + " / "
+ + sdf.formatPercentage(percentageSingletonsInRegions));
+
+
+ globalsInRegions.addRow("Correct strand reads",
+ sdf.formatLong(numCorrectStrandReads) + " / " +
+ sdf.formatPercentage(percentageCorrectStrandReads) );
+
+
+ globalsInRegions.addRow("Clipped reads",
+ sdf.formatInteger(numClippedReads) + " / " +
+ sdf.formatPercentage(getPercentageClippedReads()));
+
+ if (includeIntersectingPairs) {
+ globalsInRegions.addRow("Overlapping read pairs",
+ sdf.formatLong(numOverlappingReadPairs)+ " / " +
+ sdf.formatPercentage(getPercentageOverlappingPairs()));
+ }
+
+ }
+
+ if (numDuplicatedReadsMarked > 0) {
+ globalsInRegions.addRow("Duplicated reads (flagged)", sdf.formatLong(numDuplicatedReadsMarked) + " / " +
+ sdf.formatPercentage(getPercentageDublicateReadsMarked()));
+ } else {
+ globalsInRegions.addRow("Duplicated reads (estimated)",
+ sdf.formatLong(numDuplicatedReadsEstimated) + " / " +
+ sdf.formatPercentage(getPercentageDublicateReadsEstimated()));
+ globalsInRegions.addRow("Duplication rate", sdf.formatPercentage(duplicationRate));
+ }
+
+
+ summaryStatsKeeper.addSection(globalsInRegions);
+
+ }
+
+ StatsKeeper.Section acgtContent = new StatsKeeper.Section("ACGT Content" + postfix);
+
+ acgtContent.addRow("Number/percentage of A's", sdf.formatLong(getaNumber()) +
+ " / " + sdf.formatPercentage(getaPercent()));
+ acgtContent.addRow("Number/percentage of C's",sdf.formatLong(getcNumber()) +
+ " / " + sdf.formatPercentage(getcPercent()));
+ acgtContent.addRow("Number/percentage of T's", sdf.formatLong(gettNumber()) +
+ " / " + sdf.formatPercentage(gettPercent()));
+ acgtContent.addRow("Number/percentage of G's",sdf.formatLong(getgNumber()) +
+ " / " + sdf.formatPercentage(getgPercent()));
+ acgtContent.addRow("Number/percentage of N's",sdf.formatLong(getnNumber()) +
+ " / " + sdf.formatPercentage(getnPercent()));
+ acgtContent.addRow("GC Percentage", sdf.formatPercentage(getGcPercent()));
+
+ summaryStatsKeeper.addSection(acgtContent);
+
+
+
+ StatsKeeper.Section coverageSection = new StatsKeeper.Section("Coverage" + postfix);
+ coverageSection.addRow("Mean", sdf.formatDecimal(meanCoverage));
+ coverageSection.addRow("Standard Deviation",sdf.formatDecimal(stdCoverage) );
+
+ if (numOverlappingReadPairs > 0) {
+ coverageSection.addRow("Mean (paired-end reads overlap ignored)", sdf.formatDecimal(adaptedMeanCoverage));
+ }
+
+ summaryStatsKeeper.addSection(coverageSection);
+
+ StatsKeeper.Section mappingQualitySection = new StatsKeeper.Section("Mapping Quality" + postfix);
+ mappingQualitySection.addRow("Mean Mapping Quality", sdf.formatDecimal(meanMappingQuality));
+ summaryStatsKeeper.addSection(mappingQualitySection);
+
+ if (meanInsertSize != 0)
+ {
+ StatsKeeper.Section insertSizeSection = new StatsKeeper.Section("Insert size" + postfix);
+ insertSizeSection.addRow("Mean", sdf.formatDecimal(meanInsertSize));
+ insertSizeSection.addRow("Standard Deviation", sdf.formatDecimal(stdInsertSize));
+ insertSizeSection.addRow("P25/Median/P75", sdf.formatDecimal(p25InsertSize) + " / " +
+ sdf.formatDecimal(medianInsertSize) + " / " + sdf.formatDecimal(p75InsertSize));
+ summaryStatsKeeper.addSection(insertSizeSection);
+ }
+
+ int numIndels = numInsertions + numDeletions;
+ if ( numIndels > 0 || numMismatches > 0 || alignmentErrorRate > 0) {
+ StatsKeeper.Section indelsSection = new StatsKeeper.Section("Mismatches and indels" + postfix);
+ if (alignmentErrorRate > 0) {
+ indelsSection.addRow("General error rate", sdf.formatPercentage(alignmentErrorRate * 100.0));
+ }
+ if (numMismatches > 0) {
+ indelsSection.addRow("Mismatches",sdf.formatDecimal(numMismatches));
+ }
+ //indelsSection.addRow("Total reads with indels", sdf.formatInteger(numIndels));
+ if (numIndels > 0) {
+ indelsSection.addRow("Insertions",sdf.formatDecimal(numInsertions) );
+ indelsSection.addRow("Mapped reads with at least one insertion",
+ sdf.formatPercentage(readsWithInsertionPercentage));
+ indelsSection.addRow("Deletions",sdf.formatDecimal(numDeletions) );
+ indelsSection.addRow("Mapped reads with at least one deletion",
+ sdf.formatPercentage(readsWithDeletionPercentage));
+ indelsSection.addRow("Homopolymer indels",sdf.formatPercentage(homopolymerIndelFraction * 100.0) );
+ }
+
+ summaryStatsKeeper.addSection(indelsSection);
+
+ }
+
+
+ }
+
+ private void prepareChromosomeStatsKeeper(BamStats.ChromosomeInfo[] statsArray) {
+
+
+ tableDataStatsKeeper = new StatsKeeper();
+ tableDataStatsKeeper.setName("Chromosome stats" + namePostfix );
+
+ if (numMappedReads == 0) {
+ return;
+ }
+
+ StatsKeeper.Section headerSection = new StatsKeeper.Section(Constants.TABLE_STATS_HEADER);
+ String[] header = {
+ "Name", "Length", "Mapped bases", "Mean coverage", "Standard deviation"
+ };
+ headerSection.addRow(header);
+ tableDataStatsKeeper.addSection(headerSection);
+
+
+ StatsKeeper.Section dataSection = new StatsKeeper.Section(Constants.TABLE_STATS_DATA);
+
+ for (BamStats.ChromosomeInfo statsRecord : statsArray) {
+ String[] row = new String[5];
+ row[0] = statsRecord.getName();
+ row[1] = Long.toString(statsRecord.getLength());
+ row[2] = Long.toString(statsRecord.getNumBases());
+ row[3] = StringUtils.decimalFormat(statsRecord.getCovMean(),"#,###,###,###.##");
+ row[4] = StringUtils.decimalFormat(statsRecord.getCovStd(),"#,###,###,###.##");
+
+ dataSection.addRow(row);
+ }
+
+ tableDataStatsKeeper.addSection(dataSection);
+
+ }
+
+ public XYVector getGenomeGcContentHistogram() {
+ XYVector res = new XYVector();
+ try {
+
+ String pathToGC = Constants.pathResources + BamStatsAnalysis.getGcContentFileMap().get(genomeGCContentName);
+
+ //System.out.println("Path to genome is " + pathToGC);
+
+ BufferedReader reader = new BufferedReader(
+ new InputStreamReader( getClass().getResourceAsStream( pathToGC ) ) );
+
+ String line;
+
+ double acum = 0;
+ int counter = -1;
+ double index = 1;
+ while ( (line = reader.readLine()) != null ) {
+ if (line.isEmpty() || line.startsWith("#")) {
+ continue;
+ }
+ String[] vals = line.split(" : ");
+ double value = Double.parseDouble(vals[1].trim());
+ // skip the zero value
+ //if (index == 0.0) {
+ // continue;
+ //}
+ acum += value;
+ counter++;
+ if (counter == 10) {
+ res.addItem(new XYItem(index, acum));
+ acum = 0;
+ counter = 0;
+ index += 1;
+ }
+ }
+
+ } catch (IOException e) {
+ e.printStackTrace();
+
+ }
+
+ return res;
+ }
+
+ public Properties generateBamQcProperties() {
+
+ Properties prop = new Properties();
+
+
+ List<StatsKeeper.Section> summarySections = getSummaryDataSections();
+ for (StatsKeeper.Section s : summarySections) {
+ String sectionName = s.getName().toUpperCase().replaceAll("\\s","_");
+ for (String[] row : s.getRows()) {
+ StringBuilder builder = new StringBuilder();
+ builder.append(sectionName).append("_").append(row[0].replaceAll("\\s","_"));
+ prop.setProperty(builder.toString(), row[1].replaceAll("\\s", ""));
+ }
+ }
+
+ /*prop.setProperty("refSize", referenceSize.toString());
+ prop.setProperty("numContigs", contigsNumber.toString());
+ prop.setProperty("numRegions", Integer.toString(numSelectedRegions));
+
+ // globals
+ prop.setProperty("numWindows", numWindows.toString());
+ prop.setProperty("numReads", numReads.toString());
+ prop.setProperty("numMappedReads", numMappedReads.toString());
+ prop.setProperty("percentMappedReads", percentMappedReads.toString());
+ prop.setProperty("numMappedBases", numMappedBases.toString());
+ prop.setProperty("numSequencedBases", numSequencedBases.toString());
+ prop.setProperty("numAlignedBases", numAlignedBases.toString());
+ prop.setProperty("numPairedReads", Integer.toString(numPairedReads));
+ prop.setProperty("numSingletons", Integer.toString(numSingletons));
+ prop.setProperty("duplicationRate", Double.toString(duplicationRate));
+
+ // regions related
+ prop.setProperty("refSizeInRegions", Long.toString(numBasesInsideRegions));
+ prop.setProperty("numMappedReadsInRegions", Integer.toString(numMappedReadsInRegions));
+ prop.setProperty("percentMappedReadsInRegions", Double.toString(percentageMappedReadsInRegions));
+ prop.setProperty("numPairedReadsInRegions", Integer.toString(numPairedReadsInRegions));
+ prop.setProperty("numSingletonsInRegions", Integer.toString(numSingletonsInRegions));
+
+ // coverageData
+ prop.setProperty("meanCoverage", meanCoverage.toString());
+ prop.setProperty("stdCoverage", stdCoverage.toString());
+
+ // mapping quality
+ prop.setProperty("meanMappingQuality", meanMappingQuality.toString());
+
+ // insert size
+ prop.setProperty("meanInsertSize", meanInsertSize.toString());
+
+ // actg content
+ prop.setProperty("aNumber", aNumber.toString());
+ prop.setProperty("aPercent", aPercent.toString());
+ prop.setProperty("cNumber", cNumber.toString());
+ prop.setProperty("cPercent", cPercent.toString());
+ prop.setProperty("tNumber", tNumber.toString());
+ prop.setProperty("tPercent", tPercent.toString());
+ prop.setProperty("gNumber", gNumber.toString());
+ prop.setProperty("gPercent", gPercent.toString());
+ prop.setProperty("nNumber", nNumber.toString());
+ prop.setProperty("nPercent", nPercent.toString());
+ prop.setProperty("gcPercent", gcPercent.toString()); */
+
+
+ // per reference stats
+ StatsKeeper.Section dataSection = tableDataStatsKeeper.getSections().get(1);
+
+ for (String[] row : dataSection.getRows() ) {
+ prop.setProperty(row[0], Arrays.toString(ArrayUtils.subarray(row, 1, row.length - 1)) );
+ }
+
+
+ return prop;
+ }
+
+
+ public double getSelectedRegionsPercentage() {
+ return (numBasesInsideRegions / (double) referenceSize) * 100.0;
+ }
+
+
+}
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/beans/BamQCXYHistogramChart.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/beans/BamQCXYHistogramChart.java
new file mode 100644
index 0000000..2087982
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/beans/BamQCXYHistogramChart.java
@@ -0,0 +1,278 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.beans;
+
+import java.awt.Color;
+import java.awt.Font;
+import java.io.BufferedWriter;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+
+import org.jfree.chart.ChartFactory;
+import org.jfree.chart.JFreeChart;
+import org.jfree.chart.axis.NumberAxis;
+import org.jfree.chart.axis.NumberTickUnit;
+import org.jfree.chart.plot.PlotOrientation;
+import org.jfree.chart.plot.XYPlot;
+import org.jfree.chart.renderer.xy.XYBarRenderer;
+import org.jfree.chart.title.TextTitle;
+import org.jfree.data.xy.XYSeries;
+import org.jfree.data.xy.XYSeriesCollection;
+import org.jfree.ui.RectangleInsets;
+
+public class BamQCXYHistogramChart extends ChartRawDataWriter {
+ // org.bioinfo.ntools.main params
+ private String title;
+ private String subTitle;
+ private String xLabel;
+ private String yLabel;
+
+ // histogram series
+ private List<String> names;
+ private List<XYVector> histograms;
+ private List<Color> colors;
+
+ // chart
+ private JFreeChart chart;
+
+ private int numberOfBins;
+ private boolean cumulative;
+ private boolean zoomed;
+ private double maxValue;
+ private boolean rangeAxisIntegerTicks;
+ private boolean domainAxisIntegerTicks;
+ private boolean adjustDomainAxisLimits;
+ private double domainAxisTickUnitSize;
+
+ public BamQCXYHistogramChart(String title,String subTitle, String xLabel, String yLabel){
+
+ // main params
+ this.title = title;
+ this.subTitle = subTitle;
+ this.xLabel = xLabel;
+ this.yLabel = yLabel;
+
+ //
+ names = new ArrayList<String>();
+ histograms = new ArrayList<XYVector>();
+ colors = new ArrayList<Color>();
+ numberOfBins = 50;
+ maxValue = 100;
+ adjustDomainAxisLimits = true;
+
+ }
+
+
+ public void addHistogram(String name, XYVector histogram, Color color){
+ names.add(name);
+ histograms.add(histogram);
+ colors.add(color);
+ }
+
+
+ public void render() throws IOException{
+
+ // init chart
+ chart = ChartFactory.createXYBarChart(title,xLabel,false,yLabel, null, PlotOrientation.VERTICAL, true, true, false);
+
+ // title
+ TextTitle textTitle = new TextTitle(title);
+ textTitle.setFont(new Font(Font.SANS_SERIF,Font.BOLD,18));
+ textTitle.setPaint(Color.darkGray);
+ chart.setTitle(textTitle);
+
+ // subtitle
+ TextTitle sub = new TextTitle(subTitle);
+ Font subFont = new Font(Font.SANS_SERIF,Font.PLAIN,12);
+ sub.setFont(subFont);
+ sub.setPadding(5, 5, 15, 5);
+ sub.setPaint(Color.darkGray);
+ chart.setSubtitles(Arrays.asList(sub));
+
+ // other params
+ chart.setPadding(new RectangleInsets(30,20,30,20));
+
+ XYPlot plot = chart.getXYPlot();
+ // axis style
+ Font axisFont = new Font(Font.SANS_SERIF,Font.PLAIN,11);
+ plot.getDomainAxis().setLabelFont(axisFont);
+ plot.getRangeAxis().setLabelFont(axisFont);
+ Font tickFont = new Font(Font.SANS_SERIF,Font.PLAIN,10);
+ plot.getDomainAxis().setTickLabelFont(tickFont);
+ plot.getRangeAxis().setTickLabelFont(tickFont);
+ if(domainAxisIntegerTicks){
+ NumberAxis numberaxis = (NumberAxis)chart.getXYPlot().getDomainAxis();
+ numberaxis.setAutoRangeIncludesZero(false);
+ numberaxis.setStandardTickUnits(NumberAxis.createIntegerTickUnits());
+
+ }
+
+ if (domainAxisTickUnitSize != 0) {
+ NumberAxis numberaxis = (NumberAxis)chart.getXYPlot().getDomainAxis();
+ numberaxis.setTickLabelFont(new Font(Font.SANS_SERIF,Font.PLAIN,8));
+ numberaxis.setTickUnit( new NumberTickUnit(domainAxisTickUnitSize));
+ }
+
+ if(rangeAxisIntegerTicks){
+ NumberAxis numberaxis = (NumberAxis)chart.getXYPlot().getRangeAxis();
+ numberaxis.setAutoRangeIncludesZero(false);
+ numberaxis.setStandardTickUnits(NumberAxis.createIntegerTickUnits());
+ }
+
+
+ // grid
+ plot.setBackgroundPaint(Color.WHITE);
+ chart.setBackgroundPaint(new Color(230,230,230));
+ plot.setDomainGridlinePaint(new Color(214,139,74));
+ plot.setRangeGridlinePaint(new Color(214,139,74));
+
+ // prepare series
+ if(!zoomed && histograms.get(0).getSize() > 0) {
+ maxValue = histograms.get(0).get(histograms.get(0).getSize()-1).getX();
+ }
+
+ double inc = maxValue/(double)numberOfBins;
+ double [] covs = new double[numberOfBins+1];
+ for(int i=0; i<covs.length; i++){
+ covs[i] = inc*i;
+ }
+
+ // convert to bins
+ double [] values = new double[numberOfBins+1];
+ double [] rfreqs = new double[numberOfBins+1];
+ XYItem item;
+ int pos;
+ double total = 0;
+
+ for(int i=0; i<histograms.get(0).getSize(); i++){
+ item = histograms.get(0).get(i);
+// if(item.getX()>0){
+ pos = (int)Math.floor(item.getX()/inc);
+ if(pos<covs.length){
+ values[pos] = values[pos] + item.getY();
+ rfreqs[pos] = rfreqs[pos] + 1;
+ }
+ total+=item.getY();
+// }
+ }
+
+
+
+ XYSeries series = new XYSeries("frequencies");
+ double acum = 0;
+ double next;
+
+ for(int i=0; i<values.length; i++){
+ if(cumulative){
+ acum += (values[i]/total)*100.0;
+ next = acum;
+ } else {
+ next = values[i];
+ }
+ series.add(covs[i],next);
+ }
+
+ // mean dataset
+ chart.getXYPlot().setDataset(0, new XYSeriesCollection(series));
+
+ // mean renderer
+ XYBarRenderer renderer = new XYBarRenderer();
+ BamXYBarPainter barPainter = new BamXYBarPainter();
+ renderer.setBarPainter(barPainter);
+ plot.setRenderer(renderer);
+
+ // adjust axis limits
+ if(adjustDomainAxisLimits && histograms.get(0).getSize() > 0){
+ double minDomainAxis = histograms.get(0).get(0).getX() - inc/2.0;
+ double maxDomainAxis = maxValue + inc/2.0;
+ chart.getXYPlot().getDomainAxis().setRange(minDomainAxis,maxDomainAxis);
+ }
+ }
+
+
+ public void zoom(double maxValue){
+ this.maxValue = maxValue;
+ zoomed = true;
+ }
+
+ /**
+ * @return the chart
+ */
+ public JFreeChart getChart() {
+ return chart;
+ }
+
+
+ /**
+ * @param numberOfBins the numberOfBins to set
+ */
+ public void setNumberOfBins(int numberOfBins) {
+ this.numberOfBins = numberOfBins;
+ }
+
+
+ /**
+ * @param rangeAxisIntegerTicks the rangeAxisIntegerTicks to set
+ */
+ public void setRangeAxisIntegerTicks(boolean rangeAxisIntegerTicks) {
+ this.rangeAxisIntegerTicks = rangeAxisIntegerTicks;
+ }
+
+
+ /**
+ * @param domainAxisIntegerTicks the domainAxisIntegerTicks to set
+ */
+ public void setDomainAxisIntegerTicks(boolean domainAxisIntegerTicks) {
+ this.domainAxisIntegerTicks = domainAxisIntegerTicks;
+ }
+
+
+ public void setDomainAxisTickUnitSize(double domainAxisTickUnitSize) {
+ this.domainAxisTickUnitSize = domainAxisTickUnitSize;
+ }
+
+ @Override
+ void exportData(BufferedWriter dataWriter) throws IOException {
+
+ dataWriter.write("#" + xLabel);
+
+ //Export whole data set
+
+ for (String name : names) {
+ dataWriter.write("\t" + name);
+ }
+ dataWriter.write("\n");
+
+ int len = histograms.get(0).getSize();
+ double[] xData = histograms.get(0).getXVector();
+
+ for (int i = 0; i < len; ++i) {
+ dataWriter.write(Double.toString(xData[i]));
+ for (XYVector data : histograms) {
+ dataWriter.write("\t" + data.get(i).getY());
+ }
+ dataWriter.write("\n");
+ }
+
+ }
+}
\ No newline at end of file
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/beans/BamStats.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/beans/BamStats.java
new file mode 100644
index 0000000..178c334
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/beans/BamStats.java
@@ -0,0 +1,1947 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.beans;
+
+import java.io.*;
+import java.util.*;
+
+import org.bioinfo.commons.utils.ArrayUtils;
+import org.bioinfo.commons.utils.ListUtils;
+import org.bioinfo.commons.utils.StringUtils;
+import org.bioinfo.math.util.MathUtils;
+import org.bioinfo.ngs.qc.qualimap.process.ReadStatsCollector;
+import org.bioinfo.ngs.qc.qualimap.common.ReadStartsHistogram;
+
+public class BamStats implements Serializable {
+ private String name;
+ private String sourceFile;
+ //private String referenceFile;
+
+ // globals
+ private long numberOfMappedBases;
+ private long numberOfSequencedBases;
+ private long numberOfAlignedBases;
+ private long numberOfReads;
+ private long numberOfMappedReads;
+ private long numberOfPairedReads;
+ private long numberOfSingletons;
+ private long numberOfMappedFirstOfPair;
+ private long numberOfMappedSecondOfPair;
+
+ // regions related
+ private long numberOfMappedReadsInRegions;
+ private long numberOfPairedReadsInRegions;
+ private long numberOfSingletonsInRegions;
+ private long numberOfMappedFirstOfPairInRegions;
+ private long numberOfMappedSecondOfPairInRegions;
+ private long numCorrectStrandReads;
+
+ private ArrayList<Long> numMappedBasesPerWindow;
+ private ArrayList<Long> coveragePerWindow, coverageSquaredPerWindow;
+ private ArrayList<Long> windowLengthes;
+
+
+ /*
+ *
+ * Reference params
+ *
+ */
+
+ private long referenceSize;
+ private long numberOfReferenceContigs;
+
+ private long inRegionReferenceSize;
+ private int numSelectedRegions;
+
+ /*
+ // A content
+ private long numberOfAsInReference;
+ private double meanAContentPerWindowInReference;
+ private double meanARelativeContentPerWindowInReference;
+ private List<Double> aContentInReference;
+ private List<Double> aRelativeContentInReference;
+
+ // C content
+ private long numberOfCsInReference;
+ private double meanCContentPerWindowInReference;
+ private double meanCRelativeContentPerWindowInReference;
+ private List<Double> cContentInReference;
+ private List<Double> cRelativeContentInReference;
+
+ // T content
+ private long numberOfTsInReference;
+ private double meanTContentPerWindowInReference;
+ private double meanTRelativeContentPerWindowInReference;
+ private List<Double> tContentInReference;
+ private List<Double> tRelativeContentInReference;
+
+ // G content
+ private long numberOfGsInReference;
+ private double meanGContentPerWindowInReference;
+ private double meanGRelativeContentPerWindowInReference;
+ private List<Double> gContentInReference;
+ private List<Double> gRelativeContentInReference;
+
+ // N content
+ private long numberOfNsInReference;
+ private double meanNContentPerWindowInReference;
+ private double meanNRelativeContentPerWindowInReference;
+ private List<Double> nContentInReference;
+ private List<Double> nRelativeContentInReference;
+
+ // GC content
+ private double meanGcContentInReference;
+ private double meanGcContentPerWindowInReference;
+ private double meanGcRelativeContentPerWindowInReference;
+ private List<Double> gcContentInReference;
+ private List<Double> gcRelativeContentInReference;
+
+ // AT content
+ private double meanAtContentInReference;
+ private double meanAtContentPerWindowInReference;
+ private double meanAtRelativeContentPerWindowInReference;
+ private List<Double> atContentInReference;
+ private List<Double> atRelativeContentInReference;
+ */
+
+ /*
+ *
+ * Sample params
+ *
+ */
+
+ // coverageData
+ private double meanCoverage;
+ private double stdCoverage;
+ private List<Double> coverageAcrossReference;
+ private List<Double> stdCoverageAcrossReference;
+ private HashMap<Long,Long> coverageHistogramMap;
+ private long[] coverageHistogramCache;
+ private XYVector coverageHistogram;
+ private XYVector acumCoverageHistogram;
+ private ReadStartsHistogram readStartsHistogram;
+ private XYVector uniqueReadStartsHistogram;
+ private XYVector balancedCoverageHistogram;
+ private int maxCoverageQuota;
+ private XYVector coverageQuotes;
+ private Map<Double, String> balancedCoverageBarNames;
+ double duplicationRate;
+
+ // quality
+ private double meanMappingQualityPerWindow;
+ private List<Double> mappingQualityAcrossReference;
+ private HashMap<Long,Long> mappingQualityHistogramMap;
+ private long[] mappingQualityHistogramCache;
+ private XYVector mappingQualityHistogram;
+
+ // A content
+ private long numberOfAs;
+ private double meanAContentPerWindow;
+ private double meanARelativeContentPerWindow;
+ private double meanARelativeContent;
+ private List<Double> aContentAcrossReference;
+ private List<Double> aRelativeContentAcrossReference;
+
+ // C content
+ private long numberOfCs;
+ private double meanCContentPerWindow;
+ private double meanCRelativeContentPerWindow;
+ private double meanCRelativeContent;
+ private List<Double> cContentAcrossReference;
+ private List<Double> cRelativeContentAcrossReference;
+
+ // T content
+ private long numberOfTs;
+ private double meanTContentPerWindow;
+ private double meanTRelativeContentPerWindow;
+ private double meanTRelativeContent;
+ private List<Double> tContentAcrossReference;
+ private List<Double> tRelativeContentAcrossReference;
+
+ // G content
+ private long numberOfGs;
+ private double meanGContentPerWindow;
+ private double meanGRelativeContentPerWindow;
+ private double meanGRelativeContent;
+ private List<Double> gContentAcrossReference;
+ private List<Double> gRelativeContentAcrossReference;
+
+ // N content
+ private long numberOfNs;
+ private double meanNContentPerWindow;
+ private double meanNRelativeContentPerWindow;
+ private double meanNRelativeContent;
+ private List<Double> nContentAcrossReference;
+ private List<Double> nRelativeContentAcrossReference;
+
+ // GC content
+ private double meanGcContent;
+ private double meanGcContentPerWindow;
+ private double meanGcRelativeContentPerWindow;
+ private double meanGcRelativeContent;
+ private List<Double> gcContentAcrossReference;
+ private List<Double> gcRelativeContentAcrossReference;
+
+ // insert size
+ private double meanInsertSize;
+ private int p25InsertSize, medianInsertSize, p75InsertSize;
+ private double stdInsertSize;
+ private List<Double> insertSizeAcrossReference;
+ private XYVector insertSizeHistogram;
+ private ArrayList<Integer> insertSizeArray;
+ private HashMap<Long,Long> insertSizeHistogramMap;
+ private long[] insertSizeHistogramCache;
+
+ // reads stats
+ double readMeanSize;
+ int readMaxSize, readMinSize;
+ int numClippedReads, numReadsWithInsertion, numReadsWithDeletion;
+ List<Long> readsAsData;
+ List<Long> readsCsData;
+ List<Long> readsGsData;
+ List<Long> readsTsData;
+ List<Long> readsNsData;
+ List<Long> readsClippingData;
+ XYVector readsAsHistogram;
+ XYVector readsCsHistogram;
+ XYVector readsGsHistogram;
+ XYVector readsTsHistogram;
+ XYVector readsNsHistogram;
+ XYVector readsClippingProfileHistogram;
+ int[] homopolymerIndelsData;
+ private boolean reportNonZeroCoverageOnly;
+
+ private long numDetectedDuplcateReads, numEstimatedDuplicateReads;
+ private double adaptedMeanCoverage;
+
+ private boolean reportOverlappingReadPairs;
+ private long numOverlappingReadPairs, numOfIntersectingMappedBases;
+
+ public long getNumMismatches() {
+ return numMismatches;
+ }
+
+ public double getErrorRate() {
+ double errorRate = 0.;
+ if (acumEditDistance > 0 && numberOfMappedBases > 0) {
+ errorRate = ( (double)acumEditDistance / numberOfMappedBases);
+ }
+
+ return errorRate;
+ }
+
+ public long getNumDetectedDuplicatedReads() {
+ return numDetectedDuplcateReads;
+ }
+
+ public long getNumDuplicatedReadsEstimated() {
+ return numEstimatedDuplicateReads;
+ }
+
+ public void setNumDetectedDuplcateReads(long numReads) {
+ this.numDetectedDuplcateReads = numReads;
+ }
+
+ public void setNumberOfIntersectingReadPairs(long numIntersectingReadPairs, long numIntersectingBases) {
+ this.reportOverlappingReadPairs = true;
+ this.numOverlappingReadPairs = numIntersectingReadPairs;
+ this.numOfIntersectingMappedBases = numIntersectingBases;
+ }
+
+ public boolean reportOverlappingReadPairs() {
+ return reportOverlappingReadPairs;
+ }
+
+ public long getNumOverlappingReadPairs() {
+ return numOverlappingReadPairs;
+ }
+
+ public double getAdaptedMeanCoverage() {
+ return adaptedMeanCoverage;
+ }
+
+ // chromosome stats
+ public class ChromosomeInfo {
+ String name;
+ long length, numBases;
+ double covMean,covStd;
+
+ public String getName() {
+ return name;
+ }
+
+ public long getLength() {
+ return length;
+ }
+
+ public long getNumBases() {
+ return numBases;
+ }
+
+ public double getCovMean() {
+ return covMean;
+ }
+
+ public double getCovStd() {
+ return covStd;
+ }
+ }
+
+ public ChromosomeInfo[] getChromosomeStats() {
+ return chromosomeStats;
+ }
+
+
+ ChromosomeInfo[] chromosomeStats;
+
+
+ // windows
+ private int numberOfWindows;
+ private int numberOfProcessedWindows;
+ private int numberOfInitializedWindows;
+ private long[] windowSizes;
+ private long[] windowStarts;
+ private long[] windowEnds;
+ private String[] windowNames;
+
+ // reporting
+ private boolean activeWindowReporting;
+ transient private PrintWriter windowReport;
+ private boolean activeCoverageReporting;
+ transient private PrintWriter coverageReport;
+ private long sumCoverageSquared, sumCoverage;
+ private final int CACHE_SIZE = 2000;
+ private Map<String,String> warnings;
+ GenomeLocator locator;
+
+
+ // gc content histogram
+ public static int NUM_BINS = 1000;
+ static int SMOOTH_DISTANCE = 0;
+ private double[] gcContentHistogram;
+ boolean avaialableGenomeGcContentData;
+ long sampleCount;
+
+ private int numInsertions;
+ private int numDeletions;
+
+ private long numMismatches, acumEditDistance;
+
+ public BamStats(String name, GenomeLocator locator, long referenceSize, int numberOfWindows){
+
+ // global
+ this.name = name;
+ this.referenceSize = referenceSize;
+ this.numberOfWindows = numberOfWindows;
+ this.locator = locator;
+ numberOfMappedBases = 0;
+ numberOfSequencedBases = 0;
+ numberOfAlignedBases = 0;
+
+ // reference
+ // ACTG across reference arrays
+ /*aContentInReference = new ArrayList<Double>(numberOfWindows);
+ aRelativeContentInReference = new ArrayList<Double>(numberOfWindows);
+ cContentInReference = new ArrayList<Double>(numberOfWindows);
+ cRelativeContentInReference = new ArrayList<Double>(numberOfWindows);
+ tContentInReference = new ArrayList<Double>(numberOfWindows);
+ tRelativeContentInReference = new ArrayList<Double>(numberOfWindows);
+ gContentInReference = new ArrayList<Double>(numberOfWindows);
+ gRelativeContentInReference = new ArrayList<Double>(numberOfWindows);
+ nContentInReference = new ArrayList<Double>(numberOfWindows);
+ nRelativeContentInReference = new ArrayList<Double>(numberOfWindows);
+ gcContentInReference = new ArrayList<Double>(numberOfWindows);
+ gcRelativeContentInReference = new ArrayList<Double>(numberOfWindows);
+ atContentInReference = new ArrayList<Double>(numberOfWindows);
+ atRelativeContentInReference = new ArrayList<Double>(numberOfWindows);*/
+
+ // coverageData across reference arrays
+ coverageAcrossReference = new ArrayList<Double>(numberOfWindows);
+ stdCoverageAcrossReference = new ArrayList<Double>(numberOfWindows);
+ coverageHistogramMap = new HashMap<Long,Long>(numberOfWindows);
+ coverageHistogramCache = new long[CACHE_SIZE];
+
+
+
+ // quality
+ mappingQualityAcrossReference = new ArrayList<Double>(numberOfWindows);
+ mappingQualityHistogramMap = new HashMap<Long,Long>(numberOfWindows);
+ mappingQualityHistogramCache = new long[CACHE_SIZE];
+
+ // ACTG across reference arrays
+ aContentAcrossReference = new ArrayList<Double>(numberOfWindows);
+ aRelativeContentAcrossReference = new ArrayList<Double>(numberOfWindows);
+ cContentAcrossReference = new ArrayList<Double>(numberOfWindows);
+ cRelativeContentAcrossReference = new ArrayList<Double>(numberOfWindows);
+ tContentAcrossReference = new ArrayList<Double>(numberOfWindows);
+ tRelativeContentAcrossReference = new ArrayList<Double>(numberOfWindows);
+ gContentAcrossReference = new ArrayList<Double>(numberOfWindows);
+ gRelativeContentAcrossReference = new ArrayList<Double>(numberOfWindows);
+ nContentAcrossReference = new ArrayList<Double>(numberOfWindows);
+ nRelativeContentAcrossReference = new ArrayList<Double>(numberOfWindows);
+ gcContentAcrossReference = new ArrayList<Double>(numberOfWindows);
+ gcRelativeContentAcrossReference = new ArrayList<Double>(numberOfWindows);
+// atContentAcrossReference = new ArrayList<Double>(numberOfWindows);
+// atRelativeContentAcrossReference = new ArrayList<Double>(numberOfWindows);
+
+ numMappedBasesPerWindow = new ArrayList<Long>(numberOfWindows);
+ coveragePerWindow = new ArrayList<Long>(numberOfWindows);
+ coverageSquaredPerWindow = new ArrayList<Long>(numberOfWindows);
+ windowLengthes = new ArrayList<Long>(numberOfWindows);
+
+
+
+ // gc content histogram
+ gcContentHistogram = new double[NUM_BINS + 1];
+ sampleCount = 0;
+ avaialableGenomeGcContentData = false;
+
+ // insert size
+ insertSizeAcrossReference = new ArrayList<Double>(numberOfWindows);
+ insertSizeHistogramMap = new HashMap<Long,Long>(numberOfWindows);
+ insertSizeHistogramCache = new long[CACHE_SIZE];
+ insertSizeArray = new ArrayList<Integer>();
+
+ // reads
+ readsAsData = new ArrayList<Long>();
+ readsCsData = new ArrayList<Long>();
+ readsGsData = new ArrayList<Long>();
+ readsTsData = new ArrayList<Long>();
+ readsNsData = new ArrayList<Long>();
+ readsClippingData = new ArrayList<Long>();
+ homopolymerIndelsData = new int[6];
+
+ // others
+ maxCoverageQuota = 50;
+ numberOfProcessedWindows = 0;
+ numberOfInitializedWindows = 0;
+
+ readStartsHistogram = new ReadStartsHistogram();
+
+ warnings = new HashMap<String, String>() ;
+
+ }
+
+ /*public void setWindowReferences(String prefix,int windowSize){
+ windowNames = new String[numberOfWindows];
+ windowSizes = new long[numberOfWindows];
+ windowStarts = new long[numberOfWindows];
+ windowEnds = new long[numberOfWindows];
+ for(int i=0; i<numberOfWindows; i++){
+ windowNames[i] = prefix + "_" + (i+1);
+ windowSizes[i] = windowSize;
+ windowStarts[i] = (long)windowSize*(long)i+1;
+ windowEnds[i] = windowStarts[i] + windowSize - 1;
+ }
+ windowPositionsAvailable=true;
+ }*/
+
+ public void setWindowReferences(String prefix, List<Long> windowPositions) {
+ windowNames = new String[numberOfWindows];
+ windowSizes = new long[numberOfWindows];
+ windowStarts = new long[numberOfWindows];
+ windowEnds = new long[numberOfWindows];
+
+ for (int i = 0; i < numberOfWindows; ++i) {
+ windowNames[i] = prefix + "_" + (i+1);
+ windowStarts[i] = windowPositions.get(i);
+ if (i + 1 == numberOfWindows ) {
+ windowEnds[i] = referenceSize;
+ } else {
+ windowEnds[i] = windowPositions.get(i+1) - 1;
+ }
+ windowSizes[i] = windowEnds[i] - windowStarts[i] + 1;
+ }
+ }
+
+
+ /*
+ *
+ * Reporting
+ *
+ */
+ public void activateWindowReporting(String windowReportFile) throws FileNotFoundException{
+ this.windowReport = new PrintWriter(new File(windowReportFile));
+ this.activeWindowReporting = true;
+ reportWindowHeader();
+ }
+
+ public void closeWindowReporting(){
+ this.windowReport.close();
+ }
+
+ public void reportWindowHeader(){
+ windowReport.println("#name\tabsolute_pos\tmapped_bases\tmean_coverage\tstd_coverage");
+ }
+
+ public void reportWindow(BamGenomeWindow window){
+ windowReport.print(window.getName() + "\t");
+ windowReport.print(window.getStart()+":"+window.getEnd() + "\t");
+ windowReport.print(window.getNumberOfMappedBases() + "\t");
+ windowReport.print(StringUtils.decimalFormat(window.getMeanCoverage(),"#,###,###,###.##") + "\t");
+ windowReport.print(StringUtils.decimalFormat(window.getStdCoverage(),"#,###,###,###.##"));
+ windowReport.println();
+ windowReport.flush();
+ }
+
+
+ public void activateCoverageReporting(String coverageReportFile, boolean nonZeroCoverageOnly) throws FileNotFoundException{
+ this.coverageReport = new PrintWriter(new File(coverageReportFile));
+ this.activeCoverageReporting = true;
+ this.reportNonZeroCoverageOnly = nonZeroCoverageOnly;
+ reportCoverageHeader();
+ }
+
+ public void closeCoverageReporting(){
+ this.coverageReport.close();
+ }
+
+ public void reportCoverageHeader(){
+ coverageReport.println("#chr\tpos\tcoverage");
+ }
+
+ public void reportCoverage(BamDetailedGenomeWindow window){
+ ContigRecord rec = locator.getContigCoordinates(window.getStart());
+ for(int i=0; i<window.getCoverageAcrossReference().length; i++){
+ int coverage = window.getCoverageAcrossReference()[i];
+ if (coverage == 0 && reportNonZeroCoverageOnly) {
+ continue;
+ }
+ coverageReport.print(rec.getName() + "\t");
+ coverageReport.print((rec.getRelative() + i) + "\t");
+ coverageReport.print(window.getCoverageAcrossReference()[i]);
+ coverageReport.println();
+ }
+ coverageReport.flush();
+ }
+
+ /*
+ * Window management
+ */
+ public synchronized void incInitializedWindows(){
+ numberOfInitializedWindows++;
+ }
+
+ public synchronized void incProcessedWindows() {
+ numberOfProcessedWindows++;
+ }
+
+ public synchronized void addWindowInformation(BamGenomeWindow window){
+
+ //TODO: bad design
+ boolean isInstanceOfBamGenomeWindow = window instanceof BamDetailedGenomeWindow;
+
+ // global
+ numberOfMappedBases+=window.getNumberOfMappedBases();
+ numberOfSequencedBases+=window.getNumberOfSequencedBases();
+ numberOfAlignedBases+=window.getNumberOfAlignedBases();
+
+ /*
+ * Reference
+ */
+
+ /*
+ // A
+ numberOfAsInReference+=window.getNumberOfAsInReference();
+ aContentInReference.add((double)window.getNumberOfAsInReference());
+ aRelativeContentInReference.add(window.getaRelativeContentInReference());
+ // C
+ numberOfCsInReference+=window.getNumberOfCsInReference();
+ cContentInReference.add((double)window.getNumberOfCsInReference());
+ cRelativeContentInReference.add(window.getcRelativeContentInReference());
+ // T
+ numberOfTsInReference+=window.getNumberOfTsInReference();
+ tContentInReference.add((double)window.getNumberOfTsInReference());
+ tRelativeContentInReference.add(window.gettRelativeContentInReference());
+ // G
+ numberOfGsInReference+=window.getNumberOfGsInReference();
+ gContentInReference.add((double)window.getNumberOfGsInReference());
+ gRelativeContentInReference.add(window.getgRelativeContentInReference());
+ // N
+ numberOfNsInReference+=window.getNumberOfNsInReference();
+ nContentInReference.add((double)window.getNumberOfNsInReference());
+ nRelativeContentInReference.add(window.getnRelativeContentInReference());
+ // GC
+ gcContentInReference.add((double)window.getNumberOfGcsInReference());
+ gcRelativeContentInReference.add(window.getGcRelativeContentInReference());
+ // AT
+ atContentInReference.add((double)window.getNumberOfAtsInReference());
+ atRelativeContentInReference.add(window.getAtRelativeContentInReference());
+ */
+
+ windowLengthes.add( window.getEffectiveWindowLength() );
+ numMappedBasesPerWindow.add(window.getNumberOfMappedBases());
+
+ /*
+ * Sample
+ */
+
+ // coverageData across reference
+ coverageAcrossReference.add(window.getMeanCoverage());
+ stdCoverageAcrossReference.add(window.getStdCoverage());
+ if (isInstanceOfBamGenomeWindow) {
+ BamDetailedGenomeWindow dWindow = (BamDetailedGenomeWindow)window;
+ coverageSquaredPerWindow.add( dWindow.getSumCoverageSquared() );
+ coveragePerWindow.add( dWindow.getSumCoverage() );
+ sumCoverageSquared += dWindow.getSumCoverageSquared();
+ sumCoverage += dWindow.getSumCoverage();
+ updateHistograms(dWindow);
+ }
+
+ // quality
+ mappingQualityAcrossReference.add(window.getMeanMappingQuality());
+ /*if(isInstanceOfBamGenomeWindow) {
+ updateHistogramFromLongVector(mappingQualityHistogramMap,((BamDetailedGenomeWindow)window).getMappingQualityAcrossReference());
+ }*/
+
+ // A
+ numberOfAs+=window.getNumberOfAs();
+ aContentAcrossReference.add(window.getMeanAContent());
+ aRelativeContentAcrossReference.add(window.getMeanARelativeContent());
+
+ // C
+ numberOfCs+=window.getNumberOfCs();
+ cContentAcrossReference.add(window.getMeanCContent());
+ cRelativeContentAcrossReference.add(window.getMeanCRelativeContent());
+
+ // T
+ numberOfTs+=window.getNumberOfTs();
+ tContentAcrossReference.add(window.getMeanTContent());
+ tRelativeContentAcrossReference.add(window.getMeanTRelativeContent());
+
+ // G
+ numberOfGs+=window.getNumberOfGs();
+ gContentAcrossReference.add(window.getMeanGContent());
+ gRelativeContentAcrossReference.add(window.getMeanGRelativeContent());
+
+ // N
+ numberOfNs+=window.getNumberOfNs();
+ nContentAcrossReference.add(window.getMeanNContent());
+ nRelativeContentAcrossReference.add(window.getMeanNRelativeContent());
+
+ // GC
+ gcContentAcrossReference.add(window.getMeanGcContent());
+ gcRelativeContentAcrossReference.add(window.getMeanGcRelativeContent());
+
+ //gcContentHistogram[ (int) window.getMeanGcRelativeContent() ]++;
+
+ // insert size
+ insertSizeAcrossReference.add(window.getMeanInsertSize());
+ /*if(isInstanceOfBamGenomeWindow){
+ updateHistogramFromLongVector(insertSizeHistogramMap,((BamDetailedGenomeWindow)window).getInsertSizeAcrossReference());
+ }*/
+
+ // reporting
+ if(activeWindowReporting) reportWindow(window);
+ if(isInstanceOfBamGenomeWindow){
+ if(activeCoverageReporting) {
+ reportCoverage((BamDetailedGenomeWindow)window);
+ }
+ }
+ }
+
+ public void computeDescriptors(){
+
+ //TODO: this can be parallel!
+
+ /* Reference */
+
+ /*
+ // A
+ meanAContentPerWindowInReference = MathUtils.mean(ListUtils.toDoubleArray(aContentInReference));
+ meanARelativeContentPerWindowInReference = MathUtils.mean(ListUtils.toDoubleArray(aRelativeContentInReference));
+
+ // C
+ meanCContentPerWindowInReference = MathUtils.mean(ListUtils.toDoubleArray(cContentInReference));
+ meanCRelativeContentPerWindowInReference = MathUtils.mean(ListUtils.toDoubleArray(cRelativeContentInReference));
+
+ // T
+ meanTContentPerWindowInReference = MathUtils.mean(ListUtils.toDoubleArray(tContentInReference));
+ meanTRelativeContentPerWindowInReference = MathUtils.mean(ListUtils.toDoubleArray(tRelativeContentInReference));
+
+ // G
+ meanGContentPerWindowInReference = MathUtils.mean(ListUtils.toDoubleArray(gContentInReference));
+ meanGRelativeContentPerWindowInReference = MathUtils.mean(ListUtils.toDoubleArray(gRelativeContentInReference));
+
+ // N
+ meanNContentPerWindowInReference = MathUtils.mean(ListUtils.toDoubleArray(nContentInReference));
+ meanNRelativeContentPerWindowInReference = MathUtils.mean(ListUtils.toDoubleArray(nRelativeContentInReference));
+
+ // GC
+ meanGcContentInReference = (double)(numberOfGsInReference+numberOfCsInReference)/(double)referenceSize;
+ meanGcContentPerWindowInReference = MathUtils.mean(ListUtils.toDoubleArray(gcContentInReference));
+ meanGcRelativeContentPerWindowInReference = MathUtils.mean(ListUtils.toDoubleArray(gcRelativeContentInReference));
+ */
+
+ /*
+ * Sample
+ */
+
+ System.out.println("numberOfMappedBases: " + numberOfMappedBases);
+ System.out.println("referenceSize: " + referenceSize);
+ System.out.println("numberOfSequencedBases: " + numberOfSequencedBases);
+ System.out.println("numberOfAs: " + numberOfAs);
+
+ long effectiveRefSize = numSelectedRegions > 0 ? inRegionReferenceSize : referenceSize;
+ meanCoverage = (double) numberOfMappedBases / (double) effectiveRefSize;
+
+ if (numOfIntersectingMappedBases > 0) {
+ adaptedMeanCoverage = (double) (numberOfMappedBases - numOfIntersectingMappedBases) / (double) effectiveRefSize;
+ }
+
+
+ if (numberOfSequencedBases != 0) {
+
+ double meanCoverageSquared = meanCoverage*meanCoverage;
+
+ double stdCoverageSquared = (double) sumCoverageSquared - 2*meanCoverage*sumCoverage +
+ meanCoverageSquared*effectiveRefSize;
+
+ stdCoverage = Math.sqrt( stdCoverageSquared / effectiveRefSize);
+
+ // quality
+ meanMappingQualityPerWindow = MathUtils.mean(ListUtils.toDoubleArray(mappingQualityAcrossReference));
+
+ // A
+ meanAContentPerWindow = MathUtils.mean(ListUtils.toDoubleArray(aContentAcrossReference));
+ meanARelativeContentPerWindow = MathUtils.mean(ListUtils.toDoubleArray(aRelativeContentAcrossReference));
+ meanARelativeContent = ((double)numberOfAs/(double)numberOfSequencedBases)*100.0;
+
+ // C
+ meanCContentPerWindow = MathUtils.mean(ListUtils.toDoubleArray(cContentAcrossReference));
+ meanCRelativeContentPerWindow = MathUtils.mean(ListUtils.toDoubleArray(cRelativeContentAcrossReference));
+ meanCRelativeContent = ((double)numberOfCs/(double)numberOfSequencedBases)*100.0;
+
+ // T
+ meanTContentPerWindow = MathUtils.mean(ListUtils.toDoubleArray(tContentAcrossReference));
+ meanTRelativeContentPerWindow = MathUtils.mean(ListUtils.toDoubleArray(tRelativeContentAcrossReference));
+ meanTRelativeContent = ((double)numberOfTs/(double)numberOfSequencedBases)*100.0;
+
+ // G
+ meanGContentPerWindow = MathUtils.mean(ListUtils.toDoubleArray(gContentAcrossReference));
+ meanGRelativeContentPerWindow = MathUtils.mean(ListUtils.toDoubleArray(gRelativeContentAcrossReference));
+ meanGRelativeContent = ((double)numberOfGs/(double)numberOfSequencedBases)*100.0;
+
+ // N
+ meanNContentPerWindow = MathUtils.mean(ListUtils.toDoubleArray(nContentAcrossReference));
+ meanNRelativeContentPerWindow = MathUtils.mean(ListUtils.toDoubleArray(nRelativeContentAcrossReference));
+ meanNRelativeContent = ((double)numberOfNs/(double)numberOfSequencedBases)*100.0;
+
+ // GC
+ meanGcContent = (double)(numberOfGs+numberOfCs)/(double)referenceSize;
+ meanGcContentPerWindow = MathUtils.mean(ListUtils.toDoubleArray(gcContentAcrossReference));
+ meanGcRelativeContentPerWindow = MathUtils.mean(ListUtils.toDoubleArray(gcRelativeContentAcrossReference));
+ meanGcRelativeContent = ((double)(numberOfGs+numberOfCs)/(double)numberOfSequencedBases)*100.0;
+
+ }
+
+
+ // reporting
+ if(activeWindowReporting) {
+ closeWindowReporting();
+ }
+
+ if(activeCoverageReporting) {
+ closeCoverageReporting();
+ }
+
+ }
+
+ /*
+ * Histograms
+ */
+
+
+ public void updateHistograms(BamDetailedGenomeWindow window){
+ for(int i=0; i<window.getCoverageAcrossReference().length; i++){
+ if ( window.selectedRegionsAvailable ) {
+ if (!window.getSelectedRegions().get(i)) {
+ continue;
+ }
+ }
+ // coverageData
+ updateHistogramValue(coverageHistogramCache, coverageHistogramMap, window.getCoverageAcrossReference()[i]);
+
+ long quality = window.getMappingQualityAcrossReference()[i];
+ if (quality != -1) {
+ updateHistogramValue(mappingQualityHistogramCache, mappingQualityHistogramMap, quality);
+ }
+ // insert size
+ /*long insertSize = window.getInsertSizeAcrossReference()[i];
+ if (insertSize > 0) {
+ //System.out.println("IS = " + insertSize);
+ updateHistogramValue(insertSizeHistogramCache, insertSizeHistogramMap, insertSize);
+ }*/
+ }
+ }
+
+ /*@SuppressWarnings("unchecked")
+ public void updateHistogramValue(@SuppressWarnings("rawtypes") HashMap map, int key){
+ if(!map.containsKey(key)){
+ map.put(key, Long.valueOf(1));
+ } else {
+ long last = (Long)map.get(key);
+ last++;
+ map.put(key,last);
+ }
+ } */
+
+
+ /*public void dumpInsertData() {
+
+ try {
+ PrintWriter writer = new PrintWriter( new FileWriter("/home/kokonech/insert_size_dump.txt"));
+
+ for ( double val : insertSizeAcrossReference) {
+ writer.println(val);
+ }
+
+ writer.close();
+ } catch (IOException ex) {
+ System.out.println("Failed to dump insert size data");
+ }
+
+ }*/
+
+ public void updateHistogramValue(long[] cache, HashMap<Long,Long> map, long key){
+ if (key < CACHE_SIZE) {
+ cache[(int)key]++;
+ } else if(!map.containsKey(key)){
+ map.put(key, 1L);
+ } else {
+ map.put(key, map.get(key) + 1);
+ }
+ }
+
+
+ public void computeHistograms() {
+
+ addCacheDataToMap(mappingQualityHistogramCache,mappingQualityHistogramMap);
+ mappingQualityHistogram = computeVectorHistogram(mappingQualityHistogramMap);
+ addCacheDataToMap(coverageHistogramCache, coverageHistogramMap);
+
+ computeInsertSizeHistogram();
+ computeCoverageHistogram();
+ computeUniqueReadStartsHistogram();
+ computeGCContentHistogram();
+ computeReadsContentHistogrmas();
+ computeReadsClippingProfileHistogram();
+
+ }
+
+ public XYVector getReadsAsHistogram() {
+ return readsAsHistogram;
+ }
+
+ public XYVector getReadsCsHistogram() {
+ return readsCsHistogram;
+ }
+
+ public XYVector getReadsGsHistogram() {
+ return readsGsHistogram;
+ }
+
+ public XYVector getReadsTsHistogram() {
+ return readsTsHistogram;
+ }
+
+ public XYVector getReadsNsHistogram() {
+ return readsNsHistogram;
+ }
+
+ public XYVector getReadsClippingProfileHistogram() {
+ return readsClippingProfileHistogram;
+ }
+
+
+ private void computeReadsClippingProfileHistogram() {
+ if (readMaxSize == 0 || !clippingIsPresent()) {
+ return;
+ }
+
+ ensureListSize(readsClippingData, readMaxSize);
+
+ double totalBasesClipped = 0;
+ for (long val : readsClippingData) {
+ totalBasesClipped += val;
+ }
+
+ readsClippingProfileHistogram = new XYVector();
+
+ for (int pos = 0; pos < readMaxSize; ++pos) {
+ double val = (readsClippingData.get(pos) / totalBasesClipped) * 100.0;
+ readsClippingProfileHistogram.addItem( new XYItem(pos, val));
+ }
+
+
+ }
+
+ private void computeReadsContentHistogrmas() {
+
+ readsAsHistogram = new XYVector();
+ readsCsHistogram = new XYVector();
+ readsGsHistogram = new XYVector();
+ readsTsHistogram = new XYVector();
+ readsNsHistogram = new XYVector();
+
+ int totalSize = readsAsData.size() + readsCsData.size() + readsGsData.size()
+ + readsTsData.size() + readsNsData.size();
+
+ if (totalSize == 0 ) {
+ }
+
+ // make sure that we have enough data
+ ensureListSize(readsAsData, readMaxSize);
+ ensureListSize(readsCsData, readMaxSize);
+ ensureListSize(readsGsData, readMaxSize);
+ ensureListSize(readsTsData, readMaxSize);
+ ensureListSize(readsNsData, readMaxSize);
+
+ for (int i = 0; i < readMaxSize; ++i ) {
+
+ long numA = readsAsData.get(i);
+ long numC = readsCsData.get(i);
+ long numG = readsGsData.get(i);
+ long numT = readsTsData.get(i);
+ long numN = readsNsData.get(i);
+ double sum = numA + numC + numG + numT + numN;
+
+ readsAsHistogram.addItem( new XYItem(i, (numA / sum) * 100.0 ));
+ readsCsHistogram.addItem( new XYItem(i, (numC / sum) * 100.0 ));
+ readsGsHistogram.addItem( new XYItem(i, (numG / sum) * 100.0 ));
+ readsTsHistogram.addItem( new XYItem(i, (numT / sum) * 100.0 ));
+ readsNsHistogram.addItem( new XYItem(i, (numN / sum) * 100.0 ));
+
+ }
+
+ }
+
+ private void computeGCContentHistogram() {
+
+
+ //normalize
+ //double normalizer = sampleCount - gcContentHistogram[0];
+ for (int i = 0; i < NUM_BINS + 1; ++i) {
+ gcContentHistogram[i] /= sampleCount;
+ }
+
+ //smooth
+ for (int i = SMOOTH_DISTANCE; i < NUM_BINS - SMOOTH_DISTANCE; ++i) {
+ double res = 0;
+ for (int j = 0; j <= 2*SMOOTH_DISTANCE; ++j) {
+ res += gcContentHistogram[i + j - SMOOTH_DISTANCE];
+ }
+ gcContentHistogram[i] = res / (double) (SMOOTH_DISTANCE*2 + 1 );
+ }
+
+
+ /*double sum = 0;
+ for (int i = 1; i < NUM_BINS + 1; ++i) {
+ sum += gcContentHistogram[i];
+ }
+
+ System.out.println("Sum is " + sum + ", sampleCount is " + sampleCount);
+ */
+
+ /*try {
+ FileWriter writer = new FileWriter("/home/kokonech/out.file");
+ for (int i = 0; i < 101; ++i) {
+ String line = "" + i + " " + gcContentHistogram[i] + "\n";
+ writer.write(line);
+ }
+ writer.close();
+ } catch (IOException e) {
+ e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates.
+ }*/
+
+ }
+
+
+ /*public int getHistogramSize(){
+ // read keys
+ Object[] raw = coverageHistogramMap.keySet().toArray();
+ int totalCoverage = 0;
+ for(int i=0; i<raw.length; i++) {
+ int key = (Integer)raw[i];
+ totalCoverage+=coverageHistogramMap.get(key);
+ }
+ return totalCoverage;
+ }*/
+
+
+ private void computeUniqueReadStartsHistogram() {
+
+ long[] uniqueReadStartsArray = readStartsHistogram.getHistorgram();
+
+ uniqueReadStartsHistogram = new XYVector();
+
+ long numPositions = 0;
+
+ for (int i = 1; i <= ReadStartsHistogram.MAX_READ_STARTS_PER_POSITION; ++i ) {
+ long val = uniqueReadStartsArray[i];
+ numPositions += val;
+ uniqueReadStartsHistogram.addItem( new XYItem(i, val));
+ }
+
+ duplicationRate = ( 1.0 - (double) (uniqueReadStartsArray[1]) / numPositions ) * 100.0d;
+
+ }
+
+ private void computeInsertSizeHistogram() {
+
+ if (insertSizeArray.isEmpty()) {
+ return;
+ }
+
+ Collections.sort(insertSizeArray);
+
+ int size = insertSizeArray.size();
+ int medianIndex = size / 2;
+ int percentile25Index = size / 4;
+ int percentile75Index = percentile25Index*3;
+
+ p25InsertSize = insertSizeArray.get(percentile25Index);
+ medianInsertSize = insertSizeArray.get(medianIndex);
+ p75InsertSize = insertSizeArray.get(percentile75Index);
+ double[] insertData = ListUtils.toDoubleArray(insertSizeArray);
+ meanInsertSize = MathUtils.mean( insertData );
+ stdInsertSize = MathUtils.standardDeviation( insertData );
+
+ double border = insertSizeArray.get(percentile75Index)*2.;
+
+ for (int val : insertSizeArray) {
+ if (val <= border) {
+ updateHistogramValue(insertSizeHistogramCache, insertSizeHistogramMap, (long) val);
+ }
+ }
+
+ addCacheDataToMap(insertSizeHistogramCache,insertSizeHistogramMap);
+ insertSizeHistogram = computeVectorHistogram(insertSizeHistogramMap);
+
+
+ }
+
+
+ private void computeCoverageHistogram(){
+
+ double[] coverages = new double[coverageHistogramMap.size()];
+ double[] freqs = new double[coverageHistogramMap.size()];
+
+ // read keys
+ Object[] raw = coverageHistogramMap.keySet().toArray();
+ for(int i=0; i<raw.length; i++) {
+ coverages[i] = (Long)raw[i];
+ freqs[i] = coverageHistogramMap.get(raw[i]);
+ }
+
+ // sort coverages
+ int[] index = ArrayUtils.order(coverages);
+ double[] sortedCoverages = ArrayUtils.ordered(coverages,index);
+ double[] sortedFreqs = ArrayUtils.ordered(freqs,index);
+
+ // fill output
+ coverageHistogram = new XYVector();
+ for(int i=0; i<sortedCoverages.length; i++){
+ coverageHistogram.addItem(new XYItem(sortedCoverages[i],sortedFreqs[i]));
+ }
+
+
+ //TODO: what if coverage is constant, for example 1 everywhere? This has code has to be checked
+
+ // compute balanced coverage histogram
+ balancedCoverageHistogram = new XYVector();
+ balancedCoverageBarNames = new HashMap<Double, String>();
+ double maxCoverage = sortedCoverages[coverages.length - 1];
+ double minCoverage = sortedCoverages[0];
+ int binCount = 30;
+ double n = Math.pow(maxCoverage - minCoverage, 1.0 / binCount );
+
+ int border = (int) (minCoverage);
+
+ ArrayList<Integer> balancedCoverages = new ArrayList<Integer>();
+ balancedCoverages.add(border);
+
+ int k = sortedCoverages.length > 1 ? 1 : 0;
+
+ for (int i = 0; i <= binCount; ++i) {
+ int newBorder = (int) (Math.round( Math.pow(n, i) ) + minCoverage);
+ if (newBorder > border && newBorder >= sortedCoverages[k]) {
+ balancedCoverages.add(newBorder);
+ border = newBorder;
+ while ( k < sortedCoverages.length && newBorder >= sortedCoverages[k]) {
+ ++k;
+ }
+ }
+ }
+
+ int borderIndex = 0;
+
+ if (sortedCoverages.length == 1) {
+ String barName = "" + sortedCoverages[0];
+ balancedCoverageBarNames.put(0., barName);
+ balancedCoverageHistogram.addItem(new XYItem(0, sortedFreqs[0]));
+ } else {
+ for (int i = 0; i < balancedCoverages.size(); ++i) {
+ int coverage = balancedCoverages.get(i);
+ double sum = 0;
+ int prevIndex = borderIndex;
+ while( borderIndex < sortedCoverages.length && sortedCoverages[borderIndex] <= coverage) {
+ sum += sortedFreqs[borderIndex];
+ ++borderIndex;
+ }
+ //System.out.println("i = " + i + " ,borderIndex = " + borderIndex + " ,sum= " + sum) ;
+ String barName = borderIndex == prevIndex + 1 ? (int)sortedCoverages[prevIndex] + "" :
+ (int)sortedCoverages[prevIndex] +" - " + (int)sortedCoverages[(borderIndex - 1)];
+ //System.out.println("Bar name is " + barName);
+ balancedCoverageBarNames.put((double)i, barName);
+ balancedCoverageHistogram.addItem(new XYItem(i, sum));
+
+ }
+ }
+
+
+ // compute acum histogram
+ acumCoverageHistogram = new XYVector();
+ double acum = 0.0;
+ for(int i=0; i<sortedCoverages.length; i++){
+ acum+=sortedFreqs[i];
+ acumCoverageHistogram.addItem(new XYItem(sortedCoverages[i],acum));//(acum/(double)totalCoverage)*100.0));
+ }
+
+ // coverageData quotes
+ coverageQuotes = new XYVector();
+ double total = acum;
+ acum = 0;
+ for(long i=0; i<=maxCoverageQuota; i++){
+ if(coverageHistogramMap.containsKey(i)){
+ acum+=(coverageHistogramMap.get(i)/total)*100.0;
+ }
+ coverageQuotes.addItem(new XYItem(i+1, Math.max(0,100.0-acum)));
+ }
+
+
+ }
+
+
+ private void addCacheDataToMap(long[] cache, HashMap<Long,Long> map) {
+ for (int i = 0; i < CACHE_SIZE; ++i) {
+ long val = cache[i];
+ if (val > 0) {
+ map.put((long)i,val);
+ }
+ }
+ }
+
+ private XYVector computeVectorHistogram(HashMap<Long,Long> map){
+
+ double[] coverages = new double[map.size()];
+ double[] freqs = new double[map.size()];
+
+ // read keys
+ Object[] raw = map.keySet().toArray();
+ for(int i=0; i<raw.length; i++) {
+ coverages[i] = (Long)raw[i];
+ freqs[i] = (double) map.get(raw[i]);
+ }
+
+ // sort coverageData
+ int[] index = ArrayUtils.order(coverages);
+ double[] sortedCoverages = ArrayUtils.ordered(coverages,index);
+ double[] sortedFreqs = ArrayUtils.ordered(freqs,index);
+
+ // fill output
+ XYVector vectorHistogram = new XYVector();
+ for(int i=0; i<sortedCoverages.length; i++){
+ vectorHistogram.addItem(new XYItem(sortedCoverages[i],sortedFreqs[i]));
+ }
+
+ return vectorHistogram;
+
+ }
+
+ public String getWindowName(int index){
+ return windowNames[index];
+ }
+
+ public long getWindowStart(int index){
+ return windowStarts[index];
+ }
+
+ public long getWindowEnd(int index){
+ return windowEnds[index];
+ }
+
+ public String getCurrentWindowName(){
+ return windowNames[numberOfProcessedWindows];
+ }
+
+ public long getCurrentWindowStart(){
+ return windowStarts[numberOfProcessedWindows];
+ }
+
+ public long getCurrentWindowEnd(){
+ return windowEnds[numberOfProcessedWindows];
+ }
+
+ /**
+ * @return the name
+ */
+ public String getName() {
+ return name;
+ }
+
+ /**
+ * @return the sourceFile
+ */
+ public String getSourceFile() {
+ return sourceFile;
+ }
+
+ /**
+ * @param sourceFile the sourceFile to set
+ */
+ public void setSourceFile(String sourceFile) {
+ this.sourceFile = sourceFile;
+ }
+
+ /**
+ * @return the numberOfMappedBases
+ */
+ public long getNumberOfMappedBases() {
+ return numberOfMappedBases;
+ }
+
+ /**
+ * @return the numberOfAlignedBases
+ */
+ public long getNumberOfAlignedBases() {
+ return numberOfAlignedBases;
+ }
+
+ public long getNumberOfSequencedBases() {
+ return numberOfSequencedBases;
+ }
+
+ /**
+ * @return the numberOfReads
+ */
+ public long getNumberOfReads() {
+ return numberOfReads;
+ }
+
+ /**
+ * @param numberOfReads the numberOfReads to set
+ */
+ public void setNumberOfReads(long numberOfReads) {
+ this.numberOfReads = numberOfReads;
+ }
+
+ /**
+ * @return the numberOfMappedReads
+ */
+ public long getNumberOfMappedReads() {
+ return numberOfMappedReads;
+ }
+
+ /**
+ * @param numberOfMappedReads the numberOfMappedReads to set
+ */
+ public void setNumberOfMappedReads(long numberOfMappedReads) {
+ this.numberOfMappedReads = numberOfMappedReads;
+ }
+
+ /**
+ * @return the percentageOfMappedReads
+ */
+ public double getPercentageOfMappedReads() {
+ return ( numberOfMappedReads / (double) numberOfReads) * 100.0;
+ }
+
+ public XYVector getUniqueReadStartsHistogram() {
+ return uniqueReadStartsHistogram;
+ }
+
+ /**
+ * @return the referenceSize
+ */
+ public long getReferenceSize() {
+ return referenceSize;
+ }
+
+ /**
+ * @param referenceSize the referenceSize to set
+ */
+ public void setReferenceSize(long referenceSize) {
+ this.referenceSize = referenceSize;
+ }
+
+ /**
+ * @return the numberOfReferenceContigs
+ */
+ public long getNumberOfReferenceContigs() {
+ return numberOfReferenceContigs;
+ }
+
+ /**
+ * @param numberOfReferenceContigs the numberOfReferenceContigs to set
+ */
+ public void setNumberOfReferenceContigs(long numberOfReferenceContigs) {
+ this.numberOfReferenceContigs = numberOfReferenceContigs;
+ }
+
+ /**
+ * @return the coverageAcrossReference
+ */
+ public List<Double> getCoverageAcrossReference() {
+ return coverageAcrossReference;
+ }
+
+ public List<Double> getStdCoverageAcrossReference() {
+ return stdCoverageAcrossReference;
+ }
+
+
+ /**
+ * @return the coverageHistogram
+ */
+ public XYVector getCoverageHistogram() {
+ return coverageHistogram;
+ }
+
+ /**
+ * @return the coverageQuotes
+ */
+ public XYVector getCoverageQuotes() {
+ return coverageQuotes;
+ }
+
+ /**
+ * @return the meanMappingQualityPerWindow
+ */
+ public double getMeanMappingQualityPerWindow() {
+ return meanMappingQualityPerWindow;
+ }
+
+ /**
+ * @return the mappingQualityAcrossReference
+ */
+ public List<Double> getMappingQualityAcrossReference() {
+ return mappingQualityAcrossReference;
+ }
+
+ /**
+ * @return the mappingQualityHistogram
+ */
+ public XYVector getMappingQualityHistogram() {
+ return mappingQualityHistogram;
+ }
+
+ /**
+ * @return the numberOfAs
+ */
+ public long getNumberOfAs() {
+ return numberOfAs;
+ }
+
+
+ /**
+ * @return the meanARelativeContent
+ */
+ public double getMeanARelativeContent() {
+ return meanARelativeContent;
+ }
+
+ /**
+ * @return the numberOfCs
+ */
+ public long getNumberOfCs() {
+ return numberOfCs;
+ }
+
+
+ /**
+ * @return the meanCRelativeContent
+ */
+ public double getMeanCRelativeContent() {
+ return meanCRelativeContent;
+ }
+
+ /**
+ * @return the numberOfTs
+ */
+ public long getNumberOfTs() {
+ return numberOfTs;
+ }
+
+
+ /**
+ * @return the meanTRelativeContent
+ */
+ public double getMeanTRelativeContent() {
+ return meanTRelativeContent;
+ }
+
+ /**
+ * @return the numberOfGs
+ */
+ public long getNumberOfGs() {
+ return numberOfGs;
+ }
+
+ /**
+ * @return the meanGRelativeContent
+ */
+ public double getMeanGRelativeContent() {
+ return meanGRelativeContent;
+ }
+
+ /**
+ * @return the numberOfNs
+ */
+ public long getNumberOfNs() {
+ return numberOfNs;
+ }
+
+ /**
+ * @return the meanNRelativeContent
+ */
+ public double getMeanNRelativeContent() {
+ return meanNRelativeContent;
+ }
+
+ /**
+ * @return the meanGcRelativeContentPerWindow
+ */
+ public double getMeanGcRelativeContentPerWindow() {
+ return meanGcRelativeContentPerWindow;
+ }
+
+ /**
+ * @return the meanGcRelativeContent
+ */
+ public double getMeanGcRelativeContent() {
+ return meanGcRelativeContent;
+ }
+
+
+ /**
+ * @return the gcRelativeContentAcrossReference
+ */
+ public List<Double> getGcRelativeContentAcrossReference() {
+ return gcRelativeContentAcrossReference;
+ }
+
+ /**
+ * @return the numberOfWindows
+ */
+ public int getNumberOfWindows() {
+ return numberOfWindows;
+ }
+
+ /**
+ * @return the numberOfProcessedWindows
+ */
+ public int getNumberOfProcessedWindows() {
+ return numberOfProcessedWindows;
+ }
+
+ /**
+ * @return the numberOfInitializedWindows
+ */
+ public int getNumberOfInitializedWindows() {
+ return numberOfInitializedWindows;
+ }
+
+ public double getMeanCoverage() {
+ return meanCoverage;
+ }
+
+ public double getStdCoverage() {
+ return stdCoverage;
+ }
+
+
+ /**
+ * @return the meanInsertSize
+ */
+ public double getMeanInsertSize() {
+ return meanInsertSize;
+ }
+
+
+ /**
+ * @return the insertSizeAcrossReference
+ */
+ public List<Double> getInsertSizeAcrossReference() {
+ return insertSizeAcrossReference;
+ }
+
+ /**
+ * @return the insertSizeHistogram
+ */
+ public XYVector getInsertSizeHistogram() {
+ return insertSizeHistogram;
+ }
+
+ public long getInRegionReferenceSize() {
+ return inRegionReferenceSize;
+ }
+
+ public void setInRegionReferenceSize(long inRegionReferenceSize) {
+ this.inRegionReferenceSize = inRegionReferenceSize;
+ }
+
+ public int getNumSelectedRegions() {
+ return numSelectedRegions;
+ }
+
+ public void setNumSelectedRegions(int numSelectedRegions) {
+ this.numSelectedRegions = numSelectedRegions;
+ }
+
+ public long getNumberOfMappedReadsInRegions() {
+ return numberOfMappedReadsInRegions;
+ }
+
+ public void setNumberOfMappedReadsInRegions(long numberOfMappedReadsInRegions) {
+ this.numberOfMappedReadsInRegions = numberOfMappedReadsInRegions;
+ }
+ public double getPercentageOfInsideMappedReads() {
+ return (numberOfMappedReadsInRegions / (double) numberOfReads) * 100.0;
+ }
+
+
+ public XYVector getGcContentHistogram() {
+ XYVector result = new XYVector();
+
+ int iterCount = NUM_BINS / 100;
+ int counter = 0;
+ double acum = 0;
+ double index = 1;
+ for (int i = 1; i < NUM_BINS + 1; ++i) {
+ counter++;
+ acum += gcContentHistogram[i];
+ if (counter == iterCount) {
+ result.addItem( new XYItem(index, acum));
+ counter = 0;
+ acum = 0;
+ index++;
+ }
+ }
+
+ return result;
+ }
+
+ public void addReadStatsData(ReadStatsCollector readStatsCollector) {
+
+
+ addReadsAsData(readStatsCollector.getReadsAContent());
+ addReadsCsData(readStatsCollector.getReadsCContent());
+ addReadsGsData(readStatsCollector.getReadsGContent());
+ addReadsTsData(readStatsCollector.getReadsTContent());
+ addReadsNsData(readStatsCollector.getReadsNContent());
+ addReadsClippingInfo(readStatsCollector.getReadsClippingInfo());
+
+ ArrayList<Float> readsGcContent = readStatsCollector.getReadsGcContent();
+ for (float val : readsGcContent) {
+ //System.out.println(val);
+ gcContentHistogram[ (int) (val * NUM_BINS) ]++;
+ }
+ sampleCount += readsGcContent.size();
+
+ numClippedReads += readStatsCollector.getNumClippedReads();
+ numReadsWithInsertion += readStatsCollector.getNumReadsWithInsertion();
+ numReadsWithDeletion += readStatsCollector.getNumReadsWithDeletion();
+
+ int[] homopolymerIndels = readStatsCollector.getHomopolymerIndels();
+ int numHomopolymerIndels = 0;
+ for (int i = 0; i < 5; ++i) {
+ homopolymerIndelsData[i] += homopolymerIndels[i];
+ numHomopolymerIndels += homopolymerIndels[i];
+ }
+
+ numInsertions += readStatsCollector.getNumInsertions();
+ numDeletions += readStatsCollector.getNumDeletions();
+ numMismatches += readStatsCollector.getNumMismatches();
+ acumEditDistance += readStatsCollector.getEditDistance();
+
+
+ homopolymerIndelsData[5] += readStatsCollector.getNumIndels() - numHomopolymerIndels;
+
+ }
+
+
+ public Collection<CategoryItem> getHomopolymerIndels() {
+ ArrayList<CategoryItem> res = new ArrayList<CategoryItem>();
+
+ res.add( new CategoryItem("polyA", homopolymerIndelsData[0] ) );
+ res.add( new CategoryItem("polyC", homopolymerIndelsData[1] ) );
+ res.add( new CategoryItem("polyG", homopolymerIndelsData[2] ) );
+ res.add( new CategoryItem("polyT", homopolymerIndelsData[3] ) );
+ res.add( new CategoryItem("polyN", homopolymerIndelsData[4] ) );
+ res.add( new CategoryItem("Non-poly", homopolymerIndelsData[5] ) );
+
+ return res;
+ }
+
+ public long getNumberOfPairedReads() {
+ return numberOfPairedReads;
+ }
+
+ public void setNumberOfPairedReads(long numberOfPairedReads) {
+ this.numberOfPairedReads = numberOfPairedReads;
+ }
+
+ public double getPercentageOfPairedReads() {
+ return (numberOfPairedReads / (double) numberOfReads) * 100.0;
+ }
+
+
+ public long getNumberOfSingletons() {
+ return numberOfSingletons;
+ }
+
+ public void setNumberOfSingletons(long numberOfSingletons) {
+ this.numberOfSingletons = numberOfSingletons;
+ }
+
+ public double getPercentageOfSingletons() {
+ return (numberOfSingletons / (double) numberOfReads) * 100.0;
+ }
+
+ public void addReadsAsData(int[] readsAContent) {
+ ensureListSize(readsAsData, readsAContent.length);
+ for (int i = 0; i < readsAContent.length; ++i) {
+ long val = readsAsData.get(i);
+ val += readsAContent[i];
+ readsAsData.set(i, val);
+ }
+ }
+
+ public void addReadsCsData(int[] readsCContent) {
+ ensureListSize(readsCsData, readsCContent.length);
+ for (int i = 0; i < readsCContent.length; ++i) {
+ long val = readsCsData.get(i);
+ val += readsCContent[i];
+ readsCsData.set(i, val);
+ }
+ }
+
+ public void addReadsGsData(int[] readsGContent) {
+ ensureListSize(readsGsData, readsGContent.length);
+ for (int i = 0; i < readsGContent.length; ++i) {
+ long val = readsGsData.get(i);
+ val += readsGContent[i];
+ readsGsData.set(i, val);
+ }
+ }
+
+ public void addReadsTsData(int[] readsTContent) {
+ ensureListSize(readsTsData, readsTContent.length);
+ for (int i = 0; i < readsTContent.length; ++i) {
+ long val = readsTsData.get(i);
+ val += readsTContent[i];
+ readsTsData.set(i, val);
+ }
+ }
+
+ public void addReadsNsData(int[] readsNContent) {
+ ensureListSize(readsNsData, readsNContent.length);
+ for (int i = 0; i < readsNContent.length; ++i) {
+ long val = readsNsData.get(i);
+ val += readsNContent[i];
+ readsNsData.set(i, val);
+ }
+ }
+
+ public void addReadsClippingInfo(int[] readsClippingInfo) {
+ ensureListSize(readsClippingData, readsClippingInfo.length);
+ for (int i = 0; i < readsClippingInfo.length; ++i) {
+ long val = readsClippingData.get(i);
+ val += readsClippingInfo[i];
+ readsClippingData.set(i, val);
+ }
+ }
+
+
+ public boolean clippingIsPresent() {
+
+ for (long val : readsClippingData) {
+ if (val > 0) {
+ return true;
+ }
+ }
+
+ return false;
+ }
+
+ public int getReadMaxSize() {
+ return readMaxSize;
+ }
+
+ public void setReadMaxSize(int readMaxSize) {
+ this.readMaxSize = readMaxSize;
+ }
+
+ public double getReadMeanSize() {
+ return readMeanSize;
+ }
+
+ public void setReadMeanSize(double readMeanSize) {
+ this.readMeanSize = readMeanSize;
+ }
+
+ public int getReadMinSize() {
+ return readMinSize;
+ }
+
+ public void setReadMinSize(int minReadSize) {
+ this.readMinSize = minReadSize;
+ }
+
+
+ private static void ensureListSize(List<Long> list, int expectedSize) {
+ int listSize = list.size();
+ if (listSize < expectedSize) {
+ int numElements = expectedSize - listSize + 1;
+ for (int i = 0; i < numElements; ++i) {
+ list.add(0L);
+ }
+ }
+
+ }
+
+ public void computeChromosomeStats(GenomeLocator locator, ArrayList<Integer> chromosomeWindowIndexes) throws IOException {
+ int chromosomeCount = chromosomeWindowIndexes.size();
+ List<ContigRecord> contigRecords = locator.getContigs();
+
+ //chromoWriter.println("#name\tabsolute_pos\tmapped_bases\tmean_coverage\tstd_coverage");
+
+ chromosomeStats = new ChromosomeInfo[chromosomeCount];
+
+ for (int k = 0; k < chromosomeCount; ++k) {
+ int firstWindowIndex = chromosomeWindowIndexes.get(k);
+ int lastWindowIndex = k + 1 < chromosomeCount
+ ? chromosomeWindowIndexes.get(k + 1) - 1 : numberOfWindows - 1;
+
+
+ // Computing mean
+
+ long numBases = 0;
+ long length = 0;
+ long sumCov = 0;
+ long sumCovSquared = 0;
+ for (int i = firstWindowIndex; i <= lastWindowIndex; ++i) {
+ numBases += numMappedBasesPerWindow.get(i);
+ sumCov += coveragePerWindow.get(i);
+ sumCovSquared += coverageSquaredPerWindow.get(i);
+ length += windowLengthes.get(i);
+ }
+
+
+
+ ContigRecord contig = contigRecords.get(k);
+
+ ChromosomeInfo info = new ChromosomeInfo();
+ info.name = contig.getName();
+ if (length != 0) {
+ info.length = length;
+ info.numBases = numBases;
+ info.covMean = numBases / (double)length ;
+ double meanCoverageSquared = info.covMean*info.covMean;
+ double stdCoverageSquared = (double) sumCovSquared - 2*info.covMean*sumCov +
+ meanCoverageSquared*length;
+ info.covStd = Math.sqrt( stdCoverageSquared / length);
+
+ }
+ chromosomeStats[k] = info;
+
+ //if (length == 0) {
+ // chromoWriter.println("0\t0\t0\t");
+ //} else {
+ // chromoWriter.print(numBases + "\t");
+ // double mean = numBases / length;
+ // double std = Math.sqrt( sumCovSquared / length - mean*mean);
+ //chromoWriter.print(StringUtils.decimalFormat(mean,"#,###,###,###.##")+ "\t" );
+ //chromoWriter.println(StringUtils.decimalFormat(std, "#,###,###,###.##"));
+ //}
+ }
+
+ }
+
+ public void setCoverageMean(double covMean) {
+ this.meanCoverage = covMean;
+ }
+
+ public void setCoverageStd(double covStd) {
+ this.stdCoverage = covStd;
+ }
+
+ public void setMeanMappingQuality(double mmq) {
+ this.meanMappingQualityPerWindow = mmq;
+ }
+
+ public void setMeanGcContent(double gcContent) {
+ this.meanGcRelativeContent = gcContent;
+ }
+
+ public void setMedianInsertSize(int insertSize) {
+ this.medianInsertSize = insertSize;
+ }
+
+ public XYVector getBalancedCoverageHistogram() {
+ return balancedCoverageHistogram;
+ }
+
+ public Map<Double,String> getBalancedCoverageBarNames() {
+ return balancedCoverageBarNames;
+ }
+
+ public void addWarning(String warningIdChromosomeNotFound, String msg) {
+ warnings.put(warningIdChromosomeNotFound, msg);
+ }
+
+ public Map<String,String> getWarnings() {
+ return warnings;
+ }
+
+ public int getP25InsertSize() {
+ return p25InsertSize;
+ }
+
+ public int getMedianInsertSize() {
+ return medianInsertSize;
+ }
+
+ public int getP75InsertSize() {
+ return p75InsertSize;
+ }
+
+ public double getStdInsertSize() {
+ return stdInsertSize;
+ }
+
+ public long getNumberOfMappedFirstOfPair() {
+ return numberOfMappedFirstOfPair;
+ }
+
+ public void setNumberOfMappedFirstOfPair(long numberOfMappedFirstOfPair) {
+ this.numberOfMappedFirstOfPair = numberOfMappedFirstOfPair;
+ }
+
+ public long getNumberOfMappedSecondOfPair() {
+ return numberOfMappedSecondOfPair;
+ }
+
+ public void setNumberOfMappedSecondOfPair(long numberOfMappedSecondOfPair) {
+ this.numberOfMappedSecondOfPair = numberOfMappedSecondOfPair;
+ }
+
+ public long getNumberOfSingletonsInRegions() {
+ return numberOfSingletonsInRegions;
+ }
+
+ public void setNumberOfSingletonsInRegions(long numberOfSingletonsInRegions) {
+ this.numberOfSingletonsInRegions = numberOfSingletonsInRegions;
+ }
+
+ public long getNumberOfMappedFirstOfPairInRegions() {
+ return numberOfMappedFirstOfPairInRegions;
+ }
+
+ public void setNumberOfMappedFirstOfPairInRegions(long numberOfMappedFirstOfPairInRegions) {
+ this.numberOfMappedFirstOfPairInRegions = numberOfMappedFirstOfPairInRegions;
+ }
+
+ public long getNumberOfMappedSecondOfPairInRegions() {
+ return numberOfMappedSecondOfPairInRegions;
+ }
+
+ public void setNumberOfMappedSecondOfPairInRegions(long numberOfMappedSecondOfPairInRegions) {
+ this.numberOfMappedSecondOfPairInRegions = numberOfMappedSecondOfPairInRegions;
+ }
+
+
+ public void updateInsertSizeHistogram(int insertSize) {
+ if (insertSize >= 0 ) {
+ insertSizeArray.add(insertSize);
+ }
+ }
+
+
+ public void setNumberOfPairedReadsInRegions(long numPairedReads) {
+ numberOfPairedReadsInRegions = numPairedReads;
+ }
+
+ public long getNumberOfPairedReadsInRegions() {
+ return numberOfPairedReadsInRegions;
+ }
+
+ public double getDuplicationRate() {
+ return duplicationRate;
+ }
+
+ public boolean updateReadStartsHistogram(long position) {
+ boolean duplicate = readStartsHistogram.update(position);
+ if (duplicate) {
+ numEstimatedDuplicateReads++;
+ }
+ return duplicate;
+ }
+
+ public int getNumClippedReads() {
+ return numClippedReads;
+ }
+
+ public double getReadsWithInsertionPercentage() {
+ return (numReadsWithInsertion / (double) numberOfMappedReads) * 100.0;
+ }
+
+ public double getReadsWithDeletionPercentage() {
+ return (numReadsWithDeletion / (double) numberOfMappedReads) * 100.0;
+ }
+
+ public void setNumberOfCorrectStrandReads(long numberOfCorrectStrandReads) {
+ this.numCorrectStrandReads = numberOfCorrectStrandReads;
+ }
+
+ public long getNumCorrectStrandReads() {
+ return numCorrectStrandReads;
+ }
+
+ public int getNumIndels() {
+ return numInsertions + numDeletions;
+ }
+
+ public int getNumInsertions() {
+ return numInsertions;
+ }
+
+ public int getNumDeletions() {
+ return numDeletions;
+ }
+
+ public double getHomopolymerIndelFraction() {
+
+ return (1.0 - homopolymerIndelsData[5] / (double) (numInsertions + numDeletions));
+ }
+
+}
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/beans/BamXYBarPainter.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/beans/BamXYBarPainter.java
new file mode 100644
index 0000000..6e58ec2
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/beans/BamXYBarPainter.java
@@ -0,0 +1,70 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.beans;
+
+import java.awt.BasicStroke;
+import java.awt.Color;
+import java.awt.Graphics2D;
+import java.awt.geom.RectangularShape;
+import java.io.Serializable;
+
+import org.jfree.chart.renderer.xy.XYBarPainter;
+import org.jfree.chart.renderer.xy.XYBarRenderer;
+import org.jfree.ui.RectangleEdge;
+
+public class BamXYBarPainter implements XYBarPainter, Serializable {
+ private static Color DEFAULT_BAR_COLOR = new Color(100,100,250,150);
+ private static Color DEFAULT_BORDER_BAR_COLOR = new Color(50,50,50);
+ private Color barColor;
+ private Color borderBarColor;
+
+ public BamXYBarPainter(){
+ barColor = DEFAULT_BAR_COLOR;
+ borderBarColor = DEFAULT_BORDER_BAR_COLOR;
+ }
+
+ public BamXYBarPainter(Color color){
+ barColor = color;
+ borderBarColor = DEFAULT_BORDER_BAR_COLOR;
+ }
+
+
+ @Override
+ public void paintBar(Graphics2D g, XYBarRenderer renderer, int row, int column, RectangularShape shape, RectangleEdge edge) {
+ // create shape
+ RectangularShape myshape = (RectangularShape)shape.clone();
+
+ // fill
+ g.setColor(barColor);
+ g.fill(myshape);
+
+ // border
+ g.setColor(borderBarColor);
+ g.setStroke(new BasicStroke(1.5f));
+ g.draw(myshape);
+ }
+
+ @Override
+ public void paintBarShadow(Graphics2D arg0, XYBarRenderer arg1, int arg2, int arg3, RectangularShape arg4, RectangleEdge arg5, boolean arg6) {
+ // NOTHING TO DO
+ }
+
+}
\ No newline at end of file
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/beans/CategoryItem.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/beans/CategoryItem.java
new file mode 100644
index 0000000..a00413b
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/beans/CategoryItem.java
@@ -0,0 +1,46 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.beans;
+
+/**
+ * Created by kokonech
+ * Date: 6/27/12
+ * Time: 12:25 PM
+ */
+public class CategoryItem {
+
+ private int value;
+ private String name;
+
+ public CategoryItem(String name, int value) {
+ this.name = name;
+ this.value = value;
+ }
+
+ String getName() {
+ return name;
+ }
+
+ int getValue() {
+ return value;
+ }
+
+}
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/beans/ChartRawDataWriter.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/beans/ChartRawDataWriter.java
new file mode 100644
index 0000000..f5abeb6
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/beans/ChartRawDataWriter.java
@@ -0,0 +1,43 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.beans;
+
+import java.io.BufferedWriter;
+import java.io.FileWriter;
+import java.io.IOException;
+
+/**
+ * Created by kokonech
+ * Date: 6/13/12
+ * Time: 11:09 AM
+ */
+public abstract class ChartRawDataWriter {
+
+ public void exportDataToFile(String fileName) throws IOException{
+ BufferedWriter writer = new BufferedWriter( new FileWriter(fileName));
+ exportData(writer);
+ writer.close();
+ }
+
+ abstract void exportData(BufferedWriter dataWriter) throws IOException;
+
+
+}
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/beans/ContigRecord.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/beans/ContigRecord.java
new file mode 100644
index 0000000..bbfd9a2
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/beans/ContigRecord.java
@@ -0,0 +1,114 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.beans;
+
+import java.io.Serializable;
+
+public class ContigRecord implements Serializable {
+ private String name;
+ private long position;
+ private long relative;
+ private int size;
+
+ public ContigRecord(String name,int size){
+ this(name,1,1,size);
+ }
+
+ public ContigRecord(String name,long position,int size){
+ this(name,position,1,size);
+ }
+
+ public ContigRecord(String name,long position,long relative,int size){
+ this.name = name;
+ this.position = position;
+ this.relative = 1;
+ this.size = size;
+ }
+
+ public long getStart(){
+ return this.position;
+ }
+
+ public long getEnd(){
+ return this.position + this.size -1;
+ }
+
+
+ public String toString(){
+ return this.name + "\t" + this.position + "\t" + this.size;
+ }
+
+ /**
+ * @return the name
+ */
+ public String getName() {
+ return name;
+ }
+
+ /**
+ * @param name the name to set
+ */
+ public void setName(String name) {
+ this.name = name;
+ }
+
+ /**
+ * @return the size
+ */
+ public int getSize() {
+ return size;
+ }
+
+ /**
+ * @param size the size to set
+ */
+ public void setSize(int size) {
+ this.size = size;
+ }
+
+ /**
+ * @return the position
+ */
+ public long getPosition() {
+ return position;
+ }
+
+ /**
+ * @param position the position to set
+ */
+ public void setPosition(long position) {
+ this.position = position;
+ }
+
+ /**
+ * @return the relative
+ */
+ public long getRelative() {
+ return relative;
+ }
+
+ /**
+ * @param relative the relative to set
+ */
+ public void setRelative(long relative) {
+ this.relative = relative;
+ }
+}
\ No newline at end of file
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/beans/GenericHistogram.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/beans/GenericHistogram.java
new file mode 100644
index 0000000..0de1ae3
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/beans/GenericHistogram.java
@@ -0,0 +1,72 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.beans;
+
+/**
+ * Created by kokonech
+ * Date: 10/5/12
+ * Time: 11:21 AM
+ */
+public class GenericHistogram {
+
+
+ final int numBins;
+ double[] hist;
+ boolean normalize;
+
+ public GenericHistogram(int numBins, boolean normalize) {
+ this.numBins = numBins;
+ this.hist = new double[numBins];
+ this.normalize = normalize;
+ }
+
+ public void updateHistogram(int[] data) {
+
+ final int norm = normalize ? data.length : 1;
+
+ final int step = (int) Math.ceil( data.length / (double) numBins );
+ int binCoverage = 0;
+ int binIndex = 0;
+ int count = step;
+
+ for (int i = 0; i < data.length; ++i) {
+
+ binCoverage += data[i];
+
+ if (i + 1 == count || i == data.length - 1) {
+ hist[binIndex] += binCoverage / (double) norm;
+ ++binIndex;
+ binCoverage = 0;
+ count += step;
+
+ }
+
+ }
+
+ }
+
+
+ public double[] getHist() {
+ return hist;
+ }
+
+
+}
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/beans/GenomeLocator.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/beans/GenomeLocator.java
new file mode 100644
index 0000000..6e0c08d
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/beans/GenomeLocator.java
@@ -0,0 +1,123 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.beans;
+
+import java.io.*;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+
+public class GenomeLocator implements Externalizable {
+ private List<ContigRecord> contigs;
+ private HashMap<String,Long> positions;
+ private long totalSize;
+
+ public GenomeLocator(){
+ contigs = new ArrayList<ContigRecord>();
+ positions = new HashMap<String, Long>();
+ totalSize = 0;
+ }
+
+ public void addContig(String name, int size){
+ contigs.add(new ContigRecord(name,totalSize+1,size));
+ positions.put(name, totalSize+1);
+ totalSize+=size;
+ }
+
+ public Long getAbsoluteCoordinates(String name, int relative){
+
+ //TODO: maybe it should be possible to ignore "chr" for human genome?
+
+ /*String simplifiedName = name.replace("chr","");*/
+
+ if(positions.containsKey(name)){
+ return positions.get(name) + (relative-1);
+ } /*else if (positions.containsKey(simplifiedName)){
+ return positions.get(simplifiedName) + (relative-1);
+ } */else {
+ return (long)-1;
+ }
+ }
+
+ public ContigRecord getContigCoordinates(long absolute){
+ // empty contig list
+ if(contigs.size()==0){
+ return null;
+ }
+ // mega contig
+ else if(contigs.size()==1){
+ ContigRecord contig = contigs.get(0);
+ contig.setRelative(absolute);
+ return contig;
+ }
+ // search contig
+ else {
+ ContigRecord last = contigs.get(0);
+ for(int i=1; i<contigs.size(); i++){
+ if(contigs.get(i).getPosition()>absolute){
+ break;
+ }
+ last = contigs.get(i);
+ }
+ last.setRelative(absolute-last.getPosition()+1);
+ return last;
+ }
+ }
+
+ /**
+ * @return the contigs
+ */
+ public List<ContigRecord> getContigs() {
+ return contigs;
+ }
+
+ /**
+ * @return the totalSize
+ */
+ public long getTotalSize() {
+ return totalSize;
+ }
+
+
+ @Override
+ public void writeExternal(ObjectOutput objectOutput) throws IOException {
+ objectOutput.writeObject(contigs);
+ objectOutput.writeObject(positions);
+ objectOutput.writeLong(totalSize);
+ }
+
+ @Override
+ public void readExternal(ObjectInput objectInput) throws IOException, ClassNotFoundException {
+ contigs = (List<ContigRecord>) objectInput.readObject();
+ positions = (HashMap<String,Long>) objectInput.readObject();
+ totalSize = objectInput.readLong();
+
+ }
+
+ public boolean containsContig(String seqName) {
+ for (ContigRecord contigRecord : contigs) {
+ if (contigRecord.getName().equals(seqName)) {
+ return true;
+ }
+ }
+ return false;
+ }
+}
\ No newline at end of file
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/beans/PrincipleComponentAnalysis.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/beans/PrincipleComponentAnalysis.java
new file mode 100644
index 0000000..46ba57d
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/beans/PrincipleComponentAnalysis.java
@@ -0,0 +1,280 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.beans;
+
+/*
+ * Copyright (c) 2009-2014, Peter Abeles. All Rights Reserved.
+ *
+ * This file is part of Efficient Java Matrix Library (EJML).
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+import org.ejml.data.DenseMatrix64F;
+import org.ejml.factory.DecompositionFactory;
+import org.ejml.factory.SingularValueDecomposition;
+import org.ejml.ops.CommonOps;
+import org.ejml.ops.NormOps;
+import org.ejml.ops.SingularOps;
+
+/**
+ * <p>
+ * The following is a simple example of how to perform basic principle component analysis in EJML.
+ * </p>
+ *
+ * <p>
+ * Principal Component Analysis (PCA) is typically used to develop a linear model for a set of data
+ * (e.g. face images) which can then be used to test for membership. PCA works by converting the
+ * set of data to a new basis that is a subspace of the original set. The subspace is selected
+ * to maximize information.
+ * </p>
+ * <p>
+ * PCA is typically derived as an eigenvalue problem. However in this implementation
+ * is used instead because it will produce a more numerically stable solution. Computation using EVD requires explicitly
+ * computing the variance of each sample set. The variance is computed by squaring the residual, which can
+ * cause loss of precision.
+ * </p>
+ *
+ * <p>
+ * Usage:<br>
+ * 1) call setup()<br>
+ * 2) For each sample (e.g. an image ) call addSample()<br>
+ * 3) After all the samples have been added call computeBasis()<br>
+ * 4) Call sampleToEigenSpace() , eigenToSampleSpace() , errorMembership() , response()
+ * </p>
+ *
+ * @author Peter Abeles
+ */
+
+public class PrincipleComponentAnalysis {
+
+ // principle component subspace is stored in the rows
+ private DenseMatrix64F V_t;
+
+ // how many principle components are used
+ private int numComponents;
+
+ // where the data is stored
+ private DenseMatrix64F A = new DenseMatrix64F(1,1);
+ private int sampleIndex;
+
+ // mean values of each element across all the samples
+ double mean[];
+
+ public PrincipleComponentAnalysis() {
+ }
+
+ /**
+ * Must be called before any other functions. Declares and sets up internal data structures.
+ *
+ * @param numSamples Number of samples that will be processed.
+ * @param sampleSize Number of elements in each sample.
+ */
+ public void setup( int numSamples , int sampleSize ) {
+ mean = new double[ sampleSize ];
+ A.reshape(numSamples,sampleSize,false);
+ sampleIndex = 0;
+ numComponents = -1;
+ }
+
+ /**
+ * Adds a new sample of the raw data to internal data structure for later processing. All the samples
+ * must be added before computeBasis is called.
+ *
+ * @param sampleData Sample from original raw data.
+ */
+ public void addSample( double[] sampleData ) {
+ if( A.getNumCols() != sampleData.length )
+ throw new IllegalArgumentException("Unexpected sample size");
+ if( sampleIndex >= A.getNumRows() )
+ throw new IllegalArgumentException("Too many samples");
+
+ for( int i = 0; i < sampleData.length; i++ ) {
+ A.set(sampleIndex,i,sampleData[i]);
+ }
+ sampleIndex++;
+ }
+
+ /**
+ * Computes a basis (the principle components) from the most dominant eigenvectors.
+ *
+ * @param numComponents Number of vectors it will use to describe the data. Typically much
+ * smaller than the number of elements in the input vector.
+ */
+ public void computeBasis( int numComponents ) {
+ if( numComponents > A.getNumCols() )
+ throw new IllegalArgumentException("More components requested that the data's length.");
+ if( sampleIndex != A.getNumRows() )
+ throw new IllegalArgumentException("Not all the data has been added");
+ if( numComponents > sampleIndex )
+ throw new IllegalArgumentException("More data needed to compute the desired number of components");
+
+ this.numComponents = numComponents;
+
+ // compute the mean of all the samples
+ for( int i = 0; i < A.getNumRows(); i++ ) {
+ for( int j = 0; j < mean.length; j++ ) {
+ mean[j] += A.get(i,j);
+ }
+ }
+ for( int j = 0; j < mean.length; j++ ) {
+ mean[j] /= A.getNumRows();
+ }
+
+ // subtract the mean from the original data
+ for( int i = 0; i < A.getNumRows(); i++ ) {
+ for( int j = 0; j < mean.length; j++ ) {
+ A.set(i,j,A.get(i,j)-mean[j]);
+ }
+ }
+
+ // Compute SVD and save time by not computing U
+ SingularValueDecomposition<DenseMatrix64F> svd =
+ DecompositionFactory.svd(A.numRows, A.numCols, false, true, false);
+ if( !svd.decompose(A) )
+ throw new RuntimeException("SVD failed");
+
+ V_t = svd.getV(null,true);
+ DenseMatrix64F W = svd.getW(null);
+
+ // Singular values are in an arbitrary order initially
+ SingularOps.descendingOrder(null,false,W,V_t,true);
+
+ // strip off unneeded components and find the basis
+ V_t.reshape(numComponents,mean.length,true);
+ }
+
+ /**
+ * Returns a vector from the PCA's basis.
+ *
+ * @param which Which component's vector is to be returned.
+ * @return Vector from the PCA basis.
+ */
+ public double[] getBasisVector( int which ) {
+ if( which < 0 || which >= numComponents )
+ throw new IllegalArgumentException("Invalid component");
+
+ DenseMatrix64F v = new DenseMatrix64F(1,A.numCols);
+ CommonOps.extract(V_t,which,which+1,0,A.numCols,v,0,0);
+
+ return v.data;
+ }
+
+ /**
+ * Converts a vector from sample space into eigen space.
+ *
+ * @param sampleData Sample space data.
+ * @return Eigen space projection.
+ */
+ public double[] sampleToEigenSpace( double[] sampleData ) {
+ if( sampleData.length != A.getNumCols() )
+ throw new IllegalArgumentException("Unexpected sample length");
+ DenseMatrix64F mean = DenseMatrix64F.wrap(A.getNumCols(),1,this.mean);
+
+ DenseMatrix64F s = new DenseMatrix64F(A.getNumCols(),1,true,sampleData);
+ DenseMatrix64F r = new DenseMatrix64F(numComponents,1);
+
+ CommonOps.sub(s,mean,s);
+
+ CommonOps.mult(V_t,s,r);
+
+ return r.data;
+ }
+
+ /**
+ * Converts a vector from eigen space into sample space.
+ *
+ * @param eigenData Eigen space data.
+ * @return Sample space projection.
+ */
+ public double[] eigenToSampleSpace( double[] eigenData ) {
+ if( eigenData.length != numComponents )
+ throw new IllegalArgumentException("Unexpected sample length");
+
+ DenseMatrix64F s = new DenseMatrix64F(A.getNumCols(),1);
+ DenseMatrix64F r = DenseMatrix64F.wrap(numComponents,1,eigenData);
+
+ CommonOps.multTransA(V_t,r,s);
+
+ DenseMatrix64F mean = DenseMatrix64F.wrap(A.getNumCols(),1,this.mean);
+ CommonOps.add(s,mean,s);
+
+ return s.data;
+ }
+
+
+ /**
+ * <p>
+ * The membership error for a sample. If the error is less than a threshold then
+ * it can be considered a member. The threshold's value depends on the data set.
+ * </p>
+ * <p>
+ * The error is computed by projecting the sample into eigenspace then projecting
+ * it back into sample space and
+ * </p>
+ *
+ * @param sampleA The sample whose membership status is being considered.
+ * @return Its membership error.
+ */
+ public double errorMembership( double[] sampleA ) {
+ double[] eig = sampleToEigenSpace(sampleA);
+ double[] reproj = eigenToSampleSpace(eig);
+
+
+ double total = 0;
+ for( int i = 0; i < reproj.length; i++ ) {
+ double d = sampleA[i] - reproj[i];
+ total += d*d;
+ }
+
+ return Math.sqrt(total);
+ }
+
+ /**
+ * Computes the dot product of each basis vector against the sample. Can be used as a measure
+ * for membership in the training sample set. High values correspond to a better fit.
+ *
+ * @param sample Sample of original data.
+ * @return Higher value indicates it is more likely to be a member of input dataset.
+ */
+ public double response( double[] sample ) {
+ if( sample.length != A.numCols )
+ throw new IllegalArgumentException("Expected input vector to be in sample space");
+
+ DenseMatrix64F dots = new DenseMatrix64F(numComponents,1);
+ DenseMatrix64F s = DenseMatrix64F.wrap(A.numCols,1,sample);
+
+ CommonOps.mult(V_t,s,dots);
+
+ return NormOps.normF(dots);
+ }
+}
+
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/beans/QChart.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/beans/QChart.java
new file mode 100644
index 0000000..eb42dcb
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/beans/QChart.java
@@ -0,0 +1,107 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.beans;
+
+import org.jfree.chart.JFreeChart;
+import java.awt.image.BufferedImage;
+
+/**
+ * Created by kokonech
+ * Date: 3/29/12
+ * Time: 12:01 PM
+ */
+public class QChart {
+
+ JFreeChart chart;
+ BufferedImage bufferedImage;
+ String title, toolTip, name;
+ ChartRawDataWriter dataWriter;
+
+ public QChart(String name, JFreeChart chart) {
+
+ this.name = name;
+ this.title = chart.getTitle().getText();
+ this.chart = chart;
+ this.toolTip = chart.getTitle().getText();
+ this.bufferedImage = null;
+
+ }
+
+ public QChart(String name, JFreeChart chart, ChartRawDataWriter writer) {
+
+ this.name = name;
+ this.title = chart.getTitle().getText();
+ this.chart = chart;
+ this.toolTip = chart.getTitle().getText();
+ this.bufferedImage = null;
+ this.dataWriter = writer;
+
+ }
+
+
+ public QChart(String imageName, String title, BufferedImage image) {
+ this.name = imageName;
+ this.title = title;
+ this.chart = null;
+ this.toolTip = title;
+ this.bufferedImage = image;
+
+ }
+
+
+ public String getTitle() {
+ return title;
+ }
+
+ public String getName() {
+ return name;
+ }
+
+ public String getToolTip() {
+ return toolTip;
+ }
+
+
+ public boolean isBufferedImage() {
+ return chart == null;
+ }
+
+ public JFreeChart getJFreeChart() {
+ return chart;
+ }
+
+ public BufferedImage getBufferedImage() {
+ return bufferedImage;
+ }
+
+ public boolean canExportRawData() {
+ return dataWriter != null;
+ }
+
+
+ public ChartRawDataWriter getDataWriter() {
+ return dataWriter;
+ }
+
+ public void setDataWriter(ChartRawDataWriter dataWriter) {
+ this.dataWriter = dataWriter;
+ }
+}
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/beans/SingleReadData.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/beans/SingleReadData.java
new file mode 100644
index 0000000..6a8405e
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/beans/SingleReadData.java
@@ -0,0 +1,127 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.beans;
+
+import java.util.ArrayList;
+import java.util.List;
+
+/**
+ * Created by kokonech
+ * Date: 11/11/11
+ * Time: 11:25 AM
+ */
+public class SingleReadData {
+
+ public long numberOfSequencedBases;
+ public long numberOfMappedBases;
+ public long numberOfAs;
+ public long numberOfTs;
+ public long numberOfCs;
+ public long numberOfGs;
+ // These number denotes how many bases are aligned from sequenced bases
+ //public long numberOfAlignedBases;
+
+ public static class Cell {
+ int position;
+ int value;
+ public Cell(int position, int value) {
+ this.position = position;
+ this.value = value;
+ }
+ public int getPosition() {
+ return position;
+ }
+
+ public int getValue() {
+ return value;
+ }
+ }
+
+ public List<Integer> coverageData;
+ public List<Cell> mappingQualityData;
+
+ long windowStart;
+
+ public SingleReadData(long windowStart) {
+ this.windowStart = windowStart;
+ coverageData = new ArrayList<Integer>();
+ mappingQualityData = new ArrayList<Cell>();
+ }
+
+ public long getWindowStart() {
+ return windowStart;
+ }
+
+ public void acumBase(long relative, char base){
+ numberOfSequencedBases++;
+
+ // ATCG content
+ if(base=='A'){
+ acumA(relative);
+ } else if(base=='C'){
+ acumC(relative);
+ } else if(base=='T'){
+ acumT(relative);
+ } else if(base=='G'){
+ acumG(relative);
+ }
+
+ /*if ( insertSize != -1 ){
+ acumProperlyPairedBase(relative);
+ }*/
+
+ coverageData.add((int)relative);
+ }
+
+
+ /*public void acumProperlyPairedBase(long relative){
+ //properlyPairedCoverageAcrossReference[(int)relative] = properlyPairedCoverageAcrossReference[(int)relative] + 1;
+ }*/
+
+ public void acumA(long relative){
+ numberOfAs++;
+
+ }
+
+ public void acumC(long relative){
+ numberOfCs++;
+
+ }
+
+ public void acumT(long relative){
+ numberOfTs++;
+
+ }
+
+ public void acumG(long relative){
+ numberOfGs++;
+
+ }
+
+ public void acumMappingQuality(long relative, int mappingQuality){
+ //acumMappingQuality+=mappingQuality;
+ if (mappingQuality != 0) {
+ mappingQualityData.add( new Cell((int)relative, mappingQuality) );
+ }
+ }
+
+
+}
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/beans/StatsReporter.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/beans/StatsReporter.java
new file mode 100644
index 0000000..ed0ba8c
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/beans/StatsReporter.java
@@ -0,0 +1,237 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.beans;
+
+import org.bioinfo.ngs.qc.qualimap.common.Constants;
+import org.bioinfo.ngs.qc.qualimap.gui.panels.HtmlJPanel;
+import org.bioinfo.ngs.qc.qualimap.gui.utils.StatsKeeper;
+
+import java.util.List;
+import java.util.Map;
+
+/**
+ * Created by kokonech
+ * Date: 7/13/13
+ * Time: 2:16 PM
+ */
+public class StatsReporter {
+ protected List<QChart> charts;
+
+ protected String namePostfix, fileName;
+ protected StatsKeeper inputDataKeeper;
+ protected StatsKeeper summaryStatsKeeper;
+ protected StatsKeeper tableDataStatsKeeper;
+ protected String name;
+
+
+ public StatsReporter() {
+ name = "Results";
+ namePostfix = "";
+ fileName = "qualimapReport";
+ inputDataKeeper = new StatsKeeper();
+ summaryStatsKeeper = new StatsKeeper();
+ tableDataStatsKeeper = new StatsKeeper();
+ }
+
+ public void addInputDataSection(String name, Map<String,String> paramsMap) {
+
+ StatsKeeper.Section section = new StatsKeeper.Section(name);
+ section.addData(paramsMap);
+
+ inputDataKeeper.addSection(section);
+ }
+
+ public static void addSummarySection(StringBuffer buf, StatsKeeper.Section s, int width) {
+
+ buf.append(HtmlJPanel.COLSTART).append("<b>").append(s.getName()).append("</b>");
+ buf.append(HtmlJPanel.getTableHeader(width, "FFFFFF"));
+
+ for (String[] row : s.getRows()) {
+ buf.append(HtmlJPanel.COLSTARTFIX).append(row[0]).append(HtmlJPanel.COLMID)
+ .append(row[1]).append(HtmlJPanel.COLEND);
+ }
+
+ buf.append(HtmlJPanel.getTableFooter());
+ buf.append(HtmlJPanel.COLEND);
+
+
+ }
+
+ public static void addChromosomesSections(StringBuffer summaryHtml,
+ int width,
+ StatsKeeper chromosomeStats) {
+ List<StatsKeeper.Section> chromosomeSections = chromosomeStats.getSections();
+ summaryHtml.append(HtmlJPanel.COLSTART).append("<b>").append(chromosomeStats.getName()).append("</b>");
+ summaryHtml.append(HtmlJPanel.getTableHeader(width, "FFFFFF"));
+
+ for (StatsKeeper.Section s : chromosomeSections ) {
+ boolean header = s.getName().equals(Constants.TABLE_STATS_HEADER);
+ List<String[]> rows = s.getRows();
+ for (String[] row : rows) {
+ summaryHtml.append("<tr>");
+ for (String item : row) {
+ if (header) {
+ summaryHtml.append("<td><b>").append(item).append("</b></td>");
+ } else {
+ summaryHtml.append("<td>").append(item).append("</td>");
+ }
+ }
+ summaryHtml.append("</tr>");
+ }
+
+ }
+
+ summaryHtml.append(HtmlJPanel.getTableFooter());
+ summaryHtml.append(HtmlJPanel.COLEND);
+ }
+
+
+ public String getSummary(int width) {
+ StringBuffer summaryHtml = new StringBuffer("");
+
+ List<StatsKeeper.Section> summarySections = summaryStatsKeeper.getSections();
+ summaryHtml.append("<p align=center> <b>Summary</b></p>").append(HtmlJPanel.BR);
+ summaryHtml.append(HtmlJPanel.getTableHeader(width, "EEEEEE"));
+
+
+ for (StatsKeeper.Section s: summarySections) {
+ addSummarySection(summaryHtml, s, width);
+ }
+
+ if (tableDataStatsKeeper.getSections().size() > 0) {
+ addChromosomesSections(summaryHtml, width, tableDataStatsKeeper);
+ }
+
+
+ return summaryHtml.toString();
+ }
+
+
+ public String getInputDescription(int tableWidth) {
+
+
+ if (inputDataKeeper.getSections().isEmpty()) {
+ return null;
+ }
+
+ StringBuilder inputDesc = new StringBuilder();
+
+ inputDesc.append("<p align=center><a name=\"input\"> <b>Input data & parameters</b></p>").append(HtmlJPanel.BR);
+ inputDesc.append(HtmlJPanel.getTableHeader(tableWidth, "EEEEEE"));
+
+ List<StatsKeeper.Section> inputDataSections = inputDataKeeper.getSections();
+
+ for (StatsKeeper.Section section : inputDataSections) {
+ inputDesc.append(HtmlJPanel.COLSTART).append("<b>").append(section.getName()).append("</b>");
+ List<String[]> params = section.getRows();
+ inputDesc.append(HtmlJPanel.getTableHeader(tableWidth, "FFFFFF"));
+ for ( String[] row: params ) {
+ inputDesc.append(HtmlJPanel.COLSTARTFIX);
+ for (int i = 0; i < row.length; ++i) {
+ inputDesc.append(row[i]);
+ if (i != row.length - 1) {
+ inputDesc.append(HtmlJPanel.COLMID);
+ }
+ }
+ inputDesc.append(HtmlJPanel.COLEND) ;
+ }
+ inputDesc.append(HtmlJPanel.getTableFooter());
+ inputDesc.append(HtmlJPanel.COLEND);
+ }
+
+ inputDesc.append(HtmlJPanel.getTableFooter());
+
+ return inputDesc.toString();
+
+ }
+
+
+
+ public List<QChart> getCharts() {
+ return charts;
+ }
+
+ public void setChartList(List<QChart> chartList) {
+ charts = chartList;
+ }
+
+ public QChart findChartByName(String name) {
+ for (QChart chart : charts) {
+ if (chart.getName().equals(name)) {
+ return chart;
+ }
+ }
+
+ return null;
+ }
+
+ public boolean hasSummary() {
+ return summaryStatsKeeper.getSections().size() > 0;
+ }
+
+ public boolean hasTableData() {
+ return tableDataStatsKeeper.getSections().size() > 0;
+ }
+
+ public List<StatsKeeper.Section> getSummaryDataSections() {
+ return summaryStatsKeeper.getSections();
+ }
+
+ public List<StatsKeeper.Section> getInputDataSections() {
+ return inputDataKeeper.getSections();
+ }
+
+ public StatsKeeper getSummaryStatsKeeper() {
+ return summaryStatsKeeper;
+ }
+
+ public StatsKeeper getTableDataStatsKeeper() {
+ return tableDataStatsKeeper;
+ }
+
+ public StatsKeeper getInputDataKeeper() {
+ return inputDataKeeper;
+ }
+
+ public String getFileName() {
+ return fileName;
+ }
+
+ public void setFileName(String fileName) {
+ this.fileName = fileName;
+ }
+
+ public String getName() {
+ return name;
+ }
+
+ public void setName(String name) {
+ this.name = name;
+ }
+
+ public String getNamePostfix() {
+ return namePostfix;
+ }
+
+ public boolean hasInputDescription() {
+ return inputDataKeeper.getSections().size() > 0;
+ }
+}
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/beans/TextFileDataWriter.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/beans/TextFileDataWriter.java
new file mode 100644
index 0000000..0789d64
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/beans/TextFileDataWriter.java
@@ -0,0 +1,69 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.beans;
+
+import java.io.BufferedReader;
+import java.io.BufferedWriter;
+import java.io.FileReader;
+import java.io.IOException;
+
+/**
+ * Created by kokonech
+ * Date: 7/12/12
+ * Time: 10:51 AM
+ */
+public class TextFileDataWriter extends ChartRawDataWriter{
+
+ String[] sourceFileNames;
+ String dataPath;
+
+ /**
+ * Creates new data writer
+ * @param dataPath Path to dir containg the input files
+ * @param sourceFileName Name or several names of files, separated by semicolon
+ */
+ public TextFileDataWriter(String dataPath, String sourceFileName) {
+ this.dataPath = dataPath;
+ this.sourceFileNames = sourceFileName.split(";");
+ }
+
+ @Override
+ void exportData(BufferedWriter dataWriter) throws IOException {
+
+ for (String sourceFileName : sourceFileNames) {
+
+ dataWriter.write(sourceFileName);
+ dataWriter.write("\n");
+
+ BufferedReader reader = new BufferedReader( new FileReader(dataPath + sourceFileName));
+
+ String line;
+ while ( (line = reader.readLine()) != null) {
+ dataWriter.write(line);
+ dataWriter.write("\n");
+
+ }
+
+ reader.close();
+ }
+
+ }
+}
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/beans/XYIntervalItem.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/beans/XYIntervalItem.java
new file mode 100644
index 0000000..6d361d9
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/beans/XYIntervalItem.java
@@ -0,0 +1,92 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.beans;
+
+public class XYIntervalItem extends XYItem {
+ private double xUpDeviation;
+ private double xDownDeviation;
+ private double yUpDeviation;
+ private double yDownDeviation;
+
+ public XYIntervalItem(double x, double xDownDeviation, double xUpDeviation, double y, double yDownDeviation, double yUpDeviation){
+ super(x,y);
+ this.xDownDeviation = xDownDeviation;
+ this.xUpDeviation = xUpDeviation;
+ this.yDownDeviation = yDownDeviation;
+ this.yUpDeviation = yUpDeviation;
+ }
+
+ /**
+ * @return the xUpDeviation
+ */
+ public double getxUpDeviation() {
+ return xUpDeviation;
+ }
+
+ /**
+ * @param xUpDeviation the xUpDeviation to set
+ */
+ public void setxUpDeviation(double xUpDeviation) {
+ this.xUpDeviation = xUpDeviation;
+ }
+
+ /**
+ * @return the xDownDeviation
+ */
+ public double getxDownDeviation() {
+ return xDownDeviation;
+ }
+
+ /**
+ * @param xDownDeviation the xDownDeviation to set
+ */
+ public void setxDownDeviation(double xDownDeviation) {
+ this.xDownDeviation = xDownDeviation;
+ }
+
+ /**
+ * @return the yUpDeviation
+ */
+ public double getyUpDeviation() {
+ return yUpDeviation;
+ }
+
+ /**
+ * @param yUpDeviation the yUpDeviation to set
+ */
+ public void setyUpDeviation(double yUpDeviation) {
+ this.yUpDeviation = yUpDeviation;
+ }
+
+ /**
+ * @return the yDownDeviation
+ */
+ public double getyDownDeviation() {
+ return yDownDeviation;
+ }
+
+ /**
+ * @param yDownDeviation the yDownDeviation to set
+ */
+ public void setyDownDeviation(double yDownDeviation) {
+ this.yDownDeviation = yDownDeviation;
+ }
+}
\ No newline at end of file
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/beans/XYItem.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/beans/XYItem.java
new file mode 100644
index 0000000..7c12ebe
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/beans/XYItem.java
@@ -0,0 +1,66 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.beans;
+
+import java.io.Serializable;
+
+public class XYItem implements Serializable {
+
+ private double x;
+ private double y;
+
+ /**
+ * @param x
+ * @param y
+ */
+ public XYItem(double x, double y) {
+ this.x = x;
+ this.y = y;
+ }
+
+ /**
+ * @return the x
+ */
+ public double getX() {
+ return x;
+ }
+
+ /**
+ * @param x the x to set
+ */
+ public void setX(double x) {
+ this.x = x;
+ }
+
+ /**
+ * @return the y
+ */
+ public double getY() {
+ return y;
+ }
+
+ /**
+ * @param y the y to set
+ */
+ public void setY(double y) {
+ this.y = y;
+ }
+}
\ No newline at end of file
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/beans/XYVector.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/beans/XYVector.java
new file mode 100644
index 0000000..2535b4d
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/beans/XYVector.java
@@ -0,0 +1,115 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.beans;
+
+import java.io.Serializable;
+import java.util.ArrayList;
+import java.util.List;
+
+public class XYVector implements Serializable {
+
+ private double maxValue;
+ private List<XYItem> items;
+
+ public XYVector(){
+ items = new ArrayList<XYItem>();
+ maxValue = 0;
+ }
+
+ public XYVector(double[] x, double[] y){
+ items = new ArrayList<XYItem>();
+ for(int i=0; i<x.length; i++){
+ items.add(new XYItem(x[i], y[i]));
+ if(y[i]>maxValue) maxValue = y[i];
+ }
+ }
+
+ public XYVector(List<Double> x, List<Double> y){
+ items = new ArrayList<XYItem>();
+ for(int i=0; i<x.size(); i++){
+ items.add(new XYItem(x.get(i), y.get(i)));
+ if(y.get(i)>maxValue) maxValue = y.get(i);
+ }
+ }
+
+ public XYVector(List<Double> x, List<Double> y, List<Double> deviation){
+ this(x,y,deviation,true);
+ }
+
+ public XYVector(List<Double> x, List<Double> y, List<Double> deviation, boolean isDeviation){
+ items = new ArrayList<XYItem>();
+ double up,down;
+ for(int i=0; i<x.size(); i++){
+ if(isDeviation){
+ items.add(new XYIntervalItem(x.get(i),x.get(i),x.get(i),y.get(i),y.get(i)-deviation.get(i),y.get(i)+deviation.get(i)));
+ } else {
+ if(y.get(i)>deviation.get(i)){
+ up = y.get(i);
+ down = deviation.get(i);
+ } else {
+ up = deviation.get(i);
+ down = y.get(i);
+ }
+ items.add(new XYIntervalItem(x.get(i),x.get(i),x.get(i),y.get(i),down,up));
+ }
+ if(y.get(i)>maxValue) maxValue = y.get(i);
+ }
+ }
+
+ public void addItem(XYItem item){
+ items.add(item);
+ if(item.getY()>maxValue) maxValue = item.getY();
+ }
+
+ public double[] getXVector(){
+ double[] xs = new double[items.size()];
+ for(int i=0; i<items.size(); i++){
+ xs[i] = items.get(i).getX();
+ }
+ return xs;
+ }
+
+ public double[] getYVector(){
+ double[] ys = new double[items.size()];
+ for(int i=0; i<items.size(); i++){
+ ys[i] = items.get(i).getY();
+ }
+ return ys;
+ }
+
+ public int getSize(){
+ return items.size();
+ }
+
+ public XYItem get(int index){
+ if(index<0 || index>items.size()) return null;
+ else return items.get(index);
+ }
+
+ /**
+ * @return the maxValue
+ */
+ public double getMaxValue() {
+ return maxValue;
+ }
+
+
+}
\ No newline at end of file
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/beans/XYVectorDataWriter.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/beans/XYVectorDataWriter.java
new file mode 100644
index 0000000..61066ed
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/beans/XYVectorDataWriter.java
@@ -0,0 +1,51 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.beans;
+
+import java.io.BufferedWriter;
+import java.io.IOException;
+
+/**
+ * Created by kokonech
+ * Date: 6/13/12
+ * Time: 2:56 PM
+ */
+public class XYVectorDataWriter extends ChartRawDataWriter {
+
+ XYVector data;
+ String xName, yName;
+
+ public XYVectorDataWriter(XYVector data, String xName, String yName) {
+ this.data = data;
+ this.xName = xName;
+ this.yName = yName;
+ }
+
+ @Override
+ void exportData(BufferedWriter dataWriter) throws IOException {
+ dataWriter.write("#" + xName + "\t" + yName + "\n");
+ int len = data.getSize();
+ for (int i = 0; i < len; ++i) {
+ XYItem item = data.get(i);
+ dataWriter.write(item.getX() + "\t" + item.getY() + "\n");
+ }
+ }
+}
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/common/AnalysisType.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/common/AnalysisType.java
new file mode 100644
index 0000000..50a7c5b
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/common/AnalysisType.java
@@ -0,0 +1,59 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.common;
+
+/**
+ * Created by kokonech
+ * Date: 6/22/12
+ * Time: 4:05 PM
+ */
+
+public enum AnalysisType {
+
+ BAM_QC, RNA_SEQ_QC, COUNTS_QC, MULTISAMPLE_BAM_QC, CLUSTERING;
+
+ static final String NAME_BAM_QC = "BAM QC";
+ static final String NAME_RNA_SEQ_QC = "RNA Seq QC";
+ static final String NAME_COUNTS_QC = "Counts QC";
+ static final String NAME_MULTISAMPLE_BAM_QC = "Multi-sample BAM QC";
+ static final String NAME_CLUSTERING = "Clustering";
+ static final String UNKNOWN = "Unknown analysis";
+
+ public String toString() {
+ if (this == BAM_QC) {
+ return NAME_BAM_QC;
+ }else if (this == RNA_SEQ_QC) {
+ return NAME_RNA_SEQ_QC;
+ } else if (this == COUNTS_QC) {
+ return NAME_COUNTS_QC;
+ } else if (this == MULTISAMPLE_BAM_QC) {
+ return NAME_MULTISAMPLE_BAM_QC;
+ } else if (this == CLUSTERING ) {
+ return NAME_CLUSTERING;
+ } else {
+ return UNKNOWN;
+ }
+ }
+
+ public boolean isBamQC() {
+ return this == BAM_QC;
+ }
+}
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/common/AppSettings.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/common/AppSettings.java
new file mode 100644
index 0000000..5357950
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/common/AppSettings.java
@@ -0,0 +1,57 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.common;
+
+import java.util.Properties;
+
+/**
+ * Created by kokonech
+ * Date: 2/17/13
+ * Time: 3:29 PM
+ */
+public class AppSettings {
+
+ Properties settings;
+ static AppSettings globalSettings;
+
+ static final String PATH_TO_R_SCRIPT = "path_to_rscript";
+
+ public AppSettings() {
+ settings = new Properties();
+ }
+
+ public String getPathToRScript() {
+ return settings.getProperty(PATH_TO_R_SCRIPT, "Rscript");
+ }
+
+ public void setPathToRScript(String path) {
+ settings.setProperty(PATH_TO_R_SCRIPT, path);
+ }
+
+ public static AppSettings getGlobalSettings() {
+ return globalSettings;
+ }
+
+ public static void setGlobalSettings(AppSettings settings) {
+ globalSettings = settings;
+ }
+
+}
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/common/BamStatsCollector.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/common/BamStatsCollector.java
new file mode 100644
index 0000000..c4aab90
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/common/BamStatsCollector.java
@@ -0,0 +1,170 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.common;
+
+import net.sf.samtools.SAMRecord;
+
+import java.util.HashMap;
+import java.util.Map;
+
+/**
+ * Created by kokonech
+ * Date: 5/11/12
+ * Time: 2:17 PM
+ */
+public class BamStatsCollector {
+
+
+ class ReadAlignmentInfo{
+ int firstReadEndPos;
+ int secondReadStartPos;
+ ReadAlignmentInfo() {
+ firstReadEndPos = 0;
+ secondReadStartPos = 0;
+ }
+ }
+
+ long numMappedReads, numPairedReads;
+ long numMappedFirstInPair, numMappedSecondInPair, numSingletons;
+ boolean collectIntersectingReadPairs;
+ long numOverlappingReadPairs, numOverlappingBases;
+ Map<String,ReadAlignmentInfo> pairsCollector;
+ String curChromosome;
+ // TODO: read length might influence?
+ // int readLength;
+
+ public long getNumMappedReads() {
+ return numMappedReads;
+ }
+
+ public long getNumMappedFirstInPair() {
+ return numMappedFirstInPair;
+ }
+
+ public long getNumMappedSecondInPair() {
+ return numMappedSecondInPair;
+ }
+
+ public long getNumSingletons() {
+ return numSingletons;
+ }
+
+ public long getNumPairedReads() {
+ return numPairedReads;
+ }
+
+ public long getNumOverlappingReadPairs() {
+ return numOverlappingReadPairs;
+ }
+
+ public long getNumOverlappingBases() {
+ return numOverlappingBases;
+ }
+
+
+ public BamStatsCollector()
+ {
+ collectIntersectingReadPairs = false;
+ }
+
+ public void enableIntersectingReadsCollection() {
+ collectIntersectingReadPairs = true;
+ pairsCollector = new HashMap<String,ReadAlignmentInfo>();
+ curChromosome = "";
+
+ }
+
+
+ public void updateStats(SAMRecord read) {
+ numMappedReads++;
+ if (read.getReadPairedFlag()) {
+ numPairedReads++;
+ if (read.getFirstOfPairFlag()) {
+ numMappedFirstInPair++;
+ } else if (read.getSecondOfPairFlag()) {
+ numMappedSecondInPair++;
+ }
+ if (read.getMateUnmappedFlag()) {
+ numSingletons++;
+ } /*else if (collectIntersectingReadPairs) {
+ collectPairedReadInfo(read);
+ }*/
+ }
+
+ }
+
+ public void finalizeAlignmentInfo() {
+ if (!curChromosome.isEmpty()) {
+ //System.out.println("Collected " + pairsCollector.size() + " read pairs from chromosome " + curChromosome);
+ for (Map.Entry<String, ReadAlignmentInfo> entry : pairsCollector.entrySet()) {
+ ReadAlignmentInfo info = entry.getValue();
+ if (info.secondReadStartPos > 0) {
+ int intersectionSize = info.firstReadEndPos - info.secondReadStartPos + 1;
+ if (intersectionSize > 0 ) {
+ numOverlappingBases += intersectionSize;
+ numOverlappingReadPairs++;
+ }
+ }
+ }
+ //System.out.println("Number of intersecting pairs " + numOverlappingReadPairs);
+ }
+ }
+
+ public void collectPairedReadInfo(SAMRecord read) {
+
+ if (!read.getReadPairedFlag() || read.getMateUnmappedFlag()) {
+ return;
+ }
+
+ String chr = read.getReferenceName();
+ if (!curChromosome.equals(chr)) {
+ finalizeAlignmentInfo();
+ curChromosome = chr;
+ pairsCollector.clear();
+ }
+
+ //TODO: what if there are several alignments of the same read?
+
+ String readName = read.getReadName();
+ if (pairsCollector.containsKey(readName)){
+ ReadAlignmentInfo info = pairsCollector.get(readName);
+ info.secondReadStartPos = read.getAlignmentStart();
+ } else {
+ ReadAlignmentInfo info = new ReadAlignmentInfo();
+ info.firstReadEndPos = read.getAlignmentEnd();
+ pairsCollector.put(readName, info);
+ }
+
+ }
+
+
+ public String report() {
+ StringBuilder buf = new StringBuilder();
+ buf.append("Num mapped reads: ").append(numMappedReads).append("\n");
+ buf.append("Num mapped first of pair: ").append(numMappedFirstInPair).append("\n");
+ buf.append("Num mapped second of pair: ").append(numMappedSecondInPair).append("\n");
+ buf.append("Num singletons: ").append(numSingletons).append("\n");
+ return buf.toString();
+ }
+
+
+
+}
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/common/CommandLineBuilder.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/common/CommandLineBuilder.java
new file mode 100644
index 0000000..7d96a82
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/common/CommandLineBuilder.java
@@ -0,0 +1,73 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.common;
+
+import java.util.ArrayList;
+
+/**
+ * Created by kokonech
+ * Date: 7/14/14
+ * Time: 5:49 PM
+ */
+
+public class CommandLineBuilder {
+
+ ArrayList<String[]> options;
+ String head;
+ public CommandLineBuilder(String head) {
+ this.head = head;
+ options = new ArrayList<String[]>();
+ }
+
+ public void append(String name, String value) {
+ String[] option = { name, value };
+ options.add(option);
+ }
+
+ public void append(String name, int value) {
+ String[] option = { name, Integer.toString(value) };
+ options.add(option);
+ }
+
+ public void append(String name) {
+ String[] option = { name };
+ options.add(option);
+ }
+
+ public String getCmdLine() {
+ StringBuilder cmd = new StringBuilder();
+ cmd.append(head);
+ for (String[] option : options) {
+ if (option.length == 1) {
+ cmd.append(" -").append(option[0]);
+ } else if( option.length == 2) {
+ cmd.append(" -").append(option[0]).append(" ").append(option[1]);
+ }
+ }
+
+
+
+ return cmd.toString();
+ }
+
+
+
+}
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/common/Constants.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/common/Constants.java
new file mode 100644
index 0000000..9797b2f
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/common/Constants.java
@@ -0,0 +1,149 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.common;
+
+import java.util.HashMap;
+import java.util.Map;
+
+public final class Constants {
+ public static final int DEFAULT_NUMBER_OF_WINDOWS = 400;
+ public static final int DEFAULT_CHUNK_SIZE = 1000;
+ public static final int DEFAULT_HOMOPOLYMER_SIZE = 3;
+
+ public static final int GRAPHIC_TO_SAVE_WIDTH = 1024;
+ public static final int GRAPHIC_TO_SAVE_HEIGHT = 768;
+
+
+ /** Path to locate the images when the application is running in a jar file */
+ public static final String pathImages = "/org/bioinfo/ngs/qc/qualimap/gui/images/";
+
+ /** Path to locate the resources of the application */
+ public static final String pathResources = "/org/bioinfo/ngs/qc/qualimap/";
+
+
+ //******************************************************************************************
+ //******************************* FILE EXTENSION CONSTANTS *********************************
+ //******************************************************************************************
+ // Extension for the data Input File
+ public static final String FILE_EXTENSION_BAM = "BAM";
+ public static final String FILE_EXTENSION_SAM = "SAM";
+
+
+ // Extension for the Region Input File
+ public static final Map<String, String> FILE_EXTENSION_REGION = new HashMap<String, String>();
+ static{
+ FILE_EXTENSION_REGION.put("GFF", "GFF");
+ FILE_EXTENSION_REGION.put("GTF", "GTF");
+ FILE_EXTENSION_REGION.put("BED", "BED");
+ }
+
+ // Extension for the PDF File
+ public static final String FILE_EXTENSION_PDF_FILE = "PDF";
+
+ //******************************************************************************************
+ //******************************* GRAPHICS NAMES CONSTANTS *********************************
+ //******************************************************************************************
+
+ public static final String PLOT_TITLE_COVERAGE_ACROSS_REFERENCE = "Coverage Across Reference";
+ public static final String PLOT_TITLE_COVERAGE_HISTOGRAM = "Coverage Histogram";
+ public static final String PLOT_TITLE_COVERAGE_HISTOGRAM_0_50 = "Coverage Histogram (0-50X)";
+ public static final String PLOT_TITLE_MAPPING_QUALITY_ACROSS_REFERENCE = "Mapping Quality Across Reference";
+ public static final String PLOT_TITLE_MAPPING_QUALITY_HISTOGRAM = "Mapping Quality Histogram";
+ public static final String PLOT_TITLE_INSERT_SIZE_ACROSS_REFERENCE = "Insert Size Across Reference";
+ public static final String PLOT_TITLE_INSERT_SIZE_HISTOGRAM = "Insert Size Histogram";
+ public static final String PLOT_TITLE_READS_NUCLEOTIDE_CONTENT = "Mapped Reads Nucleotide Content";
+ public static final String PLOT_TITLE_READS_CLIPPING_PROFILE = "Mapped Reads Clipping Profile";
+ public static final String PLOT_TITLE_GENOME_FRACTION_COVERAGE = "Genome Fraction Coverage";
+ public static final String PLOT_TITLE_READS_GC_CONTENT = "Mapped Reads GC-content Distribution";
+ public static final String PLOT_TITLE_DUPLICATION_RATE_HISTOGRAM = "Duplication Rate Histogram";
+ public static final String PLOT_TITLE_HOMOPOLYMER_INDELS = "Homopolymer Indels";
+
+ //******************************************************************************************
+ //*********************************** TYPES OF SPECIES *************************************
+ //******************************************************************************************
+ public static final String TYPE_COMBO_SPECIES_HUMAN = "HUMAN.ENS68";
+ public static final String TYPE_COMBO_SPECIES_MOUSE = "MOUSE.ENS68";
+
+ //******************************************************************************************
+ //*********************************** FILES OF SPECIES *************************************
+ //******************************************************************************************
+ public static final String FILE_SPECIES_INFO_HUMAN = "human.64.genes.biotypes.txt";
+ public static final String FILE_SPECIES_GROUPS_HUMAN = "human.biotypes.groups.txt";
+ public static final String FILE_SPECIES_INFO_MOUSE = "mouse.64.genes.biotypes.txt";
+ public static final String FILE_SPECIES_GROUPS_MOUSE = "mouse.biotypes.groups.txt";
+ public static final String FILE_SPECIES_INFO_HUMAN_ENS68 = "human.ens68.txt";
+ public static final String FILE_SPECIES_INFO_MOUSE_ENS68 = "mouse.ens68.txt";
+
+ // GUI commands
+ public static final String OK_COMMAND = "ok";
+ public static final String CANCEL_COMMAND = "cancel";
+ public static final String COMMAND_ADD_ITEM = "add_item";
+ public static final String COMMAND_REMOVE_ITEM = "delete_item";
+ public static final String COMMAND_EDIT_ITEM = "edit_item";
+ public static final String COMMAND_IMPORT_CONFIG = "import_config";
+ public static final String COMMAND_RUN_ANALYSIS = "run_analysis";
+ public static final String COMMAND_BROWSE_GFF = "browse_gff";
+
+ public static final String VIZ_TYPE_HEATMAP = "heatmap";
+ public static final String VIZ_TYPE_LINE = "line";
+
+ // This is a SAM record custom field, has to be 2 characters
+ public static final String READ_IN_REGION = "XX";
+ public static final String READ_WEIGHT_ATTR = "XW";
+
+ // Reporting
+ public static final String REPORT_TYPE_HTML = "HTML";
+ public static final String REPORT_TYPE_PDF = "PDF";
+ public static final String TABLE_STATS_HEADER = "header";
+ public static final String TABLE_STATS_DATA = "data";
+ public static final String TABLE_SECTION_QUALIMAP_CMDLINE = "QualiMap command line";
+
+ // Tool names
+ public static final String TOOL_NAME_BAMQC = "bamqc";
+ public static final String TOOL_NAME_COUNTS_QC = "counts";
+ public static final String TOOL_NAME_MULTISAMPLE_BAM_QC = "multi-bamqc";
+ public static final String TOOL_NAME_RNASEQ_QC = "rnaseq";
+ public static final String TOOL_NAME_CLUSTERING = "clustering";
+ public static final String TOOL_NAME_COMPUTE_COUNTS = "comp-counts";
+ public static final String TOOL_NAME_GC_CONTENT = "gc-content";
+ public static final String TOOL_NAME_INDEL_COUNT = "indel-count";
+
+ // Tool command line options
+
+ public static final String CMDLINE_OPTION_LIBRARY_PROTOCOL = "p";
+
+ public static final String BAMQC_OPTION_BAM_FILE = "bam";
+ public static final String BAMQC_OPTION_GFF_FILE = "gff";
+ public static final String BAMQC_OPTION_COMPARE_WITH_GENOME_DISTRIBUTION = "gd";
+ public static final String BAMQC_OPTION_PAINT_CHROMOSOMES = "c";
+ public static final String BAMQC_OPTION_NUM_WINDOWS = "nw";
+ public static final String BAMQC_OPTION_CHUNK_SIZE = "nr";
+ public static final String BAMQC_OPTION_NUM_THREADS = "nt";
+ public static final String BAMQC_OPTION_OUTSIDE_STATS = "os";
+ public static final String BAMQC_OPTION_MIN_HOMOPOLYMER_SIZE = "hm";
+ public static final String BAMQC_OPTION_COVERAGE_REPORT_FILE = "oc";
+ public static final String BAMQC_OPTION_SKIP_DUPLICATED = "sd";
+ public static final String BAMQC_OPTION_COLLECT_OVERLAP_PAIRS = "ip";
+
+
+
+
+}
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/common/DocumentUtils.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/common/DocumentUtils.java
new file mode 100644
index 0000000..bf20002
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/common/DocumentUtils.java
@@ -0,0 +1,193 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.common;
+
+import org.apache.commons.io.FilenameUtils;
+
+import java.io.BufferedReader;
+import java.io.FileReader;
+
+/**
+ * Created by kokonech
+ * Date: 4/18/12
+ * Time: 11:34 AM
+ */
+public class DocumentUtils {
+
+ static final int MAX_SCORE = 100;
+
+ public static String validateTabDelimitedFile(String fileName, int expectedNumFields) {
+
+ int countRecords = 0;
+
+ try {
+ BufferedReader br = new BufferedReader(new FileReader(fileName));
+ while (countRecords < 1000) {
+ String line = br.readLine();
+ if (line == null) {
+ break;
+ }
+
+ if (line.startsWith("#") || line.isEmpty()) {
+ // skip comments and empty lines
+ continue;
+ }
+
+ String[] items = line.split("\t");
+
+ if (items.length < expectedNumFields) {
+ throw new RuntimeException("Tab-delimited file format error in " + fileName + ": not enough fields.");
+ }
+
+ countRecords++;
+ }
+
+ br.close();
+
+ } catch (Exception e) {
+ return e.getMessage();
+ }
+
+ return countRecords > 0 ? "" : "Tab-delimited file format error in " + fileName + ": file is empty.";
+ }
+
+
+ public static String validateCountsFile(String fileName) {
+ int countRecords = 0;
+
+ try {
+ BufferedReader br = new BufferedReader(new FileReader(fileName));
+ while (countRecords < 1000) {
+ String line = br.readLine();
+ if (line == null) {
+ break;
+ }
+
+ if (line.startsWith("#") || line.isEmpty()) {
+ // skip comments and empty lines
+ }
+
+ String[] items = line.split("\\s+");
+
+ if (items.length != 2) {
+ throw new RuntimeException("Counts file format error in " + fileName);
+ }
+
+ countRecords++;
+ }
+
+ br.close();
+
+ } catch (Exception e) {
+ return e.getMessage();
+ }
+
+ return countRecords > 0 ? "" : "Counts file format error in " + fileName + ": file is empty.";
+
+
+ }
+
+
+ public static FeatureFileFormat guessFeaturesFileFormat(String fileName) {
+
+ String fileExt = FilenameUtils.getExtension(fileName);
+
+ if (fileExt.equalsIgnoreCase("bed")) {
+ return FeatureFileFormat.BED;
+ } else if (fileExt.equalsIgnoreCase("gff") ) {
+ return FeatureFileFormat.GFF;
+ } else if (fileExt.equalsIgnoreCase("gtf")) {
+ return FeatureFileFormat.GTF;
+ } else {
+ // try guessing format, read 100 lines and collect scores
+ int scoreBed = 0, scoreGff = 0, scoreGtf = 0, countRecords = 0;
+ try {
+ BufferedReader br = new BufferedReader(new FileReader(fileName));
+ while (countRecords < MAX_SCORE) {
+ String line = br.readLine();
+ if (line == null) {
+ break;
+ }
+
+ if (line.startsWith("#") || line.isEmpty()) {
+ // skip comments and empty lines
+ }
+
+ String[] items = line.split("\t");
+
+ if (items.length >= 9) {
+ try {
+ Integer.parseInt(items[3]);
+ } catch (NumberFormatException ex) {
+ --scoreGff;
+ }
+ ++scoreGff;
+
+ String attrs = items[8];
+ if (attrs.contains("gene_id") && attrs.contains("transcript_id")) {
+ scoreGtf++;
+ }
+
+ }
+
+ if (items.length >= 3) {
+ try {
+ Integer.parseInt(items[1]);
+ } catch (NumberFormatException ex) {
+ --scoreBed;
+ }
+ ++scoreBed;
+ }
+
+ ++countRecords;
+ }
+
+ br.close();
+ } catch (Exception ex) {
+ System.err.println("Failed to guess feature file format.");
+ return FeatureFileFormat.UNKNOWN;
+ }
+
+ if (scoreBed == countRecords) {
+ return FeatureFileFormat.BED;
+ } if (scoreGff == countRecords) {
+ if (scoreGtf > 0) {
+ return FeatureFileFormat.GTF;
+ } else {
+ return FeatureFileFormat.GFF;
+ }
+ } else {
+ return FeatureFileFormat.UNKNOWN;
+ }
+
+
+
+
+ }
+
+
+
+
+ }
+
+
+
+}
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/common/FeatureFileFormat.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/common/FeatureFileFormat.java
new file mode 100644
index 0000000..466a5ce
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/common/FeatureFileFormat.java
@@ -0,0 +1,33 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.common;
+
+/**
+ * Created by kokonech
+ * Date: 6/8/12
+ * Time: 6:36 PM
+ */
+public enum FeatureFileFormat {
+ UNKNOWN,
+ GFF,
+ GTF,
+ BED
+}
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/common/GenomicFeature.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/common/GenomicFeature.java
new file mode 100644
index 0000000..70af097
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/common/GenomicFeature.java
@@ -0,0 +1,75 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.common;
+
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.Map;
+import net.sf.picard.util.Interval;
+
+/**
+ * Created by kokonech
+ * Date: 6/8/12
+ * Time: 6:00 PM
+ */
+public class GenomicFeature {
+
+ Interval interval;
+ Map<String,String> attributes;
+
+ public GenomicFeature(String seqName, int start, int end, boolean isNegative, String featureName ) {
+ interval = new Interval(seqName, start, end, isNegative, featureName);
+ attributes = new HashMap<String, String>();
+ }
+
+ public int getStart() {
+ return interval.getStart();
+ }
+
+ public int getEnd() {
+ return interval.getEnd();
+ }
+
+ public String getSequenceName() {
+ return interval.getSequence();
+ }
+
+ public boolean isPositiveStrand() {
+ return interval.isPositiveStrand();
+ }
+
+
+ public void addAttribute(String name, String value) {
+ attributes.put(name, value);
+ }
+
+ public String getFeatureName() {
+ return interval.getName();
+ }
+
+ public String getAttribute(String attrName) {
+ return attributes.get(attrName);
+ }
+
+ public Collection<String> getAttributeNames() {
+ return attributes.keySet();
+ }
+}
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/common/GenomicFeatureStreamReader.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/common/GenomicFeatureStreamReader.java
new file mode 100644
index 0000000..2afb4d4
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/common/GenomicFeatureStreamReader.java
@@ -0,0 +1,220 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.common;
+
+import java.io.BufferedReader;
+import java.io.FileReader;
+import java.io.IOException;
+
+/**
+ * Created by kokonech
+ * Date: 6/8/12
+ * Time: 5:55 PM
+ */
+public class GenomicFeatureStreamReader {
+
+ static abstract class FeatureRecordParser {
+
+ abstract GenomicFeature parseFeatureRecord(String record) throws RuntimeException;
+
+ }
+
+ static FeatureRecordParser getFeatureRecordParser(FeatureFileFormat format) {
+ if (format.equals(FeatureFileFormat.GFF)) {
+ return new FeatureRecordParser() {
+ @Override
+ GenomicFeature parseFeatureRecord(String line) {
+
+ String[] items = line.split("\t");
+
+ if (items.length < 8) {
+ throw new RuntimeException("GFF format error, not enough fields.\n" +
+ "Problematic line:\n" + line);
+ }
+
+ String seqName = items[0];
+ String featureName = items[2];
+ int start = Integer.parseInt(items[3]); // 1-based
+ int end = Integer.parseInt(items[4]); // 1-based, inclusive
+ boolean isNegativeStrand = items[6].equals("-");
+
+ return new GenomicFeature(seqName, start, end, isNegativeStrand, featureName);
+ }
+ };
+ } else if (format.equals(FeatureFileFormat.BED)) {
+ return new FeatureRecordParser() {
+ @Override
+ GenomicFeature parseFeatureRecord(String line) {
+
+ String[] items = line.split("\t");
+
+ if (items.length < 6) {
+ throw new RuntimeException("BED format error, there should be at least 6 fields.\n" +
+ "Problematic line:\n" + line);
+ }
+
+ String seqName = items[0];
+ int start = Integer.parseInt(items[1]) + 1; // 0-based
+ int end = Integer.parseInt(items[2]); //0-based, not-inclusive
+ String featureName = items[3];
+ boolean isNegativeStrand = items[5].equals("-");
+
+ return new GenomicFeature(seqName, start, end, isNegativeStrand, featureName);
+ }
+ };
+
+ } else if (format.equals(FeatureFileFormat.GTF)) {
+ return new FeatureRecordParser() {
+ @Override
+ GenomicFeature parseFeatureRecord(String line) throws RuntimeException {
+
+ String[] items = line.split("\t");
+
+ if (items.length != 9) {
+ throw new RuntimeException("GTF format error: there should " +
+ "9 tab-separated fields in each record.\n" +
+ "Problematic line:\n" + line);
+ }
+
+ String seqName = items[0];
+ String featureName = items[2];
+ int start = Integer.parseInt(items[3]); // 1-based
+ int end = Integer.parseInt(items[4]); // 1-based, inclusive
+ boolean isNegativeStrand = items[6].equals("-");
+
+ GenomicFeature feature = new GenomicFeature(seqName, start, end, isNegativeStrand, featureName);
+
+ String[] attrs = items[8].trim().split(" ");
+
+ int len = attrs.length;
+ if (len % 2 != 0) {
+ throw new RuntimeException("Warning! Line with wrong attributes is skipped:\n" + line);
+ }
+
+ for (int i = 0; i < len; i += 2) {
+ String atrName = attrs[i];
+ String atrVal = attrs[i+1];
+ if (atrVal.endsWith(";")) {
+ atrVal = atrVal.substring(0, atrVal.length() - 1);
+ } else {
+ throw new RuntimeException("Warning! Line with wrong attributes:\n" + line);
+ }
+ if (atrVal.startsWith("\"") && atrVal.endsWith("\"")) {
+ atrVal = atrVal.substring(1, atrVal.length() - 1);
+ }
+ feature.addAttribute(atrName, atrVal);
+
+ }
+
+ return feature;
+
+ }
+ };
+
+ }
+ else {
+ throw new RuntimeException("Unknown feature file format! ");
+ }
+
+ }
+
+ String fileName;
+ BufferedReader fileReader;
+ FeatureRecordParser recordParser;
+
+ public GenomicFeatureStreamReader(String fileName, FeatureFileFormat formatName ) throws IOException {
+ this.fileName = fileName;
+ this.fileReader = new BufferedReader(new FileReader(fileName));
+ this.recordParser = getFeatureRecordParser(formatName);
+
+ }
+
+ /**
+ * This method returns true until there are records remaining in feature file
+ * @return False if end of file is reached, otherwise True
+ * @throws IOException File reader exception
+ */
+ public boolean skipNextRecord() throws IOException {
+ String line;
+ while (true) {
+ line = fileReader.readLine();
+ if (line == null) {
+ return false;
+ }
+ if (line.startsWith("#") || line.isEmpty()) {
+ // skip comments and empty lines
+ } else {
+ break;
+ }
+ }
+
+ return true;
+ }
+
+
+ public GenomicFeature readNextRecord() throws IOException {
+
+ String line;
+ while (true) {
+ line = fileReader.readLine();
+ if (line == null) {
+ return null;
+ }
+ if (line.startsWith("#") || line.isEmpty()) {
+ // skip comments and empty lines
+ } else {
+
+ try {
+ return recordParser.parseFeatureRecord(line);
+ } catch (RuntimeException e) {
+
+ if (e.getMessage().startsWith("Warning")) {
+ System.err.println(e.getMessage());
+ } else {
+ throw e;
+ }
+ }
+
+ }
+ }
+
+ //return f;
+ //return recordParser.parseFeatureRecord(line);
+
+ }
+
+ public void close() throws IOException {
+ fileReader.close();
+ }
+
+ public void reset() throws IOException {
+ fileReader.close();
+ fileReader = new BufferedReader( new FileReader(fileName));
+ }
+
+
+
+
+
+
+
+
+}
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/common/GenomicRegionSet.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/common/GenomicRegionSet.java
new file mode 100644
index 0000000..552a6cd
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/common/GenomicRegionSet.java
@@ -0,0 +1,146 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.common;
+
+import net.sf.picard.util.Interval;
+import net.sf.picard.util.IntervalTree;
+import org.apache.commons.collections15.MultiMap;
+import org.apache.commons.collections15.multimap.MultiHashMap;
+
+import java.util.*;
+
+/**
+ * Created by kokonech
+ * Date: 12/20/11
+ * Time: 12:43 PM
+ */
+public class GenomicRegionSet {
+
+ public static class Feature {
+
+ String name;
+ boolean positiveStrand;
+
+ public Feature(String name, boolean positiveStrand) {
+ this.name = name;
+ this.positiveStrand = positiveStrand;
+ }
+
+ public String getName() {
+ return name;
+ }
+
+ public boolean isPositiveStrand() {
+ return positiveStrand;
+ }
+ }
+
+
+ IntervalTree<Set<Feature>> intervalTree;
+ MultiMap<String,Interval> featureIntervalMap;
+ Set<Interval> ambiguousRegions;
+
+ /* concatenates intersecting intervals */
+ private static Interval concatenateIntervals(Interval i1, Interval i2) {
+ int start = Math.min(i1.getStart(),i2.getStart());
+ int end = Math.max(i1.getEnd(), i2.getEnd());
+ return new Interval(i1.getSequence(), start,end, i1.isPositiveStrand(), i1.getName());
+ }
+
+ public GenomicRegionSet() {
+ intervalTree = new IntervalTree<Set<Feature>>();
+ featureIntervalMap = new MultiHashMap<String, Interval>();
+ ambiguousRegions = new HashSet<Interval>();
+ }
+
+ public void addRegion(GenomicFeature r, String featureName) {
+
+ boolean featureStrand = r.isPositiveStrand();
+
+ Interval newInterval = new Interval(r.getSequenceName(), r.getStart(), r.getEnd(), r.isPositiveStrand(), featureName);
+ List<Interval> toRemove = new ArrayList<Interval>();
+
+ //DEBUG
+ /*if (featureName.equals("ENSG00000214827") && (r.getStart() == 154292309 || r.getStart() == 154292241) ) {
+ System.out.println("It's something new here!");
+ }*/
+
+ if (featureIntervalMap.containsKey(featureName)) {
+ Collection<Interval> intervals = featureIntervalMap.get(featureName);
+ for (Interval interval: intervals ) {
+ if (newInterval.intersects(interval) || newInterval.abuts(interval)) {
+ if (newInterval.getStart() == interval.getStart() && newInterval.getEnd() == interval.getEnd()) {
+ // equal interval is already present for this feature
+ return;
+ }
+ newInterval = concatenateIntervals(newInterval, interval);
+ toRemove.add(interval);
+ }
+ }
+
+ intervals.removeAll(toRemove);
+
+ }
+
+ // If we removed intervals from featureIntervalMap, then need to update the intervalTree accordingly
+ for (Interval iv : toRemove) {
+ IntervalTree.Node<Set<Feature>> redundantInterval = intervalTree.find(iv.getStart(), iv.getEnd());
+ Set<Feature> features = redundantInterval.getValue();
+ removeFeatureByName(featureName, features);
+ if (features.isEmpty()) {
+ intervalTree.remove(iv.getStart(), iv.getEnd());
+ }
+ }
+
+ IntervalTree.Node<Set<Feature>> dublicateInterval = intervalTree.find(newInterval.getStart(), newInterval.getEnd());
+ if (dublicateInterval != null ) {
+ Set<Feature> intervalFeatures = dublicateInterval.getValue();
+ intervalFeatures.add(new Feature(featureName, featureStrand) );
+ } else {
+ Set<Feature> intervalFeatures = new HashSet<Feature>();
+ intervalFeatures.add(new Feature(featureName, featureStrand));
+ intervalTree.put(newInterval.getStart(), newInterval.getEnd(), intervalFeatures);
+ }
+ featureIntervalMap.put(featureName, newInterval);
+
+
+
+ }
+
+
+ public Iterator<IntervalTree.Node<Set<Feature>>> overlappers(int start, int end ) {
+ return intervalTree.overlappers(start, end);
+ }
+
+ static void removeFeatureByName(String featureName, Set<Feature> features) {
+ Feature toRemove = null;
+ for (Feature f :features) {
+ if (f.getName().equals(featureName)) {
+ toRemove = f;
+ break;
+ }
+ }
+ features.remove(toRemove);
+ }
+
+
+
+}
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/common/HtmlReportGenerator.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/common/HtmlReportGenerator.java
new file mode 100644
index 0000000..98f8a48
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/common/HtmlReportGenerator.java
@@ -0,0 +1,317 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.common;
+
+import org.bioinfo.ngs.qc.qualimap.beans.QChart;
+import org.bioinfo.ngs.qc.qualimap.beans.StatsReporter;
+import org.bioinfo.ngs.qc.qualimap.gui.utils.StatsKeeper;
+import org.bioinfo.ngs.qc.qualimap.gui.utils.StatsKeeper.Section;
+import org.bioinfo.ngs.qc.qualimap.main.NgsSmartMain;
+
+import java.io.File;
+import java.text.DateFormat;
+import java.text.SimpleDateFormat;
+import java.util.*;
+
+/**
+ * Created by kokonech
+ * Date: 3/13/12
+ * Time: 10:08 AM
+ */
+public class HtmlReportGenerator {
+
+ StatsReporter reporter;
+ AnalysisType analysisType;
+ String dirPath;
+ StringBuffer htmlReport;
+ List<String> plotNames, plotLinks;
+
+ public HtmlReportGenerator(StatsReporter reporter, String dirPath, AnalysisType analysisType) {
+ this.reporter = reporter;
+ this.analysisType = analysisType;
+ this.dirPath = dirPath;
+ }
+
+ public StringBuffer getReport() {
+
+ htmlReport = new StringBuffer();
+ plotNames = new ArrayList<String>();
+ plotLinks = new ArrayList<String>();
+
+ appendHeader();
+ appendBody();
+
+ return htmlReport;
+
+ }
+
+ void append(String line) {
+ htmlReport.append(line).append("\n");
+ }
+
+ void appendHeader() {
+
+ append("<!DOCTYPE HTML>");
+ append("<html>");
+ append("\t<head>");
+ append("\t\t<link rel=\"stylesheet\" href=\"css/agogo.css\" type=\"text/css\" />");
+ append("\t\t<link rel=\"stylesheet\" href=\"css/report.css\" " +
+ "type=\"text/css\" />");
+ append("\t<title>Qualimap report: " + analysisType.toString() + "</title>\n");
+ append("\t</head>");
+
+ }
+
+
+ void appendHeaderWrapper() {
+ append("\t<div class=\"header-wrapper\">");
+ append("\t\t<div class=\"header\">");
+ append("\t\t<p class=\"logo\"><a href=\"http://qualimap.bioinfo.cipf.es/\">");
+ append("\t\t<img class=\"logo\" src=\"css/qualimap_logo_small.png\" " +
+ "alt=\"Logo\"/>");
+ append("\t\t</a></p>");
+ append("<div class=\"headertitle\">" +
+ "<a href=\"\">Qualimap Report: " + analysisType.toString() + "</a></div>");
+ append("\t</div>");
+ append("</div>\n");
+ }
+
+ void appendContentWrapper() {
+ append("<div class=\"content-wrapper\">");
+ append("<div class=\"content\">");
+ appendDocument();
+ appendSideBar();
+ appendClearer();
+ append("</div>\n");
+ append("</div>\n");
+ }
+
+ private void appendClearer() {
+ append("<div class=\"clearer\"></div>");
+ }
+
+
+ void appendDocument() {
+
+ append("<div class=\"document\">");
+ append("<div class=\"documentwrapper\">");
+ append("<div class=\"bodywrapper\">");
+ append("<div class=\"body\">");
+
+ if (reporter.hasInputDescription()) {
+ appendInputData();
+ }
+
+ if (reporter.hasSummary()) {
+ appendSummary();
+ }
+
+ appendGraphs();
+
+ append("</div>\n");
+ append("</div>\n");
+ append("</div>\n");
+ append("</div>\n");
+
+ }
+
+
+ void appendSummary() {
+
+ append("<div class=section>");
+ append("<h2>Summary<a class=\"headerlink\" " +
+ "name=\"summary\" title=\"Permalink to this headline\"> </a></h2>");
+
+
+ append("<div class=summary>\n");
+
+ List<Section> summarySections = reporter.getSummaryDataSections();
+ appendTableFromStats(summarySections);
+
+ if (reporter.hasTableData()) {
+ appendChromosomeStats();
+ }
+
+ append("</div>");
+
+ append("</div> <!-- summary section -->\n");
+
+ }
+
+ void appendTableFromStats(List<Section> sections) {
+ for(Section s : sections) {
+ append("\n<div class=table-summary>");
+ append("<h3>" + s.getName() + "</h3>" );
+ append("<table class=\"summary hovertable\">");
+ for (String[] row : s.getRows()) {
+ append("<tr onmouseover=\"this.style.backgroundColor='#EEEEEC';\" " +
+ "onmouseout=\"this.style.backgroundColor='#FFFFFF';\">");
+ if (row.length == 1) {
+ append("<td class=column1>" + row[0] + "</td>");
+ } else {
+ append("<td class=column1>" + row[0] + "</td>");
+ append("<td class=column2>" + row[1] + "</td>");
+ }
+ append("</tr>");
+ }
+ append("</table>");
+ append("</div>\n");
+ }
+
+ }
+
+ void appendChromosomeStats() {
+
+ StatsKeeper chrStatsKeeper = reporter.getTableDataStatsKeeper();
+ List<Section> sections = chrStatsKeeper.getSections();
+
+ append("\n<div class=table-summary>");
+ append("<h3>" + chrStatsKeeper.getName() + "</h3>" );
+ append("<table class=\"summary hovertable\">");
+
+ for(Section s : sections) {
+ boolean sectionIsHeader = s.getName().equals(Constants.TABLE_STATS_HEADER);
+ for (String[] row : s.getRows()) {
+ append("<tr onmouseover=\"this.style.backgroundColor='#EEEEEC';\" " +
+ "onmouseout=\"this.style.backgroundColor='#FFFFFF';\">");
+ for (String item : row) {
+ if (sectionIsHeader) {
+ append("<td><b>" + item + "</b></td>");
+ } else {
+ append("<td>" + item + "</td>");
+ }
+ }
+ append("</tr>");
+ }
+ }
+
+ append("</table>");
+ append("</div>\n");
+
+ }
+
+
+ void appendInputData() {
+ append("<div class=section>");
+ append("<h2>Input data and parameters<a class=\"headerlink\" " +
+ "name=\"input\" title=\"Permalink to this headline\"> </a></h2>");
+
+
+ append("<div class=summary>\n");
+
+ List<Section> inputSections = reporter.getInputDataSections();
+ appendTableFromStats(inputSections);
+
+ append("</div>");
+
+ append("</div> <!-- summary section -->\n");
+
+ }
+
+ void appendGraphs() {
+
+ htmlReport.append("\n\n");
+ for (QChart chart : reporter.getCharts()) {
+
+ String imagePath = getImagePath(reporter,chart.getName());
+
+ plotNames.add(chart.getTitle());
+ plotLinks.add(chart.getName());
+
+ append("<div class=section>\n");
+ append("<h2>" + chart.getTitle() + "<a class=\"headerlink\" name=\""
+ + chart.getName() + "\" "
+ + "title=\"Permalink to this headline\"> </a></h2>\n");
+ append("<div><img width=100% src=\"" + imagePath + "\"></div>\n");
+ append("</div><!-- graph section -->\n\n");
+
+
+ }
+
+ }
+
+ public static String getImagePath(StatsReporter reporter, String imageName) {
+ String imagePath = "images_" + reporter.getFileName() + File.separator + imageName;
+ String extension = imageName.substring(imageName.lastIndexOf(".") + 1);
+ if (!extension.equalsIgnoreCase("png")) {
+ imagePath += ".png";
+ }
+ return imagePath;
+ }
+
+ void appendSideBar() {
+ append("\n<div class=\"sidebar\">");
+ append("<h3>Contents</h3>");
+
+ if (reporter.hasInputDescription()) {
+ append("<li class=\"toctree-l1\"><a class=\"reference internal\" href=\"#input\">Input data & parameters</a></li>");
+ }
+
+
+ if (reporter.hasSummary()) {
+ append("<li class=\"toctree-l1\"><a class=\"reference internal\" href=\"#summary\">Summary</a></li>");
+ }
+
+ int sz = plotNames.size();
+
+ for (int i = 0; i < sz; ++i) {
+ append("<li class=\"toctree-l1\"><a class=\"reference internal\" " +
+ "href=\"#" + plotLinks.get(i) + "\">" + plotNames.get(i) + "</a></li>");
+ }
+
+ append("</div> <!-- sidebar -->\n");
+ }
+
+ void appendBody() {
+ append("<body>");
+ appendHeaderWrapper();
+ appendContentWrapper();
+ appendFooter();
+ append("</body>");
+ }
+
+ private void appendFooter() {
+ append("\n<div class=\"footer-wrapper\">");
+ append("<div class=\"footer\">");
+
+ //left
+ append("<div class=\"left\">");
+ append("<div class=\"footer\">");
+ DateFormat dateFormat = new SimpleDateFormat("yyyy/MM/dd HH:mm:ss");
+ Date date = new Date();
+ append(dateFormat.format(date));
+ append("</div>");
+ append("</div>");
+
+ //right
+ append("<div class=\"right\">");
+ append("<div class=\"footer\">");
+ append("Generated by QualiMap " + NgsSmartMain.APP_VERSION );
+ append("</div");
+ append("</div>");
+
+ append("<div class=\"clearer\"></div>");
+ append("</div> <!-- footer -->");
+ append("</div>");
+ }
+
+
+}
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/common/JunctionInfo.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/common/JunctionInfo.java
new file mode 100644
index 0000000..9d51d1f
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/common/JunctionInfo.java
@@ -0,0 +1,52 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.common;
+
+/**
+ * Created by kokonech
+ * Date: 5/28/14
+ * Time: 4:51 PM
+ */
+public class JunctionInfo implements Comparable<JunctionInfo> {
+
+ Double percentage;
+ String junctionString;
+
+ public JunctionInfo(String junction, Double percentage) {
+ this.junctionString = junction;
+ this.percentage = percentage;
+ }
+
+ @Override
+ public int compareTo(JunctionInfo other) {
+ return this.percentage.compareTo( other.percentage );
+ }
+
+ public double getPercentage() {
+ return percentage;
+ }
+
+ public String getJunctionString() {
+ return junctionString;
+ }
+
+
+}
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/common/JunctionLocationMap.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/common/JunctionLocationMap.java
new file mode 100644
index 0000000..e399461
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/common/JunctionLocationMap.java
@@ -0,0 +1,87 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.common;
+
+import net.sf.picard.util.IntervalTree;
+
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Set;
+
+/**
+ * Created by kokonech
+ * Date: 8/18/14
+ * Time: 5:44 PM
+ */
+public class JunctionLocationMap {
+
+ HashMap<String, HashSet<Integer>> locationMap;
+ HashMap<String, IntervalTree<Integer>> locationIntervalTreeMap;
+
+ public JunctionLocationMap() {
+ locationMap = new HashMap<String, HashSet<Integer>>();
+ }
+
+
+ public void put(String sequence, int pos1, int pos2) {
+ if (!locationMap.containsKey(sequence)) {
+ locationMap.put(sequence, new HashSet<Integer>() );
+ }
+
+ Set<Integer> positionSet = locationMap.get(sequence);
+ positionSet.add(pos1);
+ positionSet.add(pos2);
+
+ }
+
+
+ public void setupIntervalTreeMap() {
+
+ locationIntervalTreeMap = new HashMap<String, IntervalTree<Integer>>();
+
+ for (String key : locationMap.keySet()) {
+ IntervalTree<Integer> iTree = new IntervalTree<Integer>();
+ HashSet<Integer> posSet = locationMap.get(key);
+
+ for (Integer pos : posSet) {
+ iTree.put(pos - 1, pos + 1, pos);
+ }
+ locationIntervalTreeMap.put(key, iTree );
+
+ }
+
+ }
+
+ public boolean hasOverlap(String sequence, int junctionPosition) {
+
+ IntervalTree<Integer> iTree = locationIntervalTreeMap.get(sequence);
+
+ return iTree != null && iTree.overlappers(junctionPosition, junctionPosition + 1).hasNext();
+
+
+ }
+
+
+ public int size(String seq) {
+ return locationMap.get(seq).size();
+ }
+
+}
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/common/LibraryProtocol.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/common/LibraryProtocol.java
new file mode 100644
index 0000000..834dbae
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/common/LibraryProtocol.java
@@ -0,0 +1,76 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.common;
+
+import java.util.Arrays;
+
+/**
+ * Created by kokonech
+ * Date: 6/15/12
+ * Time: 5:17 PM
+ */
+public enum LibraryProtocol {
+
+ NON_STRAND_SPECIFIC, STRAND_SPECIFIC_FORWARD, STRAND_SPECIFIC_REVERSE;
+
+ public static final String PROTOCOL_NON_STRAND_SPECIFIC = "non-strand-specific";
+ public static final String PROTOCOL_FORWARD_STRAND = "strand-specific-forward";
+ public static final String PROTOCOL_REVERSE_STRAND = "strand-specific-reverse";
+ public static final String PROTOCOL_UNKNOWN = "unknown";
+
+ public String toString() {
+ if (this == NON_STRAND_SPECIFIC) {
+ return PROTOCOL_NON_STRAND_SPECIFIC;
+ } else if (this == STRAND_SPECIFIC_FORWARD) {
+ return PROTOCOL_FORWARD_STRAND;
+ } else if (this == STRAND_SPECIFIC_REVERSE) {
+ return PROTOCOL_REVERSE_STRAND;
+ } else {
+ return PROTOCOL_UNKNOWN;
+ }
+
+ }
+
+ public static LibraryProtocol getProtocolByName(String protocolName) {
+ if (protocolName.equals(PROTOCOL_FORWARD_STRAND)) {
+ return STRAND_SPECIFIC_FORWARD;
+ } else if (protocolName.equals(PROTOCOL_NON_STRAND_SPECIFIC)) {
+ return NON_STRAND_SPECIFIC;
+ } else if (protocolName.equals(PROTOCOL_REVERSE_STRAND)) {
+ return STRAND_SPECIFIC_REVERSE;
+ }
+
+ throw new RuntimeException("Unknown library protocol name: " + protocolName + "\n" +
+ "Supported protocols: " + Arrays.toString(getProtocolNames()) );
+ }
+
+ public static String[] getProtocolNames() {
+ return new String[] {PROTOCOL_NON_STRAND_SPECIFIC, PROTOCOL_FORWARD_STRAND, PROTOCOL_REVERSE_STRAND };
+ }
+
+ public static String getProtocolNamesString() {
+ return LibraryProtocol.PROTOCOL_FORWARD_STRAND + ", "
+ + LibraryProtocol.PROTOCOL_REVERSE_STRAND + " or "
+ + LibraryProtocol.PROTOCOL_NON_STRAND_SPECIFIC;
+ }
+
+
+}
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/common/LoggerThread.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/common/LoggerThread.java
new file mode 100644
index 0000000..3a8f0b4
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/common/LoggerThread.java
@@ -0,0 +1,61 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.common;
+
+import java.io.BufferedReader;
+import java.io.IOException;
+
+/**
+ * Created by kokonech
+ * Date: 1/31/12
+ * Time: 12:54 PM
+ */
+public abstract class LoggerThread extends Thread {
+
+ BufferedReader outputReader;
+
+ public abstract void logLine(String msg);
+
+ public void updateProgress(int progress) {
+
+ }
+
+ public void start(BufferedReader reader) {
+ this.outputReader = reader;
+ start();
+ }
+
+ public void run() {
+ String line;
+ try {
+ while ((line = outputReader.readLine()) != null) {
+ logLine(line);
+ }
+
+ } catch (IOException e) {
+ System.err.println("Failed to parse output stream.");
+ }
+ }
+
+
+
+
+}
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/common/ReadStartsHistogram.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/common/ReadStartsHistogram.java
new file mode 100644
index 0000000..0a1b852
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/common/ReadStartsHistogram.java
@@ -0,0 +1,61 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.common;
+
+/**
+ * Created by kokonech
+ * Date: 2/9/12
+ * Time: 11:14 AM
+ */
+
+public class ReadStartsHistogram {
+
+ public static final int MAX_READ_STARTS_PER_POSITION = 50;
+ long currentReadStartPosition;
+ int readStartCounter;
+ long[] readStartsHistogram;
+
+ public ReadStartsHistogram() {
+ readStartsHistogram = new long[MAX_READ_STARTS_PER_POSITION + 1];
+ readStartCounter = 1;
+ currentReadStartPosition = -1;
+ }
+
+ public boolean update( long position ) {
+ if (position == currentReadStartPosition) {
+ readStartCounter++;
+ } else {
+ int histPos = readStartCounter < MAX_READ_STARTS_PER_POSITION ? readStartCounter :
+ MAX_READ_STARTS_PER_POSITION;
+ readStartsHistogram[histPos]++;
+ readStartCounter = 1;
+ currentReadStartPosition = position;
+ }
+
+ return readStartCounter > 1;
+ }
+
+ public long[] getHistorgram() {
+ return readStartsHistogram;
+ }
+
+
+}
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/common/RegionOverlapLookupTable.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/common/RegionOverlapLookupTable.java
new file mode 100644
index 0000000..d8612d5
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/common/RegionOverlapLookupTable.java
@@ -0,0 +1,113 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.common;
+
+import java.util.*;
+
+import net.sf.picard.util.Interval;
+import net.sf.picard.util.OverlapDetector;
+
+/**
+ * Created by kokonech
+ * Date: 2/6/12
+ * Time: 3:39 PM
+ */
+public class RegionOverlapLookupTable {
+
+ public static class OverlapResult {
+
+ boolean overlaps;
+ boolean strandCorrect;
+
+ public OverlapResult(boolean intervalOverlaps, boolean strandCorrect) {
+ this.overlaps = intervalOverlaps;
+ this.strandCorrect = strandCorrect;
+ }
+
+ public boolean strandMatches() {
+ return strandCorrect;
+ }
+
+ public boolean intervalOverlaps() {
+ return overlaps;
+ }
+
+ }
+
+ static class Feature {
+ String name;
+ boolean isPositiveStrand;
+ Feature(String name, boolean isPositiveStrand) {
+ this.name = name;
+ this.isPositiveStrand = isPositiveStrand;
+ }
+ }
+
+
+ OverlapDetector<Feature> overlapDetector;
+ Set<String> sequenceNames;
+ int regionCount;
+
+
+ public RegionOverlapLookupTable() {
+ overlapDetector = new OverlapDetector<Feature>(0,0);
+ sequenceNames = new HashSet<String>();
+ regionCount = 0;
+ }
+
+ public void putRegion(int startPos, int endPos, String seqName, boolean positiveStranded) {
+ // unique feature name
+ String featureName = "region" + ++regionCount;
+ overlapDetector.addLhs( new Feature(featureName, positiveStranded), new Interval(seqName, startPos, endPos));
+ sequenceNames.add(seqName);
+ }
+
+ public boolean overlaps(int readStart, int readEnd, String seqName) {
+ Collection<Feature> overlaps = overlapDetector.getOverlaps(new Interval(seqName, readStart, readEnd));
+
+ return overlaps.size() > 0;
+ }
+
+ public OverlapResult overlaps(int readStart, int readEnd, String seqName, boolean forwardStrandExpected) {
+ Collection<Feature> overlaps = overlapDetector.getOverlaps(new Interval(seqName, readStart, readEnd));
+
+ Iterator<Feature> it = overlaps.iterator();
+
+ int numStrandMatches = 0;
+ int numMatches = 0;
+
+ while (it.hasNext()) {
+ numMatches++;
+ boolean itemHasForwardStrand = it.next().isPositiveStrand;
+ if (itemHasForwardStrand == forwardStrandExpected) {
+ ++numStrandMatches;
+ }
+ }
+
+ return new OverlapResult(numMatches > 0, numStrandMatches == numMatches && numStrandMatches > 0 );
+
+ }
+
+ public Set<String> getSequenceNames() {
+ return sequenceNames;
+ }
+
+}
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/common/TranscriptDataHandler.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/common/TranscriptDataHandler.java
new file mode 100644
index 0000000..272d168
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/common/TranscriptDataHandler.java
@@ -0,0 +1,748 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.common;
+
+import net.sf.picard.annotation.Gene;
+import net.sf.picard.util.Interval;
+import net.sf.picard.util.IntervalTreeMap;
+import net.sf.picard.util.MathUtil;
+import net.sf.samtools.SAMRecord;
+import org.apache.commons.collections15.MultiMap;
+import org.apache.commons.collections15.multimap.MultiHashMap;
+import org.apache.commons.math.stat.StatUtils;
+import org.bioinfo.ngs.qc.qualimap.beans.*;
+import org.jfree.data.general.DefaultPieDataset;
+
+import javax.imageio.ImageIO;
+import java.awt.*;
+import java.awt.image.BufferedImage;
+import java.io.File;
+import java.io.IOException;
+import java.util.*;
+import java.util.List;
+
+/**
+ * Created by kokonech
+ * Date: 7/2/12
+ * Time: 1:52 PM
+ */
+public class TranscriptDataHandler {
+
+ public static final String ATTR_NAME_TRANSCRIPT_ID = "transcript_id";
+ public static final String ATTR_NAME_GENE_ID = "gene_id";
+ public static final String FEATURE_NAME_EXON = "exon";
+
+
+ MultiMap<String, GenomicFeature> featureCache;
+ HashMap<String, Gene> geneMap;
+ HashMap<Gene.Transcript, int[]> transcriptCoverage;
+ HashMap<String, Integer> junctionSequenceMap;
+ JunctionLocationMap junctionLocationMap;
+ IntervalTreeMap<Integer> intronIntervalTreeMap;
+
+ public double getMedianFivePrimeBias() {
+ return medianFivePrimeBias;
+ }
+
+ public double getMedianThreePrimeBias() {
+ return medianThreePrimeBias;
+ }
+
+ public double getMedianFiveToThreeBias() {
+ return medianFiveToThreeBias;
+ }
+
+
+ double medianFivePrimeBias, medianThreePrimeBias, medianFiveToThreeBias;
+ long numReadsWithJunction, knownJunctions, partlyKnownJunctions;
+ long numTotalReads, numIntronicReads, numIntergenicReads, numIntersectingExonRegionReads;
+
+ int[] meanTranscriptCovHistogram;
+
+ static int min(int[] data) {
+ int res = data[0];
+
+ for (int val : data) {
+ if (val < res) {
+ res = val;
+ }
+ }
+
+ return res;
+ }
+
+ static int max(int[] data) {
+ int res = data[0];
+
+ for (int val : data) {
+ if (val > res) {
+ res = val;
+ }
+ }
+
+ return res;
+ }
+
+ public TranscriptDataHandler() {
+ featureCache = new MultiHashMap<String, GenomicFeature>();
+ geneMap = new HashMap<String, Gene>();
+ transcriptCoverage = new HashMap<Gene.Transcript, int[]>();
+ junctionSequenceMap = new HashMap<String, Integer>();
+ junctionLocationMap = new JunctionLocationMap();
+
+ }
+
+
+ public void addExonFeature(GenomicFeature feature) {
+
+ String transcriptId = feature.getAttribute(ATTR_NAME_TRANSCRIPT_ID);
+ if (transcriptId == null) {
+ throw new RuntimeException("GTF attribute \"transcript_id\" is missing.");
+ }
+ featureCache.put(transcriptId, feature );
+
+ }
+
+ public void constructTranscriptsMap() throws RuntimeException {
+
+ Set<String> transciptIds = featureCache.keySet();
+
+ for (String transcriptId : transciptIds) {
+ Collection<GenomicFeature> exonFeatures = featureCache.get(transcriptId);
+ int numExons = exonFeatures.size();
+
+ int[] exonStarts = new int[numExons];
+ int[] exonEnds = new int[numExons];
+
+ GenomicFeature firstFeature = null;
+ int exonCount = 0;
+ for (GenomicFeature exonFeature : exonFeatures) {
+ if (firstFeature == null) {
+ firstFeature = exonFeature;
+ }
+ exonStarts[exonCount] = exonFeature.getStart();
+ exonEnds[exonCount] = exonFeature.getEnd();
+ exonCount++;
+ }
+
+ int transcriptStart = min(exonStarts);
+ int transcriptEnd = max(exonEnds);
+
+ if (firstFeature == null) {
+ throw new RuntimeException("No exons detected for transcript " + transcriptId);
+ }
+
+
+ String geneName = firstFeature.getAttribute(ATTR_NAME_GENE_ID);
+ Gene gene = geneMap.get(geneName);
+ if (gene == null) {
+ gene = new Gene(firstFeature.getSequenceName(), transcriptStart, transcriptEnd,
+ !firstFeature.isPositiveStrand(), geneName );
+ geneMap.put(geneName, gene);
+ }
+
+ Gene.Transcript t = gene.addTranscript(transcriptId, transcriptStart, transcriptEnd,
+ transcriptStart, transcriptEnd, numExons);
+
+ for (int i = 0; i < numExons; ++i ) {
+ t.addExon(exonStarts[i], exonEnds[i]);
+ }
+
+
+ }
+
+ featureCache.clear();
+
+ createHelperMaps();
+
+
+ }
+
+ public void addCoverage(String geneId, int startPos, int endPos) {
+ Gene gene = geneMap.get(geneId);
+ for (Gene.Transcript t : gene) {
+ int[] coverage = transcriptCoverage.get(t);
+ if (coverage == null) {
+ coverage = new int[t.length()];
+ transcriptCoverage.put(t, coverage);
+ }
+ t.addCoverageCounts(startPos, endPos, coverage );
+ }
+ }
+
+
+ public void validateAttributes(String attrName, ArrayList<String> allowedFeatureList) {
+ if (!attrName.equals(ATTR_NAME_GENE_ID)) {
+ throw new RuntimeException("Wrong attribute name \"" + attrName +
+ "\", for 5'-3' bias calculation only \"gene_id\" is supported.");
+ }
+
+ if (allowedFeatureList.size() != 1 || !allowedFeatureList.get(0).equals(FEATURE_NAME_EXON)) {
+ throw new RuntimeException("Wrong feature type \"" + allowedFeatureList.get(0) +
+ "\", for 5'-3' bias calculation only \"exon\' is supported.");
+ }
+ }
+
+
+
+ // The three methods below are based on sf.picard.analysis.directed.RnaMetricsCollector
+
+ static private double[] copyAndReverse(final double[] in) {
+ final double[] out = new double[in.length];
+ for (int i=0, j=in.length-1; i<in.length; ++i, --j) out[j] = in[i];
+ return out;
+ }
+
+ public void calculateCoverageBias() {
+
+ if (transcriptCoverage.size() == 0) {
+ return;
+ }
+
+ final Map<Gene.Transcript,int[]> transcripts = pickTranscripts();
+
+ int numTranscripts = transcripts.size();
+
+ double[] fivePrimeBias = new double[numTranscripts];
+ double[] threePrimeBias = new double[numTranscripts];
+ double[] fiveToThreePrimeBias = new double[numTranscripts];
+
+
+ int count = 0;
+ for (final Map.Entry<Gene.Transcript,int[]> entry : transcripts.entrySet()) {
+ final Gene.Transcript tx = entry.getKey();
+ final double[] coverage;
+ {
+ final double[] tmp = MathUtil.promote(entry.getValue());
+ if (tx.getGene().isPositiveStrand()) {
+ coverage = tmp;
+ } else {
+ coverage = copyAndReverse(tmp);
+ }
+ }
+ final double mean = MathUtil.mean(coverage, 0, coverage.length);
+
+ final int PRIME_BASES = 100;
+ final double fivePrimeCoverage = MathUtil.mean(coverage, 0, PRIME_BASES);
+ final double threePrimeCoverage = MathUtil.mean(coverage, coverage.length - PRIME_BASES, coverage.length);
+
+ fivePrimeBias[count] = fivePrimeCoverage / mean;
+ threePrimeBias[count] = threePrimeCoverage / mean;
+ fiveToThreePrimeBias[count] = fivePrimeCoverage /threePrimeCoverage;
+ count++;
+
+ }
+
+ medianFivePrimeBias = StatUtils.percentile(fivePrimeBias, 50);
+ medianThreePrimeBias = StatUtils.percentile(threePrimeBias, 50);
+ medianFiveToThreeBias = StatUtils.percentile(fiveToThreePrimeBias, 50);
+
+ }
+
+
+ public Map<Gene.Transcript, int[]> pickTranscripts() {
+
+ Collection<Gene> genes = geneMap.values();
+ final int minimumLength = 500;
+ final Map<Gene.Transcript, Double> bestPerGene = new HashMap<Gene.Transcript, Double>();
+
+ // Make a map of the best transcript per gene to it's mean coverage
+ for (final Gene gene : genes) {
+
+ Gene.Transcript best = null;
+ double bestMean = 0;
+
+ for (final Gene.Transcript tx : gene) {
+ final int[] cov = transcriptCoverage.get(tx);
+
+ if (tx.length() < Math.max(minimumLength, 100)) {
+ continue;
+ }
+
+ if (cov == null) {
+ continue;
+ }
+
+ final double mean = MathUtil.mean(MathUtil.promote(cov), 0, cov.length);
+ if (mean < 1d) {
+ continue;
+ }
+
+ if (best == null || mean > bestMean) {
+ best = tx;
+ bestMean = mean;
+ }
+ }
+
+ if (best != null) bestPerGene.put(best, bestMean);
+ }
+
+ // Find the 1000th best coverage value
+ final double[] coverages = new double[bestPerGene.size()];
+ int i=0;
+ for (final double d : bestPerGene.values()) {
+ coverages[i++] = d;
+ }
+ Arrays.sort(coverages);
+ final double min = coverages.length == 0 ? 0 : coverages[Math.max(0, coverages.length - 1001)];
+
+ // And finally build the output map
+ final Map<Gene.Transcript, int[]> retval = new HashMap<Gene.Transcript, int[]>();
+ for (final Map.Entry<Gene.Transcript,Double> entry : bestPerGene.entrySet()) {
+ final Gene.Transcript tx = entry.getKey();
+ final double coverage = entry.getValue();
+
+ if (coverage >= min) {
+ retval.put(tx, transcriptCoverage.get(tx));
+ }
+ }
+
+ return retval;
+ }
+
+
+ public void computeMeanTranscriptCoverageHist() {
+
+ // TODO: number of bins is currently fixed, however it might be interesting to support more bins
+
+ final int NUM_BINS = 51;
+
+ meanTranscriptCovHistogram = new int[NUM_BINS];
+
+ Collection<Gene> genes = geneMap.values();
+
+ for (final Gene gene : genes) {
+
+ for (final Gene.Transcript tx : gene) {
+
+ if (tx.length() == 0) {
+ continue;
+ }
+
+ final int[] cov = transcriptCoverage.get(tx);
+
+ long sum = 0;
+ if (cov != null) {
+ for (int c : cov) {
+ sum += c;
+ }
+ }
+
+ int meanCovLevel = (int) (sum / tx.length());
+
+ if (meanCovLevel < 0) {
+ System.out.println("Error with meanCovLevel: " + meanCovLevel);
+ continue;
+ }
+
+ if (meanCovLevel >= NUM_BINS) {
+ meanCovLevel = NUM_BINS - 1;
+ }
+
+ meanTranscriptCovHistogram[meanCovLevel] += 1;
+
+ }
+ }
+
+ }
+
+ TreeMap<Double, int[]> getSortedTranscriptCoverage() {
+
+ TreeMap<Double, int[]> resMap = new TreeMap<Double, int[]>();
+
+ Collection<Gene> genes = geneMap.values();
+
+ for (final Gene gene : genes) {
+
+ for (final Gene.Transcript tx : gene) {
+
+ final int[] cov = transcriptCoverage.get(tx);
+
+ if (cov == null) {
+ continue;
+ }
+
+ double meanCov = MathUtil.mean(MathUtil.promote(cov), 0, cov.length);
+ if (meanCov > 0) {
+ resMap.put(meanCov, cov);
+ }
+
+
+ }
+ }
+ return resMap;
+ }
+
+ public double[] computePerBaseTranscriptCoverageHist(TreeMap<Double, int[]> resMap, int numItems, boolean ascendingOrder) {
+
+ final int NUM_BINS = 100;
+
+ NavigableSet<Double> set = ascendingOrder ? resMap.navigableKeySet() : resMap.descendingKeySet();
+
+ GenericHistogram hist = new GenericHistogram(NUM_BINS, true);
+
+ int count = 0;
+ for (Double coverage : set) {
+ if (count >= numItems) {
+ break;
+ }
+
+ int[] cov = resMap.get(coverage);
+ hist.updateHistogram(cov);
+
+ count++;
+
+ }
+
+ return hist.getHist();
+
+
+ }
+
+ public double[] computePerBaseTranscriptCoverageHist() {
+
+ final int NUM_BINS = 100;
+
+ GenericHistogram hist = new GenericHistogram(NUM_BINS, true);
+
+ Collection<Gene> genes = geneMap.values();
+
+
+ for (final Gene gene : genes) {
+
+ for (final Gene.Transcript tx : gene) {
+
+ final int[] cov = transcriptCoverage.get(tx);
+
+ if (cov == null)
+ continue;
+
+ hist.updateHistogram(cov);
+
+
+ }
+ }
+
+ return hist.getHist();
+
+ }
+
+ public QChart createCoverageProfilePlot(double[] perBaseTranscriptCoverage, String chartName, String sampleName )
+ {
+
+ XYVector coverageData = new XYVector();
+
+ for (int i = 0; i < perBaseTranscriptCoverage.length; ++i) {
+ coverageData.addItem( new XYItem(i,perBaseTranscriptCoverage[i]));
+ }
+
+
+ BamQCChart geneCoverage = new BamQCChart(chartName,
+ sampleName, "Transcript position", " Counts ");
+ geneCoverage.addSeries("Transcript coverage profile", coverageData, new Color(255, 0, 0, 255));
+ geneCoverage.setAdjustDomainAxisLimits(false);
+ geneCoverage.setDomainAxisIntegerTicks(true);
+ geneCoverage.setShowLegend(false);
+ geneCoverage.render();
+ return new QChart(chartName, geneCoverage.getChart(), geneCoverage);
+
+ }
+
+
+ public QChart createReadsOriginPieChart(String sampleName) {
+
+ long numExonicReads = numTotalReads - numIntronicReads - numIntergenicReads;
+
+ DefaultPieDataset dataset = new DefaultPieDataset();
+ dataset.setValue("Exonic", new Double((100 * numExonicReads) / numTotalReads));
+ dataset.setValue("Intergenic", new Double( (100.*numIntergenicReads) / numTotalReads ));
+ dataset.setValue("Intronic", new Double((100.*numIntronicReads) / numTotalReads ));
+
+ String chartTitle = "Reads Genomic Origin";
+ BamQCPieChart pieChart = new BamQCPieChart(chartTitle, sampleName, dataset);
+ pieChart.render();
+
+ return new QChart(chartTitle, pieChart.getJFreeChart() );
+
+ }
+
+ public QChart createJunctionAnalysisPieChart(String sampleName) {
+
+ long novelJunctions = numReadsWithJunction - knownJunctions - partlyKnownJunctions;
+
+ DefaultPieDataset dataset = new DefaultPieDataset();
+ dataset.setValue("Known", new Double((100 * knownJunctions) / numReadsWithJunction));
+ dataset.setValue("Partly known", new Double( (100.*partlyKnownJunctions) / numReadsWithJunction ));
+ dataset.setValue("Novel", new Double((100.*novelJunctions) / numReadsWithJunction ));
+
+ String chartTitle = "Junction Analysis";
+ BamQCPieChart pieChart = new BamQCPieChart(chartTitle, sampleName, dataset);
+ pieChart.render();
+
+ return new QChart(chartTitle, pieChart.getJFreeChart() );
+
+ }
+
+
+ public List<QChart> createPlots(String sampleName) throws IOException {
+
+ ArrayList<QChart> charts = new ArrayList<QChart>();
+
+
+ if (numTotalReads > 0) {
+ QChart readsOriginChart = createReadsOriginPieChart(sampleName);
+ charts.add(readsOriginChart);
+ }
+
+ TreeMap<Double, int[]> sortedCoverageMap = getSortedTranscriptCoverage();
+
+ {
+ double[] perBaseTranscriptCoverage = computePerBaseTranscriptCoverageHist(sortedCoverageMap,
+ sortedCoverageMap.size(), true );
+ QChart chart = createCoverageProfilePlot(perBaseTranscriptCoverage,
+ "Coverage Profile Along Genes (Total)", sampleName);
+ charts.add(chart);
+ }
+
+ {
+ double[] perBaseTranscriptCoverage = computePerBaseTranscriptCoverageHist(sortedCoverageMap,
+ 500, true );
+ QChart chart = createCoverageProfilePlot(perBaseTranscriptCoverage,
+ "Coverage Profile Along Genes (Low)", sampleName);
+ charts.add(chart);
+ }
+
+ {
+ double[] perBaseTranscriptCoverage = computePerBaseTranscriptCoverageHist(sortedCoverageMap,
+ 500, false );
+ QChart chart = createCoverageProfilePlot(perBaseTranscriptCoverage,
+ "Coverage Profile Along Genes (High)", sampleName);
+ charts.add(chart);
+ }
+
+
+ {
+ computeMeanTranscriptCoverageHist();
+
+ XYVector covHist = new XYVector();
+
+ for (int i = 0; i < meanTranscriptCovHistogram.length; ++i) {
+ covHist.addItem(new XYItem(i, meanTranscriptCovHistogram[i]));
+ }
+
+ BamQCXYHistogramChart coverageHistogram =
+ new BamQCXYHistogramChart(Constants.PLOT_TITLE_COVERAGE_HISTOGRAM_0_50,
+ sampleName, "Coverage (X)", "Number of transcripts");
+ coverageHistogram.addHistogram("coverageData", covHist, Color.blue);
+ coverageHistogram.setNumberOfBins(50);
+ //coverageHistogram.zoom(maxValue);
+ coverageHistogram.setDomainAxisIntegerTicks(true);
+ coverageHistogram.setDomainAxisTickUnitSize(1.0);
+ coverageHistogram.render();
+
+ charts.add( new QChart("Transcript coverage histogram",
+ coverageHistogram.getChart() ) );
+
+ }
+
+ {
+ if (numReadsWithJunction > 0) {
+ QChart chart = createJunctionAnalysisPieChart(sampleName);
+ charts.add(chart);
+ }
+ }
+
+
+ return charts;
+
+ }
+
+ public void collectJunctionInfo(SAMRecord read, int posInRead, int clippedLength) {
+ byte[] seq = read.getReadBases();
+
+ if (seq != null && posInRead - 2 > 0 && posInRead + 1 < seq.length) {
+ char[] junction = new char[4];
+ junction[0] = (char) seq[posInRead - 2];
+ junction[1] = (char) seq[posInRead - 1];
+ junction[2] = (char) seq[posInRead];
+ junction[3] = (char) seq[posInRead + 1 ];
+ String junctionStr = new String(junction);
+
+
+ Integer count = junctionSequenceMap.get(junctionStr);
+ if (count == null) {
+ junctionSequenceMap.put(junctionStr, 1);
+ } else {
+ junctionSequenceMap.put(junctionStr, count + 1);
+ }
+
+ int alignmentStart = read.getAlignmentStart();
+ int posInRef1 = alignmentStart + posInRead;
+ int posInRef2 = posInRef1 + clippedLength;
+ String seqName = read.getReferenceName();
+
+ boolean j1 = junctionLocationMap.hasOverlap(seqName, posInRef1);
+ boolean j2 = junctionLocationMap.hasOverlap(seqName, posInRef2);
+ if (j1 && j2) {
+ knownJunctions++;
+ } else if (j1 || j2) {
+ partlyKnownJunctions++;
+ }
+
+
+ }
+
+ numReadsWithJunction += 1;
+
+ }
+
+ public List<JunctionInfo> computeSortedJunctionsMap() {
+
+ List<JunctionInfo> junctionList = new ArrayList<JunctionInfo>();
+
+ if (numReadsWithJunction == 0) {
+ return junctionList;
+ }
+
+ for (Map.Entry<String, Integer> entry : junctionSequenceMap.entrySet()) {
+
+ double percentage = (entry.getValue() * 100.) / numReadsWithJunction;
+ junctionList.add( new JunctionInfo(entry.getKey(), percentage));
+ }
+
+ Collections.sort(junctionList);
+
+ return junctionList;
+ }
+
+ public long getNumReadsWithJunctions() {
+ return numReadsWithJunction;
+ }
+
+ public long getNumIntronicReads() {
+ return numIntronicReads;
+ }
+
+ public long getNumIntergenicReads() {
+ return numIntergenicReads;
+ }
+
+ public void setNumTotalReads(long totalReadCounts) {
+ numTotalReads = totalReadCounts;
+ }
+
+ void createHelperMaps() {
+ intronIntervalTreeMap = new IntervalTreeMap<Integer>();
+ int numIntrons = 0;
+
+ for (Map.Entry<String,Gene> entry : geneMap.entrySet()) {
+ Gene gene = entry.getValue();
+ for (final Gene.Transcript tx : gene) {
+ int numExons = tx.exons.length;
+ if (numExons < 2) {
+ continue;
+ }
+ int[] breakCoords = new int[(numExons - 1)*2];
+ int k = 0;
+
+ if ( gene.isPositiveStrand() ) {
+ for (int i = 0; i < numExons; ++ i) {
+ Gene.Transcript.Exon e = tx.exons[i];
+ if (i == 0) {
+ breakCoords[k++] = e.end;
+ } else if ( i == numExons - 1) {
+ breakCoords[k++] = e.start;
+ } else {
+ breakCoords[k++] = e.start;
+ breakCoords[k++] = e.end;
+ }
+ }
+ } else {
+ // make sure there is no problem with sorting
+ Arrays.sort(tx.exons, new Comparator<Gene.Transcript.Exon>() {
+ @Override
+ public int compare(Gene.Transcript.Exon e1, Gene.Transcript.Exon e2) {
+ return e1.start > e2.start ? -1 : 1;
+ }
+ });
+
+ for (int i = numExons - 1; i >= 0; -- i) {
+ Gene.Transcript.Exon e = tx.exons[i];
+ if (i == 0) {
+ breakCoords[k++] = e.start;
+ } else if ( i == numExons - 1) {
+ breakCoords[k++] = e.end;
+ } else {
+ breakCoords[k++] = e.start;
+ breakCoords[k++] = e.end;
+ }
+ }
+ }
+
+ for (int i = 0; i < breakCoords.length; i+=2) {
+ String chrName = gene.getSequence();
+ if (breakCoords[i] >= breakCoords[i+1]) {
+ String warning = "Warning! Transcript " + tx.name +
+ " has incorrect exon coordinates. Transcript skipped...";
+
+ System.out.println(warning);
+ break;
+ }
+
+ Interval intronInterval = new Interval(chrName, breakCoords[i], breakCoords[i+1]);
+ numIntrons++;
+ intronIntervalTreeMap.put(intronInterval, numIntrons);
+ junctionLocationMap.put(chrName, breakCoords[i],breakCoords[i+1]);
+ }
+
+ }
+ }
+
+ junctionLocationMap.setupIntervalTreeMap();
+
+
+ }
+
+ public void collectNonFeatureMappedReadInfo(List<Interval> intervals) {
+ boolean liesInIntergenic = true;
+ for (Interval iv : intervals) {
+ Collection<Integer> intronOverlaps = intronIntervalTreeMap.getOverlapping(iv);
+ if (intronOverlaps.size() > 0) {
+ liesInIntergenic = false;
+ break;
+ }
+ }
+ if (liesInIntergenic) {
+ numIntergenicReads++;
+ } else {
+ numIntronicReads++;
+ }
+ }
+
+ public void increaseNumReadsIntersectingExonRegion() {
+ numIntersectingExonRegionReads++;
+ }
+
+ public long getNumReadsIntersectingExonRegion() {
+ return numIntersectingExonRegionReads;
+ }
+
+}
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/common/UniqueID.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/common/UniqueID.java
new file mode 100644
index 0000000..2353b31
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/common/UniqueID.java
@@ -0,0 +1,28 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.common;
+
+public class UniqueID {
+ static long current= System.currentTimeMillis();
+ static public synchronized long get(){
+ return current++;
+ }
+}
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/dialogs/AboutDialog.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/dialogs/AboutDialog.java
new file mode 100644
index 0000000..b44f085
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/dialogs/AboutDialog.java
@@ -0,0 +1,150 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.gui.dialogs;
+
+import java.awt.*;
+import java.awt.event.ActionEvent;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.io.IOException;
+import java.net.URI;
+import java.net.URISyntaxException;
+
+import javax.imageio.ImageIO;
+import javax.swing.AbstractAction;
+import javax.swing.ImageIcon;
+import javax.swing.JButton;
+import javax.swing.JDialog;
+import javax.swing.JLabel;
+
+import net.miginfocom.swing.MigLayout;
+import org.bioinfo.commons.log.Logger;
+import org.bioinfo.ngs.qc.qualimap.common.Constants;
+import org.bioinfo.ngs.qc.qualimap.gui.frames.HomeFrame;
+import org.bioinfo.ngs.qc.qualimap.gui.utils.PopupKeyListener;
+import org.bioinfo.ngs.qc.qualimap.main.NgsSmartMain;
+
+/**
+ * Class to show the Information of the application.
+ * @author kokonech
+ */
+public class AboutDialog extends JDialog {
+ /** Serial Version ID */
+ private static final long serialVersionUID = 8521724385994032467L;
+
+ private AbstractAction abstractActionCloseAbout;
+
+ /** Logger to print information */
+ protected Logger logger;
+
+ private HomeFrame homeFrame;
+
+ static class LinkMouseAdapter extends MouseAdapter {
+
+ String url;
+ public LinkMouseAdapter(String url) {
+ this.url = url;
+ }
+
+ @Override
+ public void mouseClicked(MouseEvent e) {
+ try {
+ Desktop.getDesktop().browse(new URI(url));
+ } catch (URISyntaxException e1) {
+ e1.printStackTrace();
+ } catch (IOException e1) {
+ e1.printStackTrace();
+ }
+ }
+ }
+
+ public AboutDialog(HomeFrame frame) {
+ super(frame, "About");
+ logger = new Logger(this.getClass().getName());
+ this.homeFrame = frame;
+ initGUI();
+ pack();
+ setResizable(false);
+ }
+
+ private void initGUI() {
+
+ PopupKeyListener keyListener = new PopupKeyListener(homeFrame, this, null);
+
+ getContentPane().setLayout(new MigLayout("insets 20"));
+
+ String aboutText = "<html><body align=\"center\">QualiMap: software for evaluating next " +
+ "generation sequencing<br> alignment data</body></html>";
+ add(new JLabel(aboutText), "align center,wrap");
+ String versionText = "Version: " + NgsSmartMain.APP_VERSION.replace("v.", "");
+ add(new JLabel(versionText), "align center,wrap");
+ String dateText = "Build date: " + NgsSmartMain.APP_BUILT_DATE;
+ add(new JLabel(dateText), "align center,wrap 20px");
+
+ try {
+
+ Image imageCipf = ImageIO.read(getClass().getResource(
+ Constants.pathImages + "cipf_alpha.gif"));
+
+ JLabel cipfLink = new JLabel(new ImageIcon(imageCipf.getScaledInstance(-1, 80, Image.SCALE_SMOOTH)),
+ JLabel.CENTER);
+ cipfLink.setCursor(new Cursor(Cursor.HAND_CURSOR));
+ cipfLink.addMouseListener(new LinkMouseAdapter("http://www.cipf.es/"));
+
+ Image imageMpiib = ImageIO.read(getClass().getResource(
+ Constants.pathImages + "mpiib.jpeg"));
+
+
+ JLabel mpiibLink = new JLabel(new ImageIcon(imageMpiib.getScaledInstance(-1, 80, Image.SCALE_SMOOTH)),
+ JLabel.CENTER);
+ mpiibLink.setCursor( new Cursor(Cursor.HAND_CURSOR));
+ mpiibLink.addMouseListener(new LinkMouseAdapter("http://www.mpiib-berlin.mpg.de/"));
+
+ add(cipfLink, "align center, wrap 20px");
+ add(mpiibLink, "align center, wrap 20px");
+
+ } catch (IOException e) {
+ e.printStackTrace();
+ }
+
+ JButton buttonOk = new JButton();
+ buttonOk.setText("OK");
+ buttonOk.setAction(getAbstractActionCloseAbout());
+ buttonOk.addKeyListener(keyListener);
+ add(buttonOk, "center");
+
+
+ }
+
+ private AbstractAction getAbstractActionCloseAbout() {
+ if(abstractActionCloseAbout == null) {
+ abstractActionCloseAbout = new AbstractAction("OK", null) {
+ private static final long serialVersionUID = 1624997520647406057L;
+
+ public void actionPerformed(ActionEvent evt) {
+ dispose();
+ }
+ };
+ }
+ return abstractActionCloseAbout;
+ }
+
+}
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/dialogs/AnalysisDialog.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/dialogs/AnalysisDialog.java
new file mode 100644
index 0000000..daf192a
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/dialogs/AnalysisDialog.java
@@ -0,0 +1,260 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.gui.dialogs;
+
+import org.bioinfo.ngs.qc.qualimap.gui.frames.HomeFrame;
+import org.bioinfo.ngs.qc.qualimap.main.NgsSmartMain;
+
+import javax.swing.*;
+import java.awt.*;
+import java.awt.event.ContainerEvent;
+import java.awt.event.ContainerListener;
+import java.awt.event.KeyEvent;
+import java.awt.event.KeyListener;
+import java.io.File;
+import java.io.PrintWriter;
+import java.io.StringWriter;
+
+/**
+ * Created by kokonech
+ * Date: 3/1/12
+ * Time: 10:29 AM
+ */
+public class AnalysisDialog extends JDialog implements ContainerListener, KeyListener
+{
+
+ protected static class ExceptionHandler implements Thread.UncaughtExceptionHandler {
+
+ AnalysisDialog dlg;
+
+ public ExceptionHandler(AnalysisDialog homeDlg) {
+ this.dlg = homeDlg;
+ }
+
+ public void uncaughtException(Thread th, Throwable ex) {
+
+ String m = ex.getMessage();
+ String errMsg = "Failed to perform " + dlg.getTitle() + "\n" + m;
+
+ StringWriter errorsWriter = new StringWriter();
+ ex.printStackTrace(new PrintWriter(errorsWriter));
+ String errorReport = errorsWriter.toString();
+
+ if (errorReport.contains("java.lang.OutOfMemoryError") ) {
+ errMsg = NgsSmartMain.OUT_OF_MEMORY_REPORT;
+ }
+
+ JOptionPane.showMessageDialog(dlg, errMsg, dlg.getTitle(), JOptionPane.ERROR_MESSAGE);
+
+ dlg.resetProgress();
+ dlg.setUiEnabled(true);
+ dlg.updateState();
+
+ }
+ }
+
+
+ protected HomeFrame homeFrame;
+
+ protected JButton startAnalysisButton;
+ protected JProgressBar progressBar;
+ protected JLabel progressStream;
+ protected JTextArea logArea;
+ protected JScrollPane logAreaScrollPane;
+
+ public AnalysisDialog(HomeFrame parent, String title) {
+ super(parent,title);
+ this.homeFrame = parent;
+ addKeyAndContainerListenerRecursively(this);
+
+ }
+
+ private void addKeyAndContainerListenerRecursively(Component c)
+ {
+ c.removeKeyListener(this);
+ c.addKeyListener(this);
+
+ if(c instanceof Container){
+
+ Container cont = (Container)c;
+ cont.removeContainerListener(this);
+ cont.addContainerListener(this);
+ Component[] children = cont.getComponents();
+
+ for(Component child : children){
+ addKeyAndContainerListenerRecursively(child);
+ }
+ }
+ }
+
+ private void removeKeyAndContainerListenerRecursively(Component c)
+ {
+ c.removeKeyListener(this);
+
+ if(c instanceof Container){
+
+ Container cont = (Container)c;
+
+ cont.removeContainerListener(this);
+
+ Component[] children = cont.getComponents();
+
+ for(Component child : children){
+ removeKeyAndContainerListenerRecursively(child);
+ }
+ }
+ }
+
+
+
+ @Override
+ public void componentAdded(ContainerEvent containerEvent) {
+ addKeyAndContainerListenerRecursively(containerEvent.getChild());
+
+ }
+
+ @Override
+ public void componentRemoved(ContainerEvent containerEvent) {
+ removeKeyAndContainerListenerRecursively(containerEvent.getChild());
+
+ }
+
+ @Override
+ public void keyTyped(KeyEvent keyEvent) {
+
+
+ }
+
+ @Override
+ public void keyPressed(KeyEvent keyEvent) {
+ int code = keyEvent.getKeyCode();
+ if(code == KeyEvent.VK_ESCAPE){
+ setVisible(false);
+ }
+ }
+
+ @Override
+ public void keyReleased(KeyEvent keyEvent) {
+
+ }
+
+
+ public HomeFrame getHomeFrame() {
+ return homeFrame;
+ }
+
+ protected void setupProgressBar() {
+ UIManager.put("ProgressBar.selectionBackground", Color.black);
+ UIManager.put("ProgressBar.selectionForeground", Color.black);
+ progressBar = new JProgressBar(0, 100);
+ progressBar.setVisible(true);
+ progressBar.setStringPainted(true);
+ progressBar.setBorderPainted(true);
+ progressBar.setForeground(new Color(244, 200, 120));
+ }
+
+ protected void setupProgressStream() {
+ progressStream = new JLabel();
+ progressStream.setVisible(true);
+ progressStream.setText("Status");
+ }
+
+ protected void setupLogArea() {
+ logArea = new JTextArea(10,40);
+ logArea.setEditable(false);
+
+ logAreaScrollPane = new JScrollPane();
+ logAreaScrollPane.setVerticalScrollBarPolicy(JScrollPane.VERTICAL_SCROLLBAR_ALWAYS);
+ logAreaScrollPane.setViewportView(logArea);
+ }
+
+ static public boolean validateInputFile(String filePath) {
+
+ if ( filePath.isEmpty() ) {
+ return false;
+ }
+
+ File inputFile = new File(filePath);
+ return inputFile.exists();
+
+
+ }
+
+ public JProgressBar getProgressBar() {
+ return progressBar;
+ }
+
+ public JLabel getProgressStream() {
+ return progressStream;
+ }
+
+ public JTextArea getLogArea() {
+ return logArea;
+ }
+
+ public void resetProgress() {
+ if (progressBar != null) {
+ progressBar.setValue(0);
+ }
+ if (progressStream != null) {
+ progressStream.setText("Status");
+ }
+ if (logArea != null) {
+ logArea.setText("");
+ }
+ }
+
+ public void setUiEnabled(boolean enabled) {
+
+ for (Component c : getContentPane().getComponents()) {
+ c.setEnabled(enabled);
+ if (c instanceof JComponent) {
+ JComponent panel = (JComponent) c;
+ for (Component subComponent : panel.getComponents()) {
+ subComponent.setEnabled(enabled);
+ }
+ }
+ }
+
+ // No matter happens these guys stay enabled
+ if (progressBar != null) {
+ progressBar.setEnabled(true);
+ }
+ if (progressStream != null) {
+ progressStream.setEnabled(true);
+ }
+
+ }
+
+
+ public void updateProgress(int progress) {
+ if (progressBar != null) {
+ progressBar.setValue(progress);
+ }
+ }
+
+ // virtual hopefully
+ public void updateState() {
+
+ }
+
+
+ }
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/dialogs/BrowseButtonActionListener.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/dialogs/BrowseButtonActionListener.java
new file mode 100644
index 0000000..502ce68
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/dialogs/BrowseButtonActionListener.java
@@ -0,0 +1,119 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.gui.dialogs;
+
+import org.bioinfo.ngs.qc.qualimap.gui.frames.HomeFrame;
+
+import javax.swing.*;
+import javax.swing.filechooser.FileFilter;
+import java.awt.*;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.io.File;
+
+/**
+ * Created by kokonech
+ * Date: 1/4/12
+ * Time: 11:24 AM
+ */
+
+public class BrowseButtonActionListener implements ActionListener {
+
+ protected JTextField pathEdit;
+ protected Component parent;
+ protected String description;
+ protected String[] extentions;
+ boolean allowDirectories;
+
+ public BrowseButtonActionListener(Component parent, JTextField field, String description, boolean allowDirs) {
+ this.parent = parent;
+ this.pathEdit = field;
+ this.description = description;
+ this.extentions = null;
+ this.allowDirectories = allowDirs;
+
+ }
+
+ public BrowseButtonActionListener(Component parent, JTextField field, String description, String ext) {
+ this.parent = parent;
+ this.pathEdit = field;
+ this.description = description;
+ this.allowDirectories = false;
+ this.extentions = new String[1];
+ extentions[0] = ext;
+ }
+
+
+ public BrowseButtonActionListener(Component parent, JTextField field, String description, String[] extentions) {
+ this.parent = parent;
+ this.pathEdit = field;
+ this.description = description;
+ this.extentions = extentions;
+ this.allowDirectories = false;
+ }
+
+
+ @Override
+ public void actionPerformed(ActionEvent actionEvent) {
+
+ JFileChooser fileOpenChooser = HomeFrame.getFileChooser();
+ if (allowDirectories) {
+ fileOpenChooser.setFileSelectionMode(JFileChooser.FILES_AND_DIRECTORIES);
+ }
+
+ FileFilter filter = new FileFilter() {
+ public boolean accept(File fileShown) {
+
+ if (extentions == null) {
+ return true;
+ }
+
+ for (String ext : extentions) {
+ if (fileShown.getName().endsWith(ext) || fileShown.isDirectory() ) {
+ return true;
+ }
+ }
+
+ return false;
+
+ }
+
+ public String getDescription() {
+ return description;
+ }
+ };
+
+ fileOpenChooser.setFileFilter(filter);
+
+ int result = fileOpenChooser.showOpenDialog(parent);
+
+ if (result == JFileChooser.APPROVE_OPTION) {
+ pathEdit.setText(fileOpenChooser.getSelectedFile().getPath());
+ validateInput();
+ }
+
+
+ }
+
+ protected void validateInput() {
+
+ }
+}
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/dialogs/ComputeCountsDialog.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/dialogs/ComputeCountsDialog.java
new file mode 100644
index 0000000..74a507d
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/dialogs/ComputeCountsDialog.java
@@ -0,0 +1,498 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.gui.dialogs;
+
+import net.miginfocom.swing.MigLayout;
+import org.bioinfo.ngs.qc.qualimap.gui.frames.HomeFrame;
+import org.bioinfo.ngs.qc.qualimap.common.Constants;
+import org.bioinfo.ngs.qc.qualimap.common.LibraryProtocol;
+import org.bioinfo.ngs.qc.qualimap.process.ComputeCountsTask;
+import org.bioinfo.ngs.qc.qualimap.common.*;
+
+import javax.swing.*;
+import javax.swing.event.CaretEvent;
+import javax.swing.event.CaretListener;
+import java.awt.*;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.io.File;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.io.PrintWriter;
+import java.util.*;
+
+/**
+ * Created by kokonech
+ * Date: 1/10/12
+ * Time: 3:03 PM
+ */
+public class ComputeCountsDialog extends AnalysisDialog implements ActionListener{
+
+
+ JTextField bamPathEdit, gffPathEdit, outputPathField, featureNameField, featureTypeField;
+ JButton browseBamButton, browseGffButton, okButton, cancelButton;
+ JComboBox<String> strandTypeCombo, countingAlgoCombo;
+ JComboBox<String> availableFeatureTypesCombo, availableFeatureNamesCombo;
+ JCheckBox saveStatsBox,advancedOptions, pairedAnalysisBox, alreadySortedBox;
+ JLabel countingMethodLabel;
+ JPanel ftPanel, fnPanel;
+ Thread countReadsThread;
+
+ static class BrowseGffButtonListener extends BrowseButtonActionListener {
+
+ ComputeCountsDialog dlg;
+ Set<String> featuresTypes, featureNames;
+ static final int NUM_LINES = 100000;
+ static final String[] extentions = { "gtf", "gff", "bed" };
+
+ public BrowseGffButtonListener(ComputeCountsDialog parent, JTextField textField) {
+ super(parent, textField, "Annotation files", extentions );
+ this.dlg = parent;
+ featuresTypes = new HashSet<String>();
+ featureNames = new HashSet<String>();
+ }
+
+ @Override
+ public void validateInput() {
+ dlg.setGtfSpecificOptionsEnabled(false);
+ dlg.availableFeatureTypesCombo.removeAllItems();
+ dlg.availableFeatureNamesCombo.removeAllItems();
+
+ String filePath = pathEdit.getText();
+ try {
+ preloadGff(filePath);
+ } catch (Exception e) {
+ return;
+ }
+
+ if (featuresTypes.isEmpty()) {
+ JOptionPane.showMessageDialog(parent,
+ "No features are found in GTF file, please make sure the file is not empty.",
+ dlg.getTitle(), JOptionPane.ERROR_MESSAGE);
+ return;
+ }
+ dlg.setGtfSpecificOptionsEnabled(true);
+
+ for (String s : featuresTypes) {
+ dlg.availableFeatureTypesCombo.addItem(s);
+ }
+ if (featuresTypes.contains(ComputeCountsTask.EXON_TYPE_ATTR)) {
+ dlg.availableFeatureTypesCombo.setSelectedItem(ComputeCountsTask.EXON_TYPE_ATTR);
+ }
+
+ for (String s : featureNames) {
+ dlg.availableFeatureNamesCombo.addItem(s);
+ }
+ if (featureNames.contains(ComputeCountsTask.GENE_ID_ATTR)) {
+ dlg.availableFeatureNamesCombo.setSelectedItem(ComputeCountsTask.GENE_ID_ATTR);
+ }
+
+ }
+
+ void preloadGff(String filePath) throws Exception {
+ GenomicFeatureStreamReader parser = new GenomicFeatureStreamReader(filePath, FeatureFileFormat.GTF);
+ for (int i = 0; i < NUM_LINES; ++i) {
+ GenomicFeature rec = parser.readNextRecord();
+ if (rec == null) {
+ break;
+ }
+ String featureType = rec.getFeatureName();
+ featuresTypes.add(featureType);
+ Collection<String> fNames = rec.getAttributeNames();
+ for (String name : fNames) {
+ featureNames.add(name);
+ }
+ }
+
+ }
+ }
+
+ private void setGtfSpecificOptionsEnabled(boolean enabled) {
+
+ for (Component c : fnPanel.getComponents()) {
+ c.setEnabled(enabled);
+ }
+
+ for (Component c : ftPanel.getComponents()) {
+ c.setEnabled(enabled);
+ }
+
+ }
+
+ static class FeatureComboBoxListener implements ActionListener {
+
+ JTextField targetField;
+ JComboBox featuresCombo;
+
+ FeatureComboBoxListener(JComboBox featuresCombo, JTextField targetField) {
+ this.featuresCombo = featuresCombo;
+ this.targetField = targetField;
+ }
+
+ @Override
+ public void actionPerformed(ActionEvent actionEvent) {
+ Object curItem = featuresCombo.getSelectedItem();
+ if (curItem == null) {
+ return;
+ }
+ if (!curItem.toString().isEmpty()) {
+ targetField.setText(curItem.toString());
+ }
+ }
+ }
+
+ public ComputeCountsDialog(HomeFrame homeFrame) {
+
+ super(homeFrame, "Compute counts");
+
+ getContentPane().setLayout(new MigLayout("insets 20"));
+
+
+ add(new JLabel("BAM file:"), "");
+
+ bamPathEdit = new JTextField(40);
+ bamPathEdit.setToolTipText("Path to BAM alignment file");
+ add(bamPathEdit, "grow");
+
+ browseBamButton = new JButton("...");
+ browseBamButton.addActionListener( new BrowseButtonActionListener(this,
+ bamPathEdit, "BAM files", "bam"));
+ add(browseBamButton, "align center, wrap");
+
+ add(new JLabel("Annotation file:"), "");
+
+ gffPathEdit = new JTextField(40);
+ gffPathEdit.setToolTipText("File with the definition of the regions for the features (GTF/GFF or BED).");
+ add(gffPathEdit, "grow");
+
+ browseGffButton = new JButton();
+ browseGffButton.setText("...");
+ browseGffButton.addActionListener(new BrowseGffButtonListener(this, gffPathEdit));
+ browseBamButton.addActionListener(this);
+ add(browseGffButton, "align center, wrap");
+
+
+ add(new JLabel("Protocol:"));
+ String[] protocolComboItems = LibraryProtocol.getProtocolNames();
+ strandTypeCombo = new JComboBox<String>(protocolComboItems);
+ strandTypeCombo.setToolTipText("Select the corresponding sequencing protocol");
+ strandTypeCombo.addActionListener(this);
+ add(strandTypeCombo, "wrap");
+
+ JLabel gtfLabel = new JLabel("GTF-specific options:");
+ gtfLabel.setToolTipText("<html>If annotations are given in GTF format, counting is performed based " +
+ "on given attributes.</html>");
+ add(gtfLabel, "wrap");
+ fnPanel = new JPanel();
+ fnPanel.setLayout(new MigLayout("insets 5"));
+ fnPanel.add(new JLabel("Feature ID:"));
+ featureNameField = new JTextField(10);
+ featureNameField.setText(ComputeCountsTask.GENE_ID_ATTR);
+ featureNameField.setToolTipText("<html>Attribute of the GTF to be used as feature ID. Regions with the same ID" +
+ "will be aggregated as part of the same feature. Default: gene_id</html>");
+ fnPanel.add(featureNameField, "");
+ fnPanel.add(new JLabel("Available feature IDs:"));
+ availableFeatureNamesCombo = new JComboBox<String>();
+ availableFeatureNamesCombo.setToolTipText("These feature IDS were found in first 1000 of the GTF file");
+ availableFeatureNamesCombo.addActionListener(
+ new FeatureComboBoxListener(availableFeatureNamesCombo, featureNameField));
+ fnPanel.add(availableFeatureNamesCombo, "wrap");
+
+ add(fnPanel, "span, wrap");
+
+
+ ftPanel = new JPanel();
+ ftPanel.setLayout(new MigLayout("insets 5"));
+ ftPanel.add(new JLabel("Feature type:"));
+ featureTypeField = new JTextField(10);
+ featureTypeField.setToolTipText("<html>Value of the third column of the GTF considered for counting. " +
+ "<br>Other types will be ignored. Default: exon</html>");
+ featureTypeField.setText(ComputeCountsTask.EXON_TYPE_ATTR);
+ ftPanel.add(featureTypeField, "");
+ ftPanel.add(new JLabel("Available feature types:"));
+ availableFeatureTypesCombo = new JComboBox<String>();
+ availableFeatureTypesCombo.addItem("");
+ availableFeatureTypesCombo.setToolTipText("These types of features were found in first 1000 of the GFF file");
+ availableFeatureTypesCombo.addActionListener(
+ new FeatureComboBoxListener(availableFeatureTypesCombo,featureTypeField));
+ ftPanel.add(availableFeatureTypesCombo, "wrap");
+
+ add(ftPanel, "span, wrap");
+
+ pairedAnalysisBox = new JCheckBox("Paired-end analysis");
+ pairedAnalysisBox.setToolTipText("<html>This option activates counting of fragments instead of counting of reads. " +
+ "<br>Only valid for paired-end sequencing experiments.</html>");
+ pairedAnalysisBox.addActionListener(this);
+ add(pairedAnalysisBox);
+
+ alreadySortedBox = new JCheckBox("Alignment is sorted by name");
+ alreadySortedBox.setToolTipText("<html>The paired-end analysis requires the BAM file to be sorted by name. " +
+ "<br>Check this box if it is the case, otherwise temporary BAM sorted by name" +
+ "<br>will be created.</html>");
+ add(alreadySortedBox, "wrap");
+
+ setGtfSpecificOptionsEnabled(false);
+
+ advancedOptions = new JCheckBox("Advanced options:");
+ advancedOptions.addActionListener(this);
+ add(advancedOptions, "wrap");
+
+ countingMethodLabel = new JLabel("Multi-mapped reads:");
+ countingMethodLabel.setToolTipText("Select method to count reads that map to several genome locations");
+ add(countingMethodLabel);
+ String[] algoComboItems = {ComputeCountsTask.COUNTING_ALGORITHM_ONLY_UNIQUELY_MAPPED,
+ ComputeCountsTask.COUNTING_ALGORITHM_PROPORTIONAL
+ };
+ countingAlgoCombo = new JComboBox<String>(algoComboItems);
+ countingAlgoCombo.addActionListener(this);
+ add(countingAlgoCombo, "wrap");
+
+
+ add(new JLabel("Output:"), "");
+ outputPathField = new JTextField(40);
+ outputPathField.setToolTipText("Path to the file which will contain output");
+ bamPathEdit.addCaretListener( new CaretListener() {
+ @Override
+ public void caretUpdate(CaretEvent caretEvent) {
+ if (!bamPathEdit.getText().isEmpty()) {
+ outputPathField.setText(bamPathEdit.getText() + ".counts");
+ }
+ }
+ });
+ add(outputPathField, "grow");
+
+ JButton browseOutputPathButton = new JButton("...");
+ browseOutputPathButton.addActionListener(new BrowseButtonActionListener(this,
+ outputPathField, "Counts file", false) );
+ add(browseOutputPathButton, "wrap");
+
+ saveStatsBox = new JCheckBox("Save computation summary");
+ saveStatsBox.setToolTipText("<html>This option controls whether to save " +
+ "overall computation statistics.</html>");
+ add(saveStatsBox, "span 2, wrap");
+
+ add(new JLabel("Log:"), "wrap");
+
+ setupLogArea();
+ add(logAreaScrollPane, "span, grow, wrap 30px");
+
+ JPanel buttonPanel = new JPanel();
+ buttonPanel.setLayout(new MigLayout("insets 20"));
+
+ okButton = new JButton("Run calculation");
+ okButton.setActionCommand(Constants.OK_COMMAND);
+ okButton.addActionListener(this);
+ buttonPanel.add(okButton);
+ cancelButton = new JButton("Close");
+ cancelButton.setActionCommand(Constants.CANCEL_COMMAND);
+ cancelButton.addActionListener(this);
+ buttonPanel.add(cancelButton);
+
+ add(buttonPanel, "span, align right, wrap");
+
+ if (System.getenv("QUALIMAP_DEBUG") != null) {
+ bamPathEdit.setText("/home/kokonech/sample_data/paired_rna_seq/pe_nssp_hg19.chr20.bam");
+ gffPathEdit.setText("/data/annotations/Homo_sapiens.GRCh37.68.chr20.gtf");
+
+ }
+
+ pack();
+ updateState();
+
+
+ }
+
+ @Override
+ public void actionPerformed(ActionEvent actionEvent) {
+ if (actionEvent.getActionCommand().equals(Constants.OK_COMMAND)) {
+ String errMsg = validateInput();
+ if (!errMsg.isEmpty()) {
+ JOptionPane.showMessageDialog(this, errMsg, getTitle(), JOptionPane.ERROR_MESSAGE);
+ return;
+ }
+ final ComputeCountsDialog frame = this;
+
+ countReadsThread = new Thread() {
+ public void run() {
+
+ frame.setUiEnabled(false);
+ logArea.setText("");
+ String bamPath = bamPathEdit.getText();
+ String gffPath = gffPathEdit.getText();
+ String featureType = featureTypeField.getText();
+ ComputeCountsTask computeCountsTask = new ComputeCountsTask(bamPath, gffPath);
+ String pName = strandTypeCombo.getSelectedItem().toString();
+ computeCountsTask.setProtocol(LibraryProtocol.getProtocolByName(pName));
+ computeCountsTask.setCountingAlgorithm(countingAlgoCombo.getSelectedItem().toString());
+ computeCountsTask.addSupportedFeatureType(featureType);
+ computeCountsTask.setAttrName(featureNameField.getText());
+ if (pairedAnalysisBox.isSelected()) {
+ computeCountsTask.setPairedEndAnalysis();
+ if (!alreadySortedBox.isSelected()) {
+ computeCountsTask.setSortingRequired();
+ }
+ }
+
+ final JTextArea loggerDestArea = logArea;
+
+ computeCountsTask.setLogger( new LoggerThread() {
+ @Override
+ public void logLine(String msg) {
+ loggerDestArea.append(msg + "\n");
+ loggerDestArea.setCaretPosition(loggerDestArea.getText().length());
+ }
+ });
+
+
+ try {
+ computeCountsTask.run();
+
+ PrintWriter outWriter = new PrintWriter(new FileWriter(outputPathField.getText()));
+
+ Map<String,Double> counts = computeCountsTask.getReadCounts();
+ for (Map.Entry<String,Double> entry: counts.entrySet()) {
+ String str = entry.getKey() + "\t" + entry.getValue().longValue();
+ outWriter.println(str);
+ }
+ outWriter.flush();
+
+ if (saveStatsBox.isSelected()) {
+ PrintWriter statsWriter = new PrintWriter(new FileWriter(outputPathField.getText() + ".stats"));
+
+ String statsMessage = computeCountsTask.getOutputStatsMessage().toString();
+ statsWriter.println(statsMessage);
+
+ statsWriter.flush();
+ }
+
+ } catch (Exception e) {
+ JOptionPane.showMessageDialog(frame, e.getMessage(),
+ getTitle(), JOptionPane.ERROR_MESSAGE);
+ e.printStackTrace();
+ frame.setUiEnabled(true);
+ return;
+ }
+
+ StringBuilder message = new StringBuilder();
+ message.append("Counts generated!\n\n");
+ message.append(computeCountsTask.getOutputStatsMessage());
+ message.append("\nResult is saved to ").append(outputPathField.getText());
+
+ JOptionPane.showMessageDialog(frame, message.toString(),
+ getTitle(), JOptionPane.INFORMATION_MESSAGE);
+ logArea.append(message.toString());
+ logArea.setCaretPosition(logArea.getText().length());
+
+ frame.setUiEnabled(true);
+
+ }
+ };
+
+ Thread.UncaughtExceptionHandler eh = new AnalysisDialog.ExceptionHandler(this);
+ countReadsThread.setUncaughtExceptionHandler(eh);
+
+ countReadsThread.start();
+
+ } else if (actionEvent.getActionCommand().equals(Constants.CANCEL_COMMAND)) {
+ setVisible(false);
+ } else {
+ updateState();
+ }
+
+
+ }
+
+ public void updateState() {
+ alreadySortedBox.setEnabled(pairedAnalysisBox.isSelected());
+
+ countingAlgoCombo.setEnabled(advancedOptions.isSelected());
+ countingMethodLabel.setEnabled(advancedOptions.isSelected());
+
+ String countingMethod = countingAlgoCombo.getSelectedItem().toString();
+ String algorithmHint = countingMethod.equals(ComputeCountsTask.COUNTING_ALGORITHM_ONLY_UNIQUELY_MAPPED) ?
+ "Only uniquely mapped reads will be consider" :
+ "<html>Each read will be weighted according to its number" +
+ " of mapped locations. <br>For example, a read with 4 mapping locations will " +
+ "<br>add 0.25 to the counts on each location.</html>";
+
+ countingAlgoCombo.setToolTipText(algorithmHint);
+
+
+ String protocol = strandTypeCombo.getSelectedItem().toString();
+ if (protocol.equals(LibraryProtocol.PROTOCOL_NON_STRAND_SPECIFIC)) {
+ strandTypeCombo.setToolTipText("Reads are counted if mapped to a feature independent of strand");
+ } else if (protocol.equals(LibraryProtocol.PROTOCOL_FORWARD_STRAND)) {
+ strandTypeCombo.setToolTipText("<html>The single-end reads must have the same strand as the feature." +
+ "<br>For paired-end reads first of a pair must have the same strand as the feature," +
+ "<br>while the second read must be on the opposite strand</html>");
+ } else {
+ strandTypeCombo.setToolTipText("<html>The single-end reads must have the strand opposite to the feature." +
+ "<br>For paired-end reads first of a pair must have on the opposite strand," +
+ "<br>while the second read must be on the same strand as the feature.</html>");
+ }
+
+
+ }
+
+
+ public void setUiEnabled(boolean enabled) {
+ super.setUiEnabled(enabled);
+
+ if (enabled) {
+ boolean gtfSpecific =
+ DocumentUtils.guessFeaturesFileFormat(gffPathEdit.getText()) == FeatureFileFormat.GTF;
+ setGtfSpecificOptionsEnabled( gtfSpecific );
+ } else {
+ setGtfSpecificOptionsEnabled(false);
+ }
+
+
+ }
+
+
+ private String validateInput() {
+
+ File bamFile = new File(bamPathEdit.getText());
+ if (!bamFile.exists()) {
+ return "BAM file is not found!";
+ }
+
+ File gffFile = new File(gffPathEdit.getText());
+ if (!gffFile.exists()) {
+ return "Annotations file is not found!";
+ }
+
+ File outputFile = new File(outputPathField.getText());
+ try {
+ if (!outputFile.exists() && !outputFile.createNewFile()) {
+ throw new IOException();
+ }
+ } catch (IOException e) {
+ return "Output file path is not valid!";
+ }
+ if (!outputFile.delete()) {
+ return "Output path is not valid! Deleting probing directory failed.";
+ }
+
+
+ return "";
+ }
+}
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/dialogs/EditCountsSampleInfoDialog.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/dialogs/EditCountsSampleInfoDialog.java
new file mode 100644
index 0000000..16983d4
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/dialogs/EditCountsSampleInfoDialog.java
@@ -0,0 +1,196 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.gui.dialogs;
+
+import net.miginfocom.swing.MigLayout;
+import org.bioinfo.ngs.qc.qualimap.gui.panels.CountsQcDialog;
+import org.bioinfo.ngs.qc.qualimap.process.CountsSampleInfo;
+
+import javax.swing.*;
+import java.awt.*;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.KeyEvent;
+import java.awt.event.KeyListener;
+import java.io.File;
+
+/**
+ * Created by kokonech
+ * Date: 5/15/14
+ * Time: 4:40 PM
+ */
+public class EditCountsSampleInfoDialog extends JDialog implements KeyListener{
+ CountsQcDialog parentDlg;
+ JTextField sampleName, pathField;
+ JButton okButton, cancelButton, browseCountsDataButton;
+ JSpinner dataColumnSpinner, conditionIndexSpinner;
+ Component frame;
+ boolean editMode;
+ int itemIndex;
+
+ public EditCountsSampleInfoDialog( CountsQcDialog parent) {
+
+ this.parentDlg = parent;
+ this.itemIndex = -1;
+ editMode = false;
+ initComponents();
+
+ int sampleIndex = parent.getItemCount() + 1;
+ sampleName.setText("Sample" + sampleIndex);
+ for (Component c : getContentPane().getComponents()) {
+ c.addKeyListener(this);
+ }
+
+ }
+
+ public EditCountsSampleInfoDialog(CountsQcDialog parent, int itemIndex) {
+
+ this.parentDlg = parent;
+ this.itemIndex = itemIndex;
+ editMode = true;
+
+ initComponents();
+
+ CountsSampleInfo itemToModify = parentDlg.getDataItem(itemIndex);
+ sampleName.setText(itemToModify.name);
+ pathField.setText(itemToModify.path);
+ dataColumnSpinner.setValue(itemToModify.columnNum);
+ conditionIndexSpinner.setValue(itemToModify.conditionIndex);
+
+
+
+ }
+
+ void initComponents() {
+ frame = this;
+
+ getContentPane().setLayout(new MigLayout("insets 20"));
+
+ add(new JLabel("Sample name:"));
+ sampleName = new JTextField(30);
+ add(sampleName, "wrap");
+
+ add(new JLabel("Path"));
+ pathField = new JTextField(30);
+ add(pathField);
+ browseCountsDataButton = new JButton("...");
+ browseCountsDataButton.addActionListener(new BrowseButtonActionListener(this, pathField, "Counts data",false));
+ add(browseCountsDataButton, "wrap");
+
+ JLabel colLabel = new JLabel("Data column index:");
+ add(colLabel);
+ dataColumnSpinner = new JSpinner(new SpinnerNumberModel(CountsSampleInfo.DEFAULT_COLUMN, 1, 1000, 1));
+ add(dataColumnSpinner, "wrap");
+
+ JLabel conditionLabel = new JLabel("Condition index:");
+ add(conditionLabel);
+ conditionIndexSpinner = new JSpinner(new SpinnerNumberModel(1, 1, 2, 1));
+ add(conditionIndexSpinner, "wrap");
+
+
+ JPanel buttonPanel = new JPanel();
+ buttonPanel.setLayout(new MigLayout("insets 10"));
+ okButton = new JButton("OK");
+ okButton.addActionListener( new ActionListener() {
+ @Override
+ public void actionPerformed(ActionEvent actionEvent) {
+ String errorMessage = validateInputData();
+ if (errorMessage.isEmpty()) {
+ CountsSampleInfo item = new CountsSampleInfo();
+ item.name = sampleName.getText();
+ item.path = pathField.getText();
+ item.columnNum = ((SpinnerNumberModel) dataColumnSpinner.getModel()).getNumber().intValue();
+ item.conditionIndex =
+ ((SpinnerNumberModel) conditionIndexSpinner.getModel()).getNumber().intValue();
+ if (editMode) {
+ parentDlg.replaceDataItem(itemIndex, item);
+ } else {
+ parentDlg.addDataItem(item);
+ }
+ setVisible(false);
+ } else {
+ JOptionPane.showMessageDialog(frame, errorMessage, "Input error", JOptionPane.ERROR_MESSAGE);
+ }
+ }
+ });
+
+ cancelButton = new JButton("Cancel");
+ cancelButton.addActionListener( new ActionListener() {
+ @Override
+ public void actionPerformed(ActionEvent actionEvent) {
+ setVisible(false);
+ }
+ });
+
+ buttonPanel.add(okButton);
+ buttonPanel.add(cancelButton, "wrap");
+
+ add(buttonPanel, "align right, span, wrap");
+
+
+ pack();
+ setTitle("Counts sample data");
+ setResizable(false);
+
+ }
+
+ @Override
+ public void keyTyped(KeyEvent e) {
+ // DO NOTHING
+ }
+
+ @Override
+ public void keyPressed(KeyEvent keyEvent) {
+ int code = keyEvent.getKeyCode();
+ if(code == KeyEvent.VK_ESCAPE){
+ setVisible(false);
+ }
+ }
+
+ @Override
+ public void keyReleased(KeyEvent e) {
+ // DO NOTHING.
+ }
+
+ String validateInputData() {
+
+ if (sampleName.getText().isEmpty()) {
+ return "Sample name is empty!";
+ }
+
+ String samplePath = pathField.getText();
+
+ if (samplePath.isEmpty()) {
+ return "Sample counts path is empty!";
+ }
+
+ File sampleDataFile = new File(samplePath);
+ if (!sampleDataFile.exists()) {
+ return "Sample counts file doesn't exist!";
+ }
+
+
+ return "";
+ }
+
+
+
+}
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/dialogs/EditEpigeneticsInputDataDialog.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/dialogs/EditEpigeneticsInputDataDialog.java
new file mode 100644
index 0000000..d9ae200
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/dialogs/EditEpigeneticsInputDataDialog.java
@@ -0,0 +1,184 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.gui.dialogs;
+
+import net.miginfocom.swing.MigLayout;
+import org.bioinfo.ngs.qc.qualimap.gui.panels.EpigeneticAnalysisDialog;
+import org.bioinfo.ngs.qc.qualimap.process.EpiAnalysis;
+
+import javax.swing.*;
+import java.awt.*;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.io.File;
+
+/**
+ * Created by kokonech
+ * Date: 1/3/12
+ * Time: 6:29 PM
+ */
+public class EditEpigeneticsInputDataDialog extends JDialog {
+
+ JTextField replicateName, medipDataField, inputDataField;
+ JButton okButton, cancelButton, browseMedipDataButton, browseInputDataButton;
+ Component frame;
+ EpigeneticAnalysisDialog parentDlg;
+ boolean editMode;
+ int itemIndex;
+
+ public EditEpigeneticsInputDataDialog(EpigeneticAnalysisDialog parent) {
+
+ this.parentDlg = parent;
+ this.itemIndex = -1;
+ editMode = false;
+ initComponents();
+
+ }
+
+ public EditEpigeneticsInputDataDialog(EpigeneticAnalysisDialog parent, int itemIndex) {
+
+ this.parentDlg = parent;
+ this.itemIndex = itemIndex;
+ editMode = true;
+
+ initComponents();
+
+ EpiAnalysis.ReplicateItem itemToModify = parentDlg.getDataItem(itemIndex);
+ replicateName.setText(itemToModify.name);
+ medipDataField.setText(itemToModify.medipPath);
+ inputDataField.setText(itemToModify.inputPath);
+
+ }
+
+ void initComponents() {
+ frame = this;
+
+ getContentPane().setLayout(new MigLayout("insets 20"));
+
+ add(new JLabel("Replicate name:"));
+ replicateName = new JTextField(30);
+ add(replicateName, "wrap");
+
+ add(new JLabel("Sample BAM file"));
+ medipDataField = new JTextField(30);
+ add(medipDataField);
+ browseMedipDataButton = new JButton("...");
+ browseMedipDataButton.addActionListener(new BrowseButtonActionListener(this,medipDataField,
+ "BAM files", "bam"));
+ add(browseMedipDataButton, "wrap");
+
+ add(new JLabel("Control BAM file"));
+ inputDataField = new JTextField(30);
+ add(inputDataField);
+ browseInputDataButton = new JButton("...");
+ browseInputDataButton.addActionListener( new BrowseButtonActionListener(this, inputDataField,
+ "BAM files", "bam"));
+ add(browseInputDataButton, "wrap");
+
+ JPanel buttonPanel = new JPanel();
+ buttonPanel.setLayout(new MigLayout("insets 10"));
+ okButton = new JButton("Ok");
+ okButton.addActionListener( new ActionListener() {
+ @Override
+ public void actionPerformed(ActionEvent actionEvent) {
+ String errorMessage = validateInputData();
+ if (errorMessage.isEmpty()) {
+ EpiAnalysis.ReplicateItem item = new EpiAnalysis.ReplicateItem();
+ item.name = replicateName.getText();
+ item.inputPath = inputDataField.getText();
+ item.medipPath = medipDataField.getText();
+
+ if (editMode) {
+ parentDlg.replaceDataItem(itemIndex, item);
+ } else {
+ parentDlg.addDataItem(item);
+ }
+ setVisible(false);
+ } else {
+ JOptionPane.showMessageDialog(frame, errorMessage, "Input error", JOptionPane.ERROR_MESSAGE);
+ }
+ }
+ });
+
+ cancelButton = new JButton("Cancel");
+ cancelButton.addActionListener( new ActionListener() {
+ @Override
+ public void actionPerformed(ActionEvent actionEvent) {
+ setVisible(false);
+ }
+ });
+
+ buttonPanel.add(okButton);
+ buttonPanel.add(cancelButton, "wrap");
+
+ add(buttonPanel, "align right, span, wrap");
+
+
+ pack();
+ setTitle("Input sample data");
+ setResizable(false);
+
+ }
+
+ String validateInputData() {
+
+ if (replicateName.getText().isEmpty()) {
+ return "Replicate name is empty!";
+ }
+
+ String medipDataPath = medipDataField.getText();
+
+ if (medipDataPath.isEmpty()) {
+ return "Medip input data path is empty!";
+ }
+
+ File medipDataFile = new File(medipDataPath);
+ if (!medipDataFile.exists()) {
+ return "Medip input data file doesn't exist!";
+ }
+
+ String inputDataPath = inputDataField.getText();
+
+ if (inputDataPath.isEmpty()) {
+ return "Control input data path is empty!";
+ }
+
+ File inputDataFile = new File(inputDataPath);
+ if (!inputDataFile.exists()) {
+ return "Control input data file doesn't exist!";
+ }
+
+
+ return "";
+ }
+
+
+
+
+
+
+
+
+
+
+
+
+}
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/dialogs/EditSampleInfoDialog.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/dialogs/EditSampleInfoDialog.java
new file mode 100644
index 0000000..4d59f27
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/dialogs/EditSampleInfoDialog.java
@@ -0,0 +1,177 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.gui.dialogs;
+
+import net.miginfocom.swing.MigLayout;
+import org.bioinfo.ngs.qc.qualimap.gui.panels.MultisampleBamQcDialog;
+import org.bioinfo.ngs.qc.qualimap.process.SampleInfo;
+
+import javax.swing.*;
+import java.awt.*;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.KeyEvent;
+import java.awt.event.KeyListener;
+import java.io.File;
+
+/**
+ * Created by kokonech
+ * Date: 6/6/14
+ * Time: 3:17 PM
+ */
+public class EditSampleInfoDialog extends JDialog implements KeyListener {
+
+ MultisampleBamQcDialog parentDlg;
+ JTextField sampleName, pathField;
+ JButton okButton, cancelButton, browseSampleButton;
+ Component frame;
+ boolean editMode;
+ int itemIndex;
+
+ public EditSampleInfoDialog( MultisampleBamQcDialog parent) {
+
+ this.parentDlg = parent;
+ this.itemIndex = -1;
+ editMode = false;
+ initComponents();
+
+ int sampleIndex = parent.getItemCount() + 1;
+ sampleName.setText("Sample" + sampleIndex);
+ for (Component c : getContentPane().getComponents()) {
+ c.addKeyListener(this);
+ }
+
+ }
+
+ public EditSampleInfoDialog(MultisampleBamQcDialog parent, int itemIndex) {
+
+ this.parentDlg = parent;
+ this.itemIndex = itemIndex;
+ editMode = true;
+
+ initComponents();
+
+ SampleInfo itemToModify = parentDlg.getDataItem(itemIndex);
+ sampleName.setText(itemToModify.name);
+ pathField.setText(itemToModify.path);
+
+
+ }
+
+ void initComponents() {
+ frame = this;
+ getContentPane().setLayout(new MigLayout("insets 20"));
+
+ add(new JLabel("Sample name:"));
+ sampleName = new JTextField(30);
+ add(sampleName, "wrap");
+
+ add(new JLabel("Path"));
+ pathField = new JTextField(30);
+ add(pathField);
+ browseSampleButton = new JButton("...");
+ browseSampleButton.addActionListener(
+ new BrowseButtonActionListener(this, pathField, "BAM QC result or raw BAM file", true) );
+ add(browseSampleButton, "wrap");
+
+ JPanel buttonPanel = new JPanel();
+ buttonPanel.setLayout(new MigLayout("insets 10"));
+ okButton = new JButton("OK");
+ okButton.addActionListener( new ActionListener() {
+ @Override
+ public void actionPerformed(ActionEvent actionEvent) {
+ String errorMessage = validateInputData();
+ if (errorMessage.isEmpty()) {
+ SampleInfo item = new SampleInfo();
+ item.name = sampleName.getText();
+ item.path = pathField.getText();
+ if (editMode) {
+ parentDlg.replaceDataItem(itemIndex, item);
+ } else {
+ parentDlg.addDataItem(item);
+ }
+ setVisible(false);
+ } else {
+ JOptionPane.showMessageDialog(frame, errorMessage, "Input error", JOptionPane.ERROR_MESSAGE);
+ }
+ }
+ });
+
+ cancelButton = new JButton("Cancel");
+ cancelButton.addActionListener( new ActionListener() {
+ @Override
+ public void actionPerformed(ActionEvent actionEvent) {
+ setVisible(false);
+ }
+ });
+
+ buttonPanel.add(okButton);
+ buttonPanel.add(cancelButton, "wrap");
+
+ add(buttonPanel, "align right, span, wrap");
+
+
+ pack();
+ setTitle("Sample data");
+ setResizable(false);
+
+ }
+
+ @Override
+ public void keyTyped(KeyEvent e) {
+ // DO NOTHING
+ }
+
+ @Override
+ public void keyPressed(KeyEvent keyEvent) {
+ int code = keyEvent.getKeyCode();
+ if(code == KeyEvent.VK_ESCAPE){
+ setVisible(false);
+ }
+ }
+
+ @Override
+ public void keyReleased(KeyEvent e) {
+ // DO NOTHING.
+ }
+
+ String validateInputData() {
+
+ if (sampleName.getText().isEmpty()) {
+ return "Sample name is empty!";
+ }
+
+ String samplePath = pathField.getText();
+
+ if (samplePath.isEmpty()) {
+ return "Sample path is empty!";
+ }
+
+ File sampleDataFile = new File(samplePath);
+ if (!sampleDataFile.exists()) {
+ return "Sample file doesn't exist!";
+ }
+
+
+ return "";
+ }
+
+}
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/dialogs/ExportGeneListDialog.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/dialogs/ExportGeneListDialog.java
new file mode 100644
index 0000000..f4552b4
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/dialogs/ExportGeneListDialog.java
@@ -0,0 +1,210 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.gui.dialogs;
+
+import net.miginfocom.swing.MigLayout;
+import org.bioinfo.ngs.qc.qualimap.common.Constants;
+
+import javax.swing.*;
+import java.awt.*;
+import java.awt.datatransfer.Clipboard;
+import java.awt.datatransfer.StringSelection;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.io.*;
+import java.util.HashMap;
+
+/**
+ * Created by kokonech
+ * Date: 1/26/12
+ * Time: 12:26 PM
+ */
+public class ExportGeneListDialog extends JDialog implements ActionListener {
+
+ JTextField outputPathField;
+ JTextArea genesTextArea;
+ JButton okButton, cancelButton, copyButton;
+ JComboBox clusterNumberBox;
+ JScrollPane scrollPane;
+ HashMap<Integer, String[]> geneListMap;
+
+
+ public ExportGeneListDialog(String exprName, String dataName) throws IOException {
+
+ geneListMap = new HashMap<Integer, String[]>();
+ loadDataFile(dataName);
+
+ getContentPane().setLayout(new MigLayout("insets 20"));
+
+ add(new JLabel("Select cluster:"), "");
+ clusterNumberBox = new JComboBox();
+ for (int geneNum : geneListMap.keySet()) {
+ clusterNumberBox.addItem(geneNum);
+ }
+ add(clusterNumberBox, "wrap");
+
+ add(new JLabel("Output:"), "");
+
+ outputPathField = new JTextField(40);
+ add(outputPathField, "grow");
+
+ JButton browseOutputPathButton = new JButton("...");
+ browseOutputPathButton.addActionListener(new BrowseButtonActionListener(this,
+ outputPathField, "Counts file", false) );
+ add(browseOutputPathButton, "wrap");
+
+ add(new JLabel("Preview"), "wrap");
+ genesTextArea = new JTextArea(10,40);
+ genesTextArea.setEditable(false);
+
+ scrollPane = new JScrollPane();
+ scrollPane.setVerticalScrollBarPolicy(JScrollPane.VERTICAL_SCROLLBAR_ALWAYS);
+
+ clusterNumberBox.addActionListener( new ActionListener() {
+ @Override
+ public void actionPerformed(ActionEvent actionEvent) {
+ int index = Integer.parseInt(clusterNumberBox.getSelectedItem().toString());
+ String[] genes = geneListMap.get(index);
+ genesTextArea.setText("");
+ for (String gene : genes) {
+ genesTextArea.append(gene + "\n");
+ }
+ JScrollBar verticalScrollBar = scrollPane.getVerticalScrollBar();
+ verticalScrollBar.setValue(verticalScrollBar.getMinimum());
+ }
+ });
+ clusterNumberBox.setSelectedIndex(0);
+
+ scrollPane.setViewportView(genesTextArea);
+ add(scrollPane, "span, wrap");
+
+ JPanel buttonPanel = new JPanel();
+ buttonPanel.setLayout(new MigLayout("insets 20"));
+
+ copyButton = new JButton("Copy");
+ copyButton.setActionCommand("COPY");
+ copyButton.addActionListener(this);
+
+ okButton = new JButton("OK");
+ okButton.setActionCommand(Constants.OK_COMMAND);
+ okButton.addActionListener(this);
+ buttonPanel.add(okButton);
+ cancelButton = new JButton("Cancel");
+ cancelButton.setActionCommand(Constants.CANCEL_COMMAND);
+ cancelButton.addActionListener(this);
+ buttonPanel.add(cancelButton);
+
+ add( copyButton, "align left" );
+ add (buttonPanel, "span 2, align right, wrap");
+
+ pack();
+
+ setResizable(false);
+ setTitle("Export feature list: " + exprName);
+
+
+ }
+
+
+ private void loadDataFile(String fileName) throws IOException {
+
+ BufferedReader br = new BufferedReader(new FileReader(fileName));
+
+ String line;
+ int lineCount = 0;
+ int curClusterNumber = 0;
+
+ while ( (line = br.readLine()) != null) {
+ if (line.isEmpty()) {
+ continue;
+ }
+
+ if (line.startsWith("START_CLUSTER=")) {
+ lineCount = 1;
+ String value = line.split("=")[1].trim();
+ curClusterNumber = Integer.parseInt(value);
+ continue;
+ }
+
+ if (lineCount == 1 && curClusterNumber != 0) {
+ String[] genes = line.split("\\s");
+ geneListMap.put(curClusterNumber, genes);
+ }
+
+ lineCount++;
+
+ }
+
+
+
+ }
+
+ @Override
+ public void actionPerformed(ActionEvent actionEvent) {
+ if (actionEvent.getActionCommand().equals(Constants.OK_COMMAND)) {
+ String errMsg = validateInput();
+ if (!errMsg.isEmpty()) {
+ JOptionPane.showMessageDialog(this, errMsg, this.getTitle(), JOptionPane.ERROR_MESSAGE);
+ return;
+ }
+
+ try {
+ genesTextArea.write(new FileWriter(outputPathField.getText()));
+ } catch (IOException e) {
+ JOptionPane.showMessageDialog(this, "Failed writing to output file.",
+ this.getTitle(), JOptionPane.ERROR_MESSAGE);
+ return;
+ }
+ setVisible(false);
+
+
+ } else if (actionEvent.getActionCommand().equals(Constants.CANCEL_COMMAND)) {
+ setVisible(false);
+ } else if (actionEvent.getActionCommand().equals("COPY")) {
+ String selection = genesTextArea.getText();
+ StringSelection data = new StringSelection(selection);
+ Clipboard clipboard = Toolkit.getDefaultToolkit().getSystemClipboard();
+ clipboard.setContents(data, data);
+ }
+
+
+
+
+ }
+
+
+
+ private String validateInput() {
+
+ File outputFile = new File(outputPathField.getText());
+ try {
+ outputFile.createNewFile();
+ } catch (IOException e) {
+ return "Output file path is not valid!";
+ }
+ outputFile.delete();
+
+ return "";
+ }
+
+
+
+}
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/frames/HomeFrame.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/frames/HomeFrame.java
new file mode 100644
index 0000000..1f14490
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/frames/HomeFrame.java
@@ -0,0 +1,880 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.gui.frames;
+
+import java.awt.*;
+import java.awt.event.*;
+import java.io.*;
+import java.net.URI;
+import java.net.URISyntaxException;
+import java.util.*;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
+import javax.swing.*;
+import javax.swing.event.ChangeEvent;
+import javax.swing.event.ChangeListener;
+
+import org.bioinfo.commons.io.utils.FileUtils;
+import org.bioinfo.commons.log.Logger;
+import org.bioinfo.ngs.qc.qualimap.common.AnalysisType;
+import org.bioinfo.ngs.qc.qualimap.common.AppSettings;
+import org.bioinfo.ngs.qc.qualimap.common.Constants;
+import org.bioinfo.ngs.qc.qualimap.gui.dialogs.AboutDialog;
+import org.bioinfo.ngs.qc.qualimap.gui.dialogs.ComputeCountsDialog;
+import org.bioinfo.ngs.qc.qualimap.gui.dialogs.ExportGeneListDialog;
+import org.bioinfo.ngs.qc.qualimap.gui.panels.*;
+import org.bioinfo.ngs.qc.qualimap.gui.utils.*;
+import org.bioinfo.ngs.qc.qualimap.main.NgsSmartMain;
+
+
+/**
+ * Class that manages the principal frames of the application.
+ *
+ * @author Luis Miguel Cruz
+ * @author kokonech
+ */
+
+public class HomeFrame extends JFrame implements WindowListener, ActionListener, MouseListener {
+ private static final long serialVersionUID = -3290549319383957609L;
+
+ public static final String outputpath =File.separator+"tmp"+File.separator + "qualimap";
+
+ public static Font defaultFont = new Font(Font.DIALOG, Font.PLAIN, 12);
+ //public static Font smallFont = new Font(Font.DIALOG, Font.PLAIN, 10);
+ public static Font defaultFontItalic = new Font(Font.DIALOG, Font.ITALIC, 12);
+ private static final int FRAME_WIDTH = 1000;
+ private static final int FRAME_HEIGHT = 600;
+ private static final String WM_COMMAND_EXPORT_GENE_LIST = "exportgenelist";
+ private static final String WM_COMMAND_EXIT = "exit";
+ private static final String WM_COMMAND_ABOUT = "about";
+ private static final String WM_COMMAND_OPEN_MANUAL = "manual";
+ private static final String WM_COMMAND_CLOSE_TABS = "closealltabs";
+ private static final String WM_COMMAND_WEB_BIOINFO = "bioinfoweb";
+ private static final String WM_COMMAND_WEB_QUALIMAP = "qualionline";
+ private int screenHeight;
+ private int screenWidth;
+
+ private static final String WM_COMMAND_EXPORT_HTML = "exporthtml";
+ private static final String WM_COMMAND_EXPORT_PDF = "exportpdf";
+
+ public static final String WM_COMMAND_BAMQC = "bamqc";
+ public static final String WM_COMMAND_RNASEQQC = "rnaseqqc";
+ public static final String WM_COMMAND_COUNTSQC = "counts";
+ public static final String WM_COMMAND_BAMQC_MS = "bamqc-multi";
+ public static final String WM_COMMAND_CLUSTERING = "clustering";
+ public static final String WM_COMMAND_CALC_COUNTS = "calc-counts";
+
+
+ // Menu items with configurable state
+ JMenuItem exportToPdfItem, exportToHtmlItem, exportGeneListItem, closeAllTabsItem;
+
+ /** Logger to print information */
+ protected Logger logger;
+
+ /**
+ * Variable to manage the path of the qualimap folder where we have the R
+ * scripts and resources without compress
+ */
+ private String qualimapFolder;
+ private Dimension dim;
+
+ /** Variable to contains the tabs of the window */
+ private JTabbedPane aTabbedPane;
+ /**
+ * Variable that contains the list of paths from the output folders for each
+ * tab in the program
+ */
+ private Map<Component,TabPageController> tabsPropertiesMap;
+
+ /** Dialog to show beside the window */
+ private JDialog popUpDialog;
+
+ public boolean isWebStart;
+ private SplashWindow splashWindow;
+ private boolean rIsAvailable;
+ private boolean countsQCPackagesAvailable;
+ private boolean clusteringPacakgesAvailble;
+
+ private static class TabbedPaneListener implements ContainerListener, ChangeListener {
+
+ HomeFrame homeFrame;
+
+ TabbedPaneListener(HomeFrame homeFrame) {
+ this.homeFrame = homeFrame;
+ }
+
+ @Override
+ public void stateChanged(ChangeEvent changeEvent) {
+ homeFrame.updateMenuBar();
+ }
+
+ @Override
+ public void componentAdded(ContainerEvent containerEvent) {
+ homeFrame.updateMenuBar();
+ }
+
+ @Override
+ public void componentRemoved(ContainerEvent containerEvent) {
+ Component componentToRemove = containerEvent.getChild();
+ homeFrame.tabsPropertiesMap.remove(componentToRemove);
+ homeFrame.updateMenuBar();
+ }
+ }
+
+
+ public static void main(String[] args) {
+ SwingUtilities.invokeLater(new Runnable() {
+ public void run() {
+ new HomeFrame(null);
+ }
+ });
+ }
+
+ public HomeFrame(String homeFolder) {
+ super("Qualimap " + NgsSmartMain.APP_VERSION);
+ isWebStart = isRunningJavaWebStart();
+ if(isWebStart){
+ copyFilesFromResourcesToFolder();
+ }
+ if(homeFolder == null){
+ setQualimapFolder(new File("").getAbsolutePath()+File.separator);
+ } else {
+ setQualimapFolder(homeFolder);
+ }
+ logger = new Logger(this.getClass().getName());
+ logger.println("Qualimap home is " + getQualimapFolder());
+ initGUI();
+ this.setLocationRelativeTo(null);
+ this.setVisible(true);
+ }
+
+ private void copyFilesFromResourcesToFolder() {
+
+ //TODO: is this ever tested?
+ String outputpath = new File("").getAbsolutePath()+File.separator+".qualimap"+File.separator;
+ this.setQualimapFolder(outputpath);
+
+ createDirectory(outputpath+"scripts"+ File.separator);
+ File newFile = new File(outputpath+"scripts"+ File.separator +"qualimapRscript.r");
+ createFile("/org/bioinfo/ngs/qc/qualimap/scripts/qualimapRscript.r",newFile);
+ newFile = new File(outputpath+"scripts"+ File.separator +"qualimapRfunctions.r");
+ createFile("/org/bioinfo/ngs/qc/qualimap/scripts/qualimapRfunctions.r",newFile);
+
+ createDirectory(outputpath+"species"+ File.separator);
+ newFile = new File(outputpath+"species"+ File.separator +Constants.FILE_SPECIES_INFO_HUMAN);
+ createFile("/org/bioinfo/ngs/qc/qualimap/species/"+Constants.FILE_SPECIES_INFO_HUMAN, newFile);
+ newFile = new File(outputpath+"species"+ File.separator +Constants.FILE_SPECIES_GROUPS_HUMAN);
+ createFile("/org/bioinfo/ngs/qc/qualimap/species/"+Constants.FILE_SPECIES_GROUPS_HUMAN, newFile);
+ newFile = new File(outputpath+"species"+ File.separator +Constants.FILE_SPECIES_INFO_MOUSE);
+ createFile("/org/bioinfo/ngs/qc/qualimap/species/"+Constants.FILE_SPECIES_INFO_MOUSE, newFile);
+ newFile = new File(outputpath+"species"+ File.separator +Constants.FILE_SPECIES_GROUPS_MOUSE);
+ createFile("/org/bioinfo/ngs/qc/qualimap/species/"+Constants.FILE_SPECIES_GROUPS_MOUSE, newFile);
+ }
+
+
+ private String checkForRScript() {
+
+ String errMsg = "";
+
+ try {
+ String testCommand = AppSettings.getGlobalSettings().getPathToRScript() + " --version";
+ Process p = Runtime.getRuntime().exec( testCommand );
+ BufferedReader outputReader = new BufferedReader( new InputStreamReader(
+ new SequenceInputStream( p.getInputStream(), p.getErrorStream() )
+ ) );
+ int res = p.waitFor();
+ if (res != 0) {
+ return "Rscript process resulted with non-zero exit code";
+ }
+
+ String output = outputReader.readLine();
+ Pattern pattern = Pattern.compile("(\\d).([\\d]+)");
+ Matcher matcher = pattern.matcher(output);
+ boolean versionOk = false;
+ if (matcher.find() ) {
+ int majorVersion = Integer.parseInt( matcher.group(1) );
+ if (majorVersion < 2 ) {
+ versionOk = false;
+ } else if (majorVersion == 2) {
+ int minorVersion = Integer.parseInt( matcher.group(2) );
+ if (minorVersion >= 14) {
+ versionOk = true;
+ }
+
+ } else {
+ versionOk = true;
+ }
+ }
+
+ if (!versionOk) {
+ errMsg = "Unsupported version of RScript " + output;
+ errMsg += "Please use RScript 2.14. or higher. Refer to documentation for details.";
+ return errMsg;
+ }
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ return "Failed to launch RScript: " + e.getMessage();
+ }
+
+ return errMsg;
+ }
+
+ /**
+ * Returns fileChooser which remembers last opened dir
+ * @return The file chooser
+ */
+
+ public static JFileChooser getFileChooser() {
+ return new LODFileChooser();
+ }
+
+ private ArrayList<String> getMissingPackages() throws Exception {
+
+ String path = getQualimapFolder() + File.separator;
+ final StringBuffer buf = new StringBuffer();
+ final ArrayList<String> missingPackages = new ArrayList<String>();
+
+ String pathToRScript = AppSettings.getGlobalSettings().getPathToRScript();
+ final Process p = Runtime.getRuntime().exec(pathToRScript + " " + path + "scripts/init.r");
+ Thread outputReadingThread = new Thread(new Runnable() { public void run() {
+ BufferedReader outputReader = new BufferedReader( new InputStreamReader ( p.getInputStream() ) );
+ String line;
+ try {
+ while ((line = outputReader.readLine()) != null) {
+ buf.append(line);
+ if (line.contains("ERROR!")) {
+ String packageName = line.split(":")[1].trim();
+ System.out.println(packageName);
+ missingPackages.add(packageName);
+ }
+ }
+ } catch (IOException e) {
+ e.printStackTrace();
+ }
+ } } );
+ outputReadingThread.start();
+ int res = p.waitFor();
+ outputReadingThread.join();
+
+ if (res != 0) {
+ System.err.print("Rscript output:\n" + buf.toString() );
+ throw new RuntimeException("R process finished with non-zero exit code.");
+ }
+
+ return missingPackages;
+
+ }
+
+ private static String reportMissingPackages(ArrayList<String> missingPacages) {
+ StringBuilder message = new StringBuilder();
+
+ message.append("The following R packages are missing:\n");
+ for (String packageName : missingPacages) {
+ message.append("-").append(packageName).append("\n");
+ }
+ message.append("Features dependent on these packages are disabled.\n");
+ message.append("See user manual for details.\n");
+
+ return message.toString();
+ }
+
+
+ private static boolean isRunningJavaWebStart() {
+ String jwsVersion = System.getProperty("javawebstart.version", null);
+ if(jwsVersion!=null) System.out.println("Java Web Start Version: "+ jwsVersion);
+ return jwsVersion != null;
+ }
+
+ private static void createDirectory(String path) {
+ path = path.substring(0, path.lastIndexOf(File.separator));
+ boolean success = (new File(path)).mkdirs();
+ if (success) {
+ System.out.println("Created directory: " + path + " ");
+ }
+ }
+
+ public void initGUI() {
+ this.tabsPropertiesMap = new HashMap<Component, TabPageController>();
+ this.setDefaultCloseOperation(WindowConstants.DO_NOTHING_ON_CLOSE);
+ this.addWindowListener(this);
+
+ String errMsg = checkForRScript();
+ rIsAvailable = errMsg.isEmpty();
+ if (!rIsAvailable) {
+ logger.error(errMsg);
+ JOptionPane.showMessageDialog(this,
+ "" + "Some features of Qualimap, relying on the R language, will be disabled.\n" +
+ "To enable them please install R v2.14 or higher and\nmake sure the Rscript command is available" +
+ " from PATH.", "Rscript is not found",
+ JOptionPane.INFORMATION_MESSAGE);
+ }
+
+ if (rIsAvailable) {
+
+ try {
+ ArrayList<String> missingPackages = getMissingPackages();
+ countsQCPackagesAvailable = !missingPackages.contains("optparse") &&
+ !missingPackages.contains("NOISeq");
+ clusteringPacakgesAvailble = missingPackages.isEmpty();
+ if (!missingPackages.isEmpty()) {
+ String message = reportMissingPackages(missingPackages);
+ JOptionPane.showMessageDialog(this, message,
+ "Checking for required R packages",
+ JOptionPane.INFORMATION_MESSAGE);
+ }
+
+
+ } catch (Exception e) {
+ JOptionPane.showMessageDialog(this,
+ "Failed to check for R dependencies! RScript process finished with errors.",
+ "Checking for required R packages",
+ JOptionPane.INFORMATION_MESSAGE);
+ }
+
+
+ }
+
+ if (this.getClass().getResource(Constants.pathImages + "qualimap_logo_medium.png") != null ) {
+ splashWindow = new SplashWindow(this.getClass().getResource(Constants.pathImages + "qualimap_logo_medium.png"), this, 4000);
+ }
+
+ try {
+ Image iconImage = new ImageIcon(getClass().getResource(Constants.pathImages + "dna.png")).getImage();
+ this.setIconImage(iconImage);
+ } catch (NullPointerException e) {
+ logger.error("Incorrect path of the icon image");
+ }
+
+ setMainFrameSize();
+ createMenuBar();
+ updateMenuBar();
+
+ aTabbedPane = new JTabbedPane();
+ TabbedPaneListener tabbedPaneListener = new TabbedPaneListener(this);
+ aTabbedPane.addMouseListener(this);
+ aTabbedPane.addContainerListener(tabbedPaneListener);
+ aTabbedPane.addChangeListener(tabbedPaneListener);
+ this.getContentPane().add(aTabbedPane);
+
+ this.pack();
+ this.validate();
+ }
+
+
+
+ private void createMenuBar() {
+
+ setJMenuBar( new JMenuBar());
+ JMenu fileMenu = getMenu("File",KeyEvent.VK_F);
+ JMenu analysisMenu = getMenu("New Analysis",KeyEvent.VK_N);
+ JMenu toolsMenu = getMenu("Tools", KeyEvent.VK_T);
+ JMenu windowsMenu = getMenu("Windows", KeyEvent.VK_W);
+ JMenu helpMenu = getMenu("Help",KeyEvent.VK_H);
+
+ analysisMenu.setIcon(new ImageIcon(this.getClass().getResource(Constants.pathImages + "report.png")));
+ fileMenu.add(analysisMenu);
+
+ fileMenu.addSeparator();
+ exportToHtmlItem = addMenuItem("Export as HTML", WM_COMMAND_EXPORT_HTML, "save_zip.png", "ctrl pressed H");
+ fileMenu.add(exportToHtmlItem);
+ exportToPdfItem = addMenuItem("Export as PDF", WM_COMMAND_EXPORT_PDF, "save_pdf.png", "ctrl pressed P");
+ fileMenu.add(exportToPdfItem);
+ exportGeneListItem = addMenuItem("Export feature list", WM_COMMAND_EXPORT_GENE_LIST, "save_zip.png", "" );
+ fileMenu.add(exportGeneListItem);
+ fileMenu.addSeparator();
+ fileMenu.add(addMenuItem("Exit QualiMap", WM_COMMAND_EXIT, "door_out.png", "ctrl pressed Q"));
+
+ analysisMenu.add(addMenuItem(AnalysisType.BAM_QC.toString() , WM_COMMAND_BAMQC,
+ "chart_curve_add.png", "ctrl pressed G"));
+ analysisMenu.add(addMenuItem(AnalysisType.RNA_SEQ_QC.toString(), WM_COMMAND_RNASEQQC,
+ "chart_curve_add.png", "ctrl pressed R"));
+ JMenuItem analyzeCountsItem = addMenuItem(AnalysisType.COUNTS_QC.toString(),
+ WM_COMMAND_COUNTSQC, "chart_curve_add.png", "ctrl pressed C");
+ analyzeCountsItem.setEnabled(countsQCPackagesAvailable);
+ analysisMenu.add(analyzeCountsItem);
+
+ JMenuItem multiBamQcItem = addMenuItem(AnalysisType.MULTISAMPLE_BAM_QC.toString(),
+ WM_COMMAND_BAMQC_MS, "chart_curve_add.png", "");
+ analysisMenu.add(multiBamQcItem);
+
+
+ closeAllTabsItem = addMenuItem("Close All Tabs", WM_COMMAND_CLOSE_TABS, "", "ctrl pressed A");
+ windowsMenu.add(closeAllTabsItem);
+
+ toolsMenu.add(addMenuItem("Compute counts", WM_COMMAND_CALC_COUNTS, "calculator_edit.png", "ctrl pressed T"));
+ JMenuItem epiMenuItem = addMenuItem(AnalysisType.CLUSTERING.toString(), WM_COMMAND_CLUSTERING,
+ "chart_curve_add.png", "ctrl pressed E");
+ epiMenuItem.setEnabled(clusteringPacakgesAvailble);
+ toolsMenu.add(epiMenuItem);
+
+
+ if (checkForUserManual()) {
+ helpMenu.add(addMenuItem("User Manual", WM_COMMAND_OPEN_MANUAL, "help.png", "F1"));
+
+ }
+ helpMenu.add(addMenuItem("QualiMap Online", WM_COMMAND_WEB_QUALIMAP, "world_go.png", ""));
+ helpMenu.add(addMenuItem("CIPF BioInfo Web", WM_COMMAND_WEB_BIOINFO, "world_go.png", ""));
+ helpMenu.add(addMenuItem("About QualiMap", WM_COMMAND_ABOUT, "help.png","F12"));
+
+ JMenuBar menuBar = getJMenuBar();
+ menuBar.add(fileMenu);
+ menuBar.add(toolsMenu);
+ menuBar.add(windowsMenu);
+ menuBar.add(helpMenu);
+
+
+ }
+
+ private boolean checkForUserManual() {
+ File manualFile = new File(qualimapFolder + File.separator + "QualimapManual.pdf");
+ return manualFile.exists();
+ }
+
+ private JMenu getMenu(String name, int vkH) {
+ JMenu m = new JMenu();
+ m.setText(name);
+ m.setMnemonic(vkH);
+ m.setSize(new Dimension(30, 30));
+ return m;
+ }
+
+ private JMenuItem addMenuItem(String text, String command, String icon, String keys){
+ JMenuItem a = new JMenuItem();
+ a.setText(text);
+ a.setActionCommand(command);
+ a.addActionListener(this);
+ if ( icon.length() > 0 ) {
+ a.setIcon(new ImageIcon(this.getClass().getResource(Constants.pathImages + icon)));
+ }
+ if ( keys.length() > 0 ) {
+ a.setAccelerator(KeyStroke.getKeyStroke(keys));
+ }
+ return a;
+ }
+
+ public void addNewPane(final String inputFileName, final TabPageController tabProperties) {
+
+ this.getPopUpDialog().setVisible(false);
+ this.remove(this.getPopUpDialog());
+
+ AnalysisType typeAnalysis = tabProperties.getTypeAnalysis();
+
+ // Cutting the file name if necessary
+ String fileName = StringUtilsSwing.formatFileName(inputFileName);
+ ImageIcon ic = new ImageIcon(getClass().getResource(Constants.pathImages + "chart_curve.png"));
+ String prefix = typeAnalysis.toString() + ": ";
+
+ OpenLoadedStatistics op = new OpenLoadedStatistics(this,tabProperties);
+ JSplitPane statisticsPane = op.getLoadedStatistics();
+ tabsPropertiesMap.put(statisticsPane, tabProperties);
+
+ aTabbedPane.addTab(null, statisticsPane);
+ aTabbedPane.setTabComponentAt( aTabbedPane.indexOfComponent(statisticsPane),
+ new ButtonTabComponent(aTabbedPane, ic, prefix + fileName) );
+
+ aTabbedPane.setSelectedComponent(statisticsPane);
+
+ op.showInitialPage();
+
+ }
+
+ /**
+ * Private function that erase from the disk the temporal directories that
+ * contains the output data generated by the application.
+ */
+ private void deleteOutputFolders() {
+ File dir = new File(HomeFrame.outputpath);
+
+ if (dir.isDirectory()) {
+ Collection<TabPageController> tabPropertiesVOList = tabsPropertiesMap.values();
+ for (TabPageController tabController : tabPropertiesVOList) {
+ deleteOutputIndivifualFolder(tabController);
+ }
+ }
+ }
+
+ /*
+ * Private function that erase from the disk the temporal directory
+ * specified
+ */
+ private void deleteOutputIndivifualFolder(TabPageController tabPageController) {
+ String path = HomeFrame.outputpath + tabPageController.getOutputFolder();
+
+ try {
+ FileUtils.checkDirectory(path);
+ File outputDir = new File(path);
+ FileUtils.deleteDirectory(outputDir);
+ } catch (IOException e) {
+ logger.debug("Cannot delete directory " + path + ". It does not exists");
+ }
+ }
+
+ public void openUrl(final String url) {
+ Desktop desktop = Desktop.getDesktop();
+ if (desktop.isSupported(Desktop.Action.BROWSE)) {
+ try {
+ desktop.browse(new URI(url));
+ } catch (IOException e) {
+ System.out.println("Problem when trying to open a Browser: " + e.getMessage());
+ } catch (URISyntaxException e) {
+ System.out.println("Problem when trying to open a Browser: " + e.getMessage());
+ }
+ }
+ }
+
+ private void setMainFrameSize() {
+ final Toolkit toolkit = Toolkit.getDefaultToolkit();
+ final Dimension dimScreen = toolkit.getScreenSize();
+ screenHeight = dimScreen.height;
+ screenWidth = dimScreen.width;
+ this.setBounds((screenWidth - FRAME_WIDTH) / 2, (screenHeight - FRAME_HEIGHT) / 2, FRAME_WIDTH, FRAME_HEIGHT);
+ //this.setExtendedState(MAXIMIZED_BOTH);
+ this.setBackground(Color.lightGray);
+ this.dim = new Dimension(FRAME_WIDTH, FRAME_HEIGHT);
+ this.setMinimumSize(new Dimension(720, 440));
+ this.setMaximumSize(new Dimension(2000, 2000));
+ this.setPreferredSize(dim);
+ this.getContentPane().setLayout(new BorderLayout());
+ this.setResizable(true);
+ this.setState(Frame.NORMAL);
+ this.setSize(dim);
+ }
+
+ public void closeHomeFrame() {
+
+ int n = 0;
+
+ if (tabsPropertiesMap.size() > 0) {
+ n = JOptionPane.showConfirmDialog(this,
+ "There are open reports. Close QualiMap?", "QualiMap", JOptionPane.OK_CANCEL_OPTION);
+ }
+
+ if (n == 0) {
+ deleteOutputFolders();
+ System.exit(0);
+ }
+ }
+
+ public void windowActivated(final WindowEvent arg0) {}
+ public void windowClosed(final WindowEvent arg0) {}
+ public void windowClosing(final WindowEvent arg0) {
+ this.closeHomeFrame();
+ }
+ public void windowDeactivated(final WindowEvent arg0) {}
+ public void windowDeiconified(final WindowEvent arg0) {}
+ public void windowIconified(final WindowEvent arg0) {}
+ public void windowOpened(final WindowEvent arg0) {}
+
+ @Override
+ public void actionPerformed(ActionEvent e) {
+ splashWindow.setVisible(false);
+ if(e.getActionCommand().equalsIgnoreCase(WM_COMMAND_EXIT) ){
+ this.closeHomeFrame();
+ }
+ else if (e.getActionCommand().equalsIgnoreCase(WM_COMMAND_ABOUT)){
+ AboutDialog about = new AboutDialog(HomeFrame.this);
+ about.setDefaultCloseOperation(JDialog.DISPOSE_ON_CLOSE);
+ about.setLocationRelativeTo(this);
+ about.setVisible(true);
+ }
+ else if(e.getActionCommand().equalsIgnoreCase(WM_COMMAND_WEB_QUALIMAP)){
+ openUrl("http://bioinfo.cipf.es/qualimap");
+ }
+ else if(e.getActionCommand().equalsIgnoreCase(WM_COMMAND_WEB_BIOINFO)){
+ openUrl("http://bioinfo.cipf.es");
+ }
+ else if(e.getActionCommand().equalsIgnoreCase(WM_COMMAND_CLOSE_TABS)){
+ if (aTabbedPane != null && aTabbedPane.getTabCount() > 0) {
+ int res = JOptionPane.showConfirmDialog(this,
+ "Close all tabs?", "QualiMap", JOptionPane.OK_CANCEL_OPTION);
+ if (res == 0) {
+ aTabbedPane.removeAll();
+ aTabbedPane = new JTabbedPane();
+ this.validate();
+ }
+ }
+ }else if(e.getActionCommand().equalsIgnoreCase(WM_COMMAND_EXPORT_HTML)){
+ if (aTabbedPane != null && aTabbedPane.getTabCount() > 0) {
+
+ TabPageController tabProperties = getSelectedTabPageController();
+
+ // We test if this tab has result values or is an input tab
+ if (tabProperties != null && tabProperties.getReporters().size() > 0) {
+ SavePanel pathSaveDialog = new SavePanel();
+ popUpDialog = pathSaveDialog.getExportToHtmlFilePanel(this);
+ popUpDialog.setModal(true);
+ popUpDialog.setDefaultCloseOperation(JDialog.DISPOSE_ON_CLOSE);
+ popUpDialog.setLocationRelativeTo(this);
+ popUpDialog.setVisible(true);
+ } else {
+ JOptionPane.showMessageDialog(this, "Can not export to HTML!", "Error", JOptionPane.ERROR_MESSAGE);
+ }
+ }
+ } else if(e.getActionCommand().equalsIgnoreCase(WM_COMMAND_EXPORT_PDF)){
+ if (aTabbedPane != null && aTabbedPane.getTabCount() > 0) {
+ TabPageController tabProperties = getSelectedTabPageController();
+
+ // We test if this tab has result values or is an input tab
+ if (tabProperties != null && tabProperties.getReporters().size() > 0) {
+ exportToPdf();
+ } else {
+ JOptionPane.showMessageDialog(this, "Can not export PDF!", "Error", JOptionPane.ERROR_MESSAGE);
+ }
+ }
+ } else if(e.getActionCommand().equalsIgnoreCase(WM_COMMAND_BAMQC)){
+ runBamQC();
+ }else if(e.getActionCommand().equalsIgnoreCase(WM_COMMAND_RNASEQQC)){
+ runRnaSeqQC();
+ }else if(e.getActionCommand().equalsIgnoreCase(WM_COMMAND_COUNTSQC)){
+ runMultisampleCountsQc();
+ }else if(e.getActionCommand().equalsIgnoreCase(WM_COMMAND_BAMQC_MS)){
+ runMultisampleBamQc();
+ }else if(e.getActionCommand().equals(WM_COMMAND_CLUSTERING)) {
+ runClusteringAnalysis();
+ } else if (e.getActionCommand().equals(WM_COMMAND_CALC_COUNTS)) {
+ showCountReadsDialog(this);
+ } else if (e.getActionCommand().equalsIgnoreCase(WM_COMMAND_EXPORT_GENE_LIST)) {
+ showExportGenesDialog(this, getSelectedTabPageController());
+ } else if (e.getActionCommand().equals(WM_COMMAND_OPEN_MANUAL)) {
+ openUserManual();
+ }
+ }
+
+
+ private void openUserManual() {
+ File manualFile = new File(qualimapFolder + File.separator + "QualimapManual.pdf");
+ try {
+ Desktop.getDesktop().open(manualFile);
+ } catch (IOException ex) {
+ JOptionPane.showMessageDialog(this,
+ "No application is registered for viewing PDF files.",
+ getTitle(),
+ JOptionPane.ERROR_MESSAGE);
+ }
+ }
+
+ public static void showExportGenesDialog(Component frame, TabPageController tabProperties) {
+ ExportGeneListDialog dlg;
+ try {
+ String exprName = tabProperties.getLoadedGraphicName();
+ if (exprName.isEmpty()) {
+ JOptionPane.showMessageDialog(frame, "There is no chart selected! Please select chart.",
+ "Export feature list", JOptionPane.ERROR_MESSAGE);
+ return;
+ }
+ String path = HomeFrame.outputpath + tabProperties.getOutputFolder() + "/" +
+ tabProperties.getLoadedGraphicName() + ".txt";
+ dlg = new ExportGeneListDialog(exprName, path);
+ dlg.setModal(true);
+ dlg.setDefaultCloseOperation(JDialog.DISPOSE_ON_CLOSE);
+ dlg.setLocationRelativeTo(frame);
+ dlg.setVisible(true);
+ } catch (IOException e) {
+ JOptionPane.showMessageDialog(frame, "Can not prepare feature list! "+ e.getMessage(),
+ "Export feature list", JOptionPane.ERROR_MESSAGE);
+ }
+
+ }
+
+
+ private void showPopUpDialog() {
+ popUpDialog.setModal(true);
+ popUpDialog.setDefaultCloseOperation(JDialog.DISPOSE_ON_CLOSE);
+ popUpDialog.setLocationRelativeTo(this);
+ popUpDialog.setVisible(true);
+ }
+
+ private void runBamQC(){
+ popUpDialog = new BamAnalysisDialog(this);
+ showPopUpDialog();
+ }
+
+ private void runRnaSeqQC(){
+ popUpDialog = new RNASeqQCDialog(this);
+ showPopUpDialog();
+ }
+
+
+ private void runMultisampleCountsQc() {
+ popUpDialog = new CountsQcDialog(this);
+ showPopUpDialog();
+ }
+
+ private void runMultisampleBamQc() {
+ popUpDialog = new MultisampleBamQcDialog(this);
+ showPopUpDialog();
+
+ }
+
+
+ static public void showCountReadsDialog(HomeFrame parent) {
+ ComputeCountsDialog dlg = new ComputeCountsDialog(parent);
+ dlg.setModal(true);
+ dlg.setDefaultCloseOperation(JDialog.DISPOSE_ON_CLOSE);
+ dlg.setLocationRelativeTo(parent);
+ dlg.setVisible(true);
+ }
+
+
+ private void runClusteringAnalysis(){
+ popUpDialog = new EpigeneticAnalysisDialog(this);
+ showPopUpDialog();
+ }
+
+ private void exportToPdf() {
+ SavePanel pathSaveDialog = new SavePanel();
+ popUpDialog = pathSaveDialog.getExportToPdfDialog(this);
+ popUpDialog.setModal(true);
+ popUpDialog.setDefaultCloseOperation(JDialog.DISPOSE_ON_CLOSE);
+ popUpDialog.setLocationRelativeTo(HomeFrame.this);
+ popUpDialog.setVisible(true);
+
+
+ }
+
+
+ public void updateMenuBar() {
+
+ boolean activeTabsAvailable = aTabbedPane != null && aTabbedPane.getTabCount() > 0;
+ boolean canExportGeneList = false;
+ if (activeTabsAvailable) {
+ TabPageController tabProperties = getSelectedTabPageController();
+ if (tabProperties != null ) {
+
+ AnalysisType typeAnalysis = tabProperties.getTypeAnalysis();
+
+ canExportGeneList = typeAnalysis == AnalysisType.CLUSTERING &&
+ !tabProperties.getLoadedGraphicName().isEmpty();
+
+ }
+ }
+
+ exportToPdfItem.setEnabled(activeTabsAvailable);
+ closeAllTabsItem.setEnabled(activeTabsAvailable);
+ exportToHtmlItem.setEnabled(activeTabsAvailable);
+ exportGeneListItem.setEnabled(canExportGeneList);
+
+
+
+ }
+
+ public TabPageController getSelectedTabPageController() {
+ Component selectedComponent = aTabbedPane.getSelectedComponent();
+ if (selectedComponent != null) {
+ return tabsPropertiesMap.get(selectedComponent);
+ } else {
+ return null;
+ }
+
+ }
+
+
+ public JFrame getCurrentInstance() {
+ return this;
+ }
+
+ public String getQualimapFolder() {
+ return qualimapFolder;
+ }
+
+ public void setQualimapFolder(String qualimapFolder) {
+ this.qualimapFolder = qualimapFolder;
+ //System.out.println("QualiMapHome: "+qualimapFolder);
+ }
+
+ public JDialog getPopUpDialog() {
+ return popUpDialog;
+ }
+
+ @Override
+ public void mouseClicked(MouseEvent event) {
+ // Events to change the tab name and close the selected tab
+ if (event.getButton() == MouseEvent.BUTTON3 && event.getClickCount() == 1 && tabsPropertiesMap.size() > 0) {
+ JPopupMenu popupMenu = new JPopupMenu();
+ JMenuItem renameBtn = new JMenuItem("Rename Tab");
+ //renameBtn.setIcon(new ImageIcon(getClass().getResource(Constants.pathImages + "chart_curve_edit.png")));
+ renameBtn.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent e) {
+ //Component tabPane =
+ ButtonTabComponent tabPane = (ButtonTabComponent) aTabbedPane.getTabComponentAt(aTabbedPane.getSelectedIndex());
+ String title = tabPane.getTitle();
+ //String title = aTabbedPane.getSelectedComponent().getName();
+ //showInputDialog(Component parentComponent, Object message, String title, int messageType, Icon icon, Object[] selectionValues, Object initialSelectionValue)
+ String temp = (String) JOptionPane.showInputDialog(null,"Enter the name for the tab", "Tab Name", JOptionPane.QUESTION_MESSAGE, null, null,title);
+ if(temp.length()>1){
+ tabPane.setTitle(temp);
+ //aTabbedPane.setTitleAt(aTabbedPane.getSelectedIndex(), temp);
+ }
+ }
+ });
+
+ popupMenu.add(renameBtn);
+ popupMenu.show(event.getComponent(), event.getX(), event.getY() - 10);
+ }
+ }
+
+ @Override
+ public void mouseEntered(MouseEvent arg0) {}
+ @Override
+ public void mouseExited(MouseEvent arg0) {}
+ @Override
+ public void mousePressed(MouseEvent arg0) {}
+ @Override
+ public void mouseReleased(MouseEvent arg0) {}
+
+
+ private boolean createFile(final String resource, final File file ) {
+ BufferedWriter bw = null;
+ BufferedReader br = null;
+ FileWriter fw;
+ InputStreamReader isr;
+ String temp;
+ try {
+ if (this.getClass().getResource(resource) != null){
+ /// write new propertyfile
+ fw = new FileWriter(file);
+ bw = new BufferedWriter(fw);
+ isr = new InputStreamReader(this.getClass().getResource(resource).openStream());
+ br = new BufferedReader(isr);
+ while ((temp = br.readLine()) != null) {
+ temp = temp.trim();
+ bw.write(temp);
+ bw.newLine();
+ }
+ }
+ return true;
+ } catch (final IOException e1) {
+ System.out.println("Error while creating file: " + file.getAbsolutePath() +"\nError: "+ e1.getMessage());
+ return false;
+ } finally{
+ try {
+ if(bw!=null)bw.close();
+ if(br!=null)br.close();
+ } catch (IOException e) {
+ e.printStackTrace();
+ }
+ }
+ }
+
+
+}
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/frames/SplashWindow.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/frames/SplashWindow.java
new file mode 100755
index 0000000..240fe02
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/frames/SplashWindow.java
@@ -0,0 +1,94 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+/*
+ * Blast2GO
+ * All Rights Reserved.
+ */
+package org.bioinfo.ngs.qc.qualimap.gui.frames;
+
+import java.awt.*;
+import java.awt.event.*;
+import java.io.File;
+import java.net.URL;
+
+import javax.swing.*;
+
+public class SplashWindow extends JWindow {
+ public SplashWindow(final File file, final HomeFrame f, final int waitTime) {
+ super(f);
+ final JLabel l = new JLabel(new ImageIcon(file.getPath()));
+ this.rest(l, f, waitTime);
+ }
+
+ public SplashWindow(final URL fileurl, final HomeFrame f, final int waitTime) {
+ super(f);
+ final JLabel l = new JLabel(new ImageIcon(fileurl));
+ this.rest(l, f, waitTime);
+ }
+
+ public SplashWindow(final String text, final HomeFrame f, final int waitTime) {
+ super(f);
+ final JLabel l = new JLabel(text);
+ l.setFont(new Font("Courier", Font.PLAIN, 6));
+ this.rest(l, f, waitTime);
+ }
+
+ private void rest(final JLabel l, final HomeFrame f, final int waitTime) {
+ this.getContentPane().add(l, BorderLayout.CENTER);
+ final Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
+ final Dimension labelSize = l.getPreferredSize();
+ this.setBounds((screenSize.width - labelSize.width) / 2, (screenSize.height - labelSize.height) / 2, labelSize.width, labelSize.height);
+ this.validate();
+ this.pack();
+ this.addMouseListener(new MouseAdapter() {
+ public void mousePressed(final MouseEvent e) {
+ SplashWindow.this.setVisible(false);
+ SplashWindow.this.dispose();
+ }
+ });
+ final int pause = waitTime;
+ final HomeFrame aMainGui = f;
+ final Runnable closerRunner = new Runnable() {
+ public void run() {
+ SplashWindow.this.setVisible(false);
+ aMainGui.setVisible(true);
+ SplashWindow.this.dispose();
+ }
+ };
+ final Runnable waitRunner = new Runnable() {
+ public void run() {
+ try {
+ Thread.sleep(pause);
+ SwingUtilities.invokeAndWait(closerRunner);
+ } catch (Exception e) {
+ System.out.println(e.getMessage());
+ // can catch InvocationTargetException
+ // can catch InterruptedException
+ }
+ }
+ };
+ this.setLocationRelativeTo(f);
+ this.setVisible(true);
+ final Thread splashThread = new Thread(waitRunner, "SplashThread");
+ splashThread.start();
+ }
+}
+
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/panels/BamAnalysisDialog.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/panels/BamAnalysisDialog.java
new file mode 100644
index 0000000..9011ff5
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/panels/BamAnalysisDialog.java
@@ -0,0 +1,484 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.gui.panels;
+
+import net.miginfocom.swing.MigLayout;
+import org.apache.commons.io.FilenameUtils;
+import org.bioinfo.commons.io.utils.FileUtils;
+import org.bioinfo.ngs.qc.qualimap.common.AnalysisType;
+import org.bioinfo.ngs.qc.qualimap.common.Constants;
+import org.bioinfo.ngs.qc.qualimap.common.LibraryProtocol;
+import org.bioinfo.ngs.qc.qualimap.gui.dialogs.AnalysisDialog;
+import org.bioinfo.ngs.qc.qualimap.gui.frames.HomeFrame;
+import org.bioinfo.ngs.qc.qualimap.gui.threads.BamAnalysisThread;
+import org.bioinfo.ngs.qc.qualimap.gui.utils.*;
+import org.bioinfo.ngs.qc.qualimap.process.BamStatsAnalysis;
+
+import javax.activation.MimetypesFileTypeMap;
+import javax.swing.*;
+import javax.swing.filechooser.FileFilter;
+import java.awt.*;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.io.File;
+import java.io.IOException;
+import java.util.*;
+
+
+/**
+ * Created by kokonech
+ * Date: 12/8/11
+ * Time: 11:18 AM
+ */
+public class BamAnalysisDialog extends AnalysisDialog implements ActionListener {
+
+ JButton pathDataFileButton, pathGffFileButton;
+ JTextField pathDataFile, pathGffFile, valueNw;
+ JSpinner numThreadsSpinner,numReadsPerBunchSpinner, minHmSizeSpinner;
+ JCheckBox drawChromosomeLimits, skipDuplicates, computeOutsideStats, advancedInfoCheckBox, analyzeRegionsCheckBox;
+ JCheckBox compareGcContentDistr, detectOverlapingPairs;
+ JComboBox<String> genomeGcContentCombo, protocolCombo;
+ JLabel labelPathDataFile, labelPathAditionalDataFile, labelNw,
+ labelNumThreads, labelNumReadsPerBunch, protocolLabel, minHmSizeLabel;
+ File inputFile, regionFile;
+
+ StringBuilder stringValidation;
+
+ final String startButtonText = ">>> Start analysis";
+
+ public BamAnalysisDialog(HomeFrame homeFrame) {
+
+ super(homeFrame, "Analyze alignment" );
+
+ getContentPane().setLayout(new MigLayout("insets 20"));
+
+ labelPathDataFile = new JLabel();
+ labelPathDataFile.setText("BAM/SAM file:");
+ add(labelPathDataFile, "");
+
+ pathDataFile = new JTextField(40);
+ pathDataFile.setToolTipText("Path to the alignment file. Note: BAM file has to be sorted by coordinate.");
+ add(pathDataFile, "grow");
+
+ pathDataFileButton = new JButton();
+ pathDataFileButton.setAction(getActionLoadBamFile());
+ pathDataFileButton.setText("...");
+ add(pathDataFileButton, "align center, wrap");
+
+ analyzeRegionsCheckBox = new JCheckBox("Analyze regions");
+ analyzeRegionsCheckBox.addActionListener(this);
+ analyzeRegionsCheckBox.setToolTipText("Check to only analyze the regions defined in the features file");
+ add(analyzeRegionsCheckBox, "wrap");
+
+ labelPathAditionalDataFile = new JLabel("Regions file (GFF/BED):");
+ add(labelPathAditionalDataFile, "");
+
+ pathGffFile = new JTextField(40);
+ pathGffFile.setToolTipText("Path to GFF/GTF or BED file containing regions of interest");
+ add(pathGffFile, "grow");
+
+ pathGffFileButton = new JButton();
+ pathGffFileButton.setAction(getActionLoadAdditionalFile());
+ pathGffFileButton.setText("...");
+ add(pathGffFileButton, "align center, wrap");
+
+ protocolLabel = new JLabel("Library strand specificity:");
+ add(protocolLabel);
+ String[] names = LibraryProtocol.getProtocolNames();
+ protocolCombo = new JComboBox<String>( names );
+ add(protocolCombo, "wrap");
+
+ computeOutsideStats = new JCheckBox("Analyze outside regions");
+ computeOutsideStats.setCursor(Cursor.getPredefinedCursor(Cursor.HAND_CURSOR));
+ computeOutsideStats.setToolTipText("<html>Check to perform a separate analysis for the genome " +
+ "<br>regions complement to those in the features file</html>");
+ add(computeOutsideStats, "wrap");
+
+
+ drawChromosomeLimits = new JCheckBox("Chromosome limits");
+ drawChromosomeLimits.setCursor(Cursor.getPredefinedCursor(Cursor.HAND_CURSOR));
+ drawChromosomeLimits.setToolTipText("Check to draw the chromosome limits");
+ drawChromosomeLimits.setSelected(true);
+ add(drawChromosomeLimits, "wrap");
+
+ skipDuplicates = new JCheckBox("Skip duplicates");
+ skipDuplicates.setCursor(Cursor.getPredefinedCursor(Cursor.HAND_CURSOR));
+ skipDuplicates.setToolTipText("Activate this option to skip duplicated alignments from analysis");
+ skipDuplicates.setSelected(false);
+ add(skipDuplicates, "");
+
+
+ detectOverlapingPairs = new JCheckBox("Detect overlapping paired-end reads");
+ detectOverlapingPairs.setCursor(Cursor.getPredefinedCursor(Cursor.HAND_CURSOR));
+ detectOverlapingPairs.setToolTipText("Activate this option to detect overlapping paired-end read" +
+ " alignments and compute adapted mean coverage.");
+ detectOverlapingPairs.setSelected(false);
+
+ add(detectOverlapingPairs, "wrap");
+
+
+ compareGcContentDistr = new JCheckBox("Compare GC content distribution with:");
+ compareGcContentDistr.addActionListener(this);
+ compareGcContentDistr.setToolTipText("Compare sample GC distribution with the corresponding genome");
+ add(compareGcContentDistr, "span 2, wrap");
+
+ Map<String,String> gcFileMap = BamStatsAnalysis.getGcContentFileMap();
+ String[] genomes = new String[gcFileMap.size()];
+ gcFileMap.keySet().toArray(genomes);
+ // small trick for human genome to be first
+ Arrays.sort(genomes);
+ genomeGcContentCombo = new JComboBox<String>( genomes );
+ add( genomeGcContentCombo, "gapleft 20, span 2, wrap" );
+
+ // Input Line of information (check to show the advance info)
+ advancedInfoCheckBox = new JCheckBox("Advanced options");
+ advancedInfoCheckBox.setCursor(Cursor.getPredefinedCursor(Cursor.HAND_CURSOR));
+ add(advancedInfoCheckBox,"wrap");
+
+ labelNw = new JLabel("Number of windows:");
+ add(labelNw, "gapleft 20");
+
+ valueNw = new JTextField(10);
+ valueNw.setDocument(new JTextFieldLimit(6, true));
+ valueNw.setText("" + Constants.DEFAULT_NUMBER_OF_WINDOWS);
+ valueNw.setToolTipText("Number of sampling windows across the genome");
+ add(valueNw, "wrap");
+
+ minHmSizeLabel = new JLabel("Homopolymer size:");
+ add(minHmSizeLabel, "gapleft 20");
+ minHmSizeSpinner = new JSpinner(new SpinnerNumberModel(Constants.DEFAULT_HOMOPOLYMER_SIZE, 2, 7, 1));
+ minHmSizeSpinner.setToolTipText("<html>Only homopolymers of this size or larger will be considered " +
+ "<br>when estimating number of homopolymer indels.</html>" );
+ add(minHmSizeSpinner, "wrap");
+
+ labelNumThreads = new JLabel("Number of threads:");
+ add(labelNumThreads, "gapleft 20");
+ int numCPUs = Runtime.getRuntime().availableProcessors();
+ numThreadsSpinner = new JSpinner(new SpinnerNumberModel(numCPUs, 1, numCPUs*2, 1));
+ numThreadsSpinner.setToolTipText("Number of computational threads");
+ add(numThreadsSpinner, "wrap");
+
+ labelNumReadsPerBunch = new JLabel("Size of the chunk:");
+ add(labelNumReadsPerBunch, "gapleft 20");
+ numReadsPerBunchSpinner = new JSpinner(new SpinnerNumberModel(Constants.DEFAULT_CHUNK_SIZE, 100, 5000, 1));
+ numReadsPerBunchSpinner.setToolTipText("<html>To speed up the computation reads are analyzed in chunks. " +
+ "Each bunch is analyzed by single thread. <br>This option controls the number of reads in the chunk." +
+ "<br>Smaller number may result in lower performance, " +
+ "but also the memory consumption will be reduced.</html>");
+ add(numReadsPerBunchSpinner, "wrap 20px");
+
+ advancedInfoCheckBox.addActionListener(this);
+
+ // Action done while the statistics graphics are loaded
+ setupProgressStream();
+ add(progressStream, "align center");
+
+ setupProgressBar();
+ add(progressBar, "grow, wrap 30px");
+
+ startAnalysisButton = new JButton();
+ startAnalysisButton.setAction(getActionLoadQualimap());
+ startAnalysisButton.setText(startButtonText);
+
+ add(new JLabel(""), "span 2");
+ add(startAnalysisButton, "wrap");
+
+ updateState();
+ pack();
+
+ setResizable(false);
+
+ }
+
+ public void updateState() {
+
+ boolean analyzeRegions = analyzeRegionsCheckBox.isSelected();
+ labelPathAditionalDataFile.setEnabled(analyzeRegions);
+ pathGffFile.setEnabled(analyzeRegions);
+ pathGffFileButton.setEnabled(analyzeRegions);
+ computeOutsideStats.setEnabled(analyzeRegions);
+ protocolCombo.setEnabled(analyzeRegions);
+ protocolLabel.setEnabled(analyzeRegions);
+
+ boolean advOptionsEnabled = advancedInfoCheckBox.isSelected();
+ valueNw.setEnabled(advOptionsEnabled);
+ labelNw.setEnabled(advOptionsEnabled);
+ labelNumThreads.setEnabled(advOptionsEnabled);
+ numThreadsSpinner.setEnabled(advOptionsEnabled);
+ numReadsPerBunchSpinner.setEnabled(advOptionsEnabled);
+ labelNumReadsPerBunch.setEnabled(advOptionsEnabled);
+ minHmSizeLabel.setEnabled(advOptionsEnabled);
+ minHmSizeSpinner.setEnabled(advOptionsEnabled);
+
+ genomeGcContentCombo.setEnabled(compareGcContentDistr.isSelected());
+ }
+
+
+ /**
+ * Action to load the input data file.
+ *
+ * @return AbstractAction with the event
+ */
+ private AbstractAction getActionLoadBamFile() {
+
+ return new AbstractAction() {
+ private static final long serialVersionUID = -8111339366112980049L;
+
+ boolean hasExtension(final String fileName, final String ext) {
+ return (fileName.substring(fileName.lastIndexOf(".") + 1).equalsIgnoreCase(ext));
+ }
+
+ public void actionPerformed(ActionEvent evt) {
+
+ JFileChooser fileChooser = HomeFrame.getFileChooser();
+
+ FileFilter filter = new FileFilter() {
+ public boolean accept(File fileShown) {
+ boolean result = true;
+
+ if (!fileShown.isDirectory() &&!hasExtension(fileShown.getName(), Constants.FILE_EXTENSION_BAM)
+ && !hasExtension(fileShown.getName(), Constants.FILE_EXTENSION_SAM) ) {
+ result = false;
+ }
+
+ return result;
+ }
+
+ public String getDescription() {
+ return ("BAM/SAM Files (*.bam, *.sam)");
+ }
+ };
+ fileChooser.setFileFilter(filter);
+
+ int valor = fileChooser.showOpenDialog(homeFrame.getCurrentInstance());
+
+ if (valor == JFileChooser.APPROVE_OPTION) {
+ pathDataFile.setText(fileChooser.getSelectedFile().getPath());
+ }
+ }
+ };
+
+ }
+
+ /**
+ * Action to calculate the qualimap with the input data.
+ *
+ * @return AbstractAction with the event
+ */
+ private AbstractAction getActionLoadQualimap() {
+
+ return new AbstractAction() {
+ private static final long serialVersionUID = 8329832238125153187L;
+
+ public void actionPerformed(ActionEvent evt) {
+ // We can load from file or from a BAM file
+ TabPageController tabPageController = new TabPageController(AnalysisType.BAM_QC);
+ if (validateInput()) {
+ // If the input has the required values, load the
+ // results
+ runAnalysis(tabPageController);
+ } else {
+ JOptionPane.showMessageDialog(null, stringValidation.toString(), "Error", 0);
+ }
+ }
+ };
+
+ }
+
+
+ /**
+ * Action to load the additional input data file.
+ *
+ * @return AbstractAction with the event
+ */
+ private AbstractAction getActionLoadAdditionalFile() {
+ return new AbstractAction() {
+ private static final long serialVersionUID = -1601146976209876607L;
+
+ public void actionPerformed(ActionEvent evt) {
+
+ JFileChooser fileChooser = HomeFrame.getFileChooser();
+
+ FileFilter filter = new FileFilter() {
+ public boolean accept(File fileShown) {
+ boolean result = true;
+
+ String ext = FilenameUtils.getExtension(fileShown.getName());
+
+ if (!fileShown.isDirectory() && !Constants.FILE_EXTENSION_REGION.containsKey(ext.toUpperCase())) {
+ result = false;
+ }
+
+ return result;
+ }
+
+ public String getDescription() {
+ return ("Region Files (*.gff *.gtf *.bed)");
+ }
+ };
+ fileChooser.setFileFilter(filter);
+ int valor = fileChooser.showOpenDialog(homeFrame.getCurrentInstance());
+
+ if (valor == JFileChooser.APPROVE_OPTION) {
+ pathGffFile.setText(fileChooser.getSelectedFile().getPath());
+ }
+ }
+ };
+
+ }
+
+ /**
+ * Test if the input data correct.
+ *
+ * @return boolean, true if the input data are correct.
+ */
+ private boolean validateInput() {
+ boolean validate = true;
+
+ stringValidation = new StringBuilder();
+
+ // Validation for the input data file
+ if ( !pathDataFile.getText().isEmpty() ) {
+ inputFile = new File(pathDataFile.getText());
+ String mimeType = new MimetypesFileTypeMap().getContentType(inputFile);
+ if (mimeType == null ) {
+ stringValidation.append(" • Incorrect MimeType for the input BAM/SAM file \n");
+ }
+ }
+
+ if (inputFile == null) {
+ stringValidation.append(" • The path to the SAM file is required \n");
+ }else {
+ try {
+ FileUtils.checkFile(inputFile);
+ } catch (IOException e) {
+ stringValidation.append(" • ").append( e.getMessage()).append(" \n");
+ }
+ }
+
+ // Validation for the regions file
+ if (analyzeRegionsCheckBox.isSelected()) {
+ if ( !pathGffFile.getText().isEmpty() ) {
+ regionFile = new File(pathGffFile.getText());
+ String mimeType = new MimetypesFileTypeMap().getContentType(regionFile);
+ if ( mimeType == null ) {
+ stringValidation.append(" • Incorrect MimeType for the regions data file \n");
+ }
+ }
+ if (regionFile == null) {
+ stringValidation.append(" • The path to the regions file is required \n");
+ } else {
+ try {
+ FileUtils.checkFile(regionFile);
+ } catch (IOException e) {
+ stringValidation.append(" • ").append(e.getMessage()).append("\n");
+ }
+ }
+ }
+
+ // If we have got any error, we reset the invalidate flag
+ if (stringValidation.length() > 0) {
+ validate = false;
+ }
+
+ return validate;
+ }
+
+ /*
+ * Function that execute the quality map program an show the results from
+ * the input data files
+ */
+ private synchronized void runAnalysis(TabPageController tabPageController) {
+ BamAnalysisThread t;
+ t = new BamAnalysisThread("BamAnalysisThread", this, tabPageController);
+
+ Thread.UncaughtExceptionHandler eh = new AnalysisDialog.ExceptionHandler(this);
+ t.setUncaughtExceptionHandler(eh);
+
+ t.start();
+
+ }
+
+ public int getNumberOfWindows() {
+ try {
+ return Integer.parseInt(valueNw.getText());
+ } catch (NumberFormatException ex) {
+ return Constants.DEFAULT_NUMBER_OF_WINDOWS;
+ }
+ }
+
+ public File getInputFile() {
+ return inputFile;
+ }
+
+ public File getRegionFile() {
+ return regionFile;
+ }
+
+ public boolean getDrawChromosomeLimits() {
+ return drawChromosomeLimits.isSelected();
+ }
+
+ public boolean getSkipDuplicatesStatus() {
+ return skipDuplicates.isSelected();
+ }
+
+ public boolean getOverlappingReadPairAlignmentStatus() {
+ return detectOverlapingPairs.isSelected();
+ }
+
+ public boolean getComputeOutsideRegions() {
+ return analyzeRegionsCheckBox.isSelected() && computeOutsideStats.isSelected();
+ }
+
+ public int getNumThreads() {
+ return ((SpinnerNumberModel)numThreadsSpinner.getModel()).getNumber().intValue();
+ }
+
+ public void addNewPane(TabPageController tabProperties) {
+ homeFrame.addNewPane(inputFile.getName(), tabProperties);
+ }
+
+ @Override
+ public void actionPerformed(ActionEvent actionEvent) {
+ updateState();
+ }
+
+ public boolean compareGcContentToPrecalculated() {
+ return compareGcContentDistr.isSelected();
+ }
+
+ public String getGenomeName() {
+ return genomeGcContentCombo.getSelectedItem().toString();
+ }
+
+ public int getBunchSize() {
+ return ((SpinnerNumberModel)numReadsPerBunchSpinner.getModel()).getNumber().intValue();
+ }
+
+ public LibraryProtocol getLibraryProtocol() {
+ return LibraryProtocol.getProtocolByName(protocolCombo.getSelectedItem().toString());
+ }
+
+ public int getMinHomopolymerSize() {
+ return ((SpinnerNumberModel) minHmSizeSpinner.getModel()).getNumber().intValue();
+ }
+}
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/panels/CountsQcDialog.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/panels/CountsQcDialog.java
new file mode 100644
index 0000000..440a8e0
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/panels/CountsQcDialog.java
@@ -0,0 +1,476 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.gui.panels;
+
+import net.miginfocom.swing.MigLayout;
+import org.bioinfo.ngs.qc.qualimap.common.AnalysisType;
+import org.bioinfo.ngs.qc.qualimap.common.Constants;
+import org.bioinfo.ngs.qc.qualimap.gui.dialogs.AnalysisDialog;
+import org.bioinfo.ngs.qc.qualimap.gui.dialogs.BrowseButtonActionListener;
+import org.bioinfo.ngs.qc.qualimap.gui.dialogs.EditCountsSampleInfoDialog;
+import org.bioinfo.ngs.qc.qualimap.gui.frames.HomeFrame;
+import org.bioinfo.ngs.qc.qualimap.gui.threads.CountsQCAnalysisThread;
+import org.bioinfo.ngs.qc.qualimap.gui.utils.TabPageController;
+import org.bioinfo.ngs.qc.qualimap.process.CountsSampleInfo;
+
+import javax.swing.*;
+import javax.swing.table.AbstractTableModel;
+import java.awt.*;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.util.*;
+import java.util.List;
+
+/**
+ * Created by kokonech
+ * Date: 5/15/14
+ * Time: 3:36 PM
+ */
+
+public class CountsQcDialog extends AnalysisDialog implements ActionListener {
+
+ private SampleDataTableModel sampleTableModel;
+ private JTable inputDataTable;
+ private JPanel buttonPanel;
+ private JButton addSampleButton, editSampleButton, removeSampleButton;
+ private JCheckBox compartativeAnalysisCheckBox, provideInfoFileCheckBox;
+ private JRadioButton infoFileButton, speciesButton;
+ private JTextField infoFileEdit, condition1NameEdit, condition2NameEdit;
+ private JLabel condition1Label, condition2Label, thresholdLabel;
+ private JSpinner thresholdSpinner;
+ private JButton browseInfoFileButton;
+ private JComboBox speciesCombo;
+
+ static final String INFO_FILE_TOOLTIP = "File containing the biological classification, " +
+ "gc content and lengths of features in the count files.";
+
+ static final String SPECIES_ITEM_TOOLTIP = "Qualimap provides the Ensembl biotype " +
+ "classification for selected species";
+
+ static class SampleDataTableModel extends AbstractTableModel {
+
+ java.util.List<CountsSampleInfo> sampleReplicateList;
+ final String[] columnNames = { "Sample name", "Path", "Column number", "Condition"};
+
+ public SampleDataTableModel() {
+ sampleReplicateList = new ArrayList<CountsSampleInfo>();
+ }
+
+ public void addItem(CountsSampleInfo item) {
+ sampleReplicateList.add(item);
+ fireTableDataChanged();
+ }
+
+ public void replaceItem(int index, CountsSampleInfo newItem) {
+ sampleReplicateList.set(index, newItem);
+ fireTableDataChanged();
+ }
+
+ public void removeItem(int index) {
+ sampleReplicateList.remove(index);
+ fireTableDataChanged();
+ }
+
+ @Override
+ public String getColumnName(int column) {
+ return columnNames[column];
+ }
+
+ @Override
+ public int getRowCount() {
+ return sampleReplicateList.size();
+ }
+
+ @Override
+ public int getColumnCount() {
+ return columnNames.length;
+ }
+
+ @Override
+ public Object getValueAt(int i, int j) {
+ CountsSampleInfo sampleInfo = sampleReplicateList.get(i);
+
+ if (j == 0) {
+ return sampleInfo.name;
+ } else if (j == 1) {
+ return sampleInfo.path;
+ } else if (j == 2) {
+ return sampleInfo.columnNum;
+ } else if (j == 3) {
+ return sampleInfo.conditionIndex;
+ } else {
+ return "";
+ }
+
+
+ }
+
+ public CountsSampleInfo getItem(int index) {
+ return sampleReplicateList.get(index);
+ }
+
+ public java.util.List<CountsSampleInfo> getItems() {
+ return sampleReplicateList;
+ }
+ }
+
+ public CountsQcDialog(HomeFrame homeFrame) {
+ super(homeFrame, "Counts QC");
+ getContentPane().setLayout(new MigLayout("insets 20"));
+
+ add(new JLabel("Samples:"), "span 2, wrap");
+
+ sampleTableModel = new SampleDataTableModel();
+ inputDataTable = new JTable(sampleTableModel);
+
+ JScrollPane scroller = new JScrollPane(inputDataTable);
+ scroller.setPreferredSize(new Dimension(700, 100));
+ add(scroller, "span, wrap");
+
+ buttonPanel = new JPanel();
+ buttonPanel.setLayout(new MigLayout("insets 0"));
+ addSampleButton = new JButton("Add");
+ addSampleButton.setActionCommand(Constants.COMMAND_ADD_ITEM);
+ addSampleButton.addActionListener(this);
+ buttonPanel.add(addSampleButton, "");
+ editSampleButton = new JButton("Edit");
+ editSampleButton.setActionCommand(Constants.COMMAND_EDIT_ITEM);
+ editSampleButton.addActionListener(this);
+ buttonPanel.add(editSampleButton, "");
+ removeSampleButton = new JButton("Remove");
+ removeSampleButton.setActionCommand(Constants.COMMAND_REMOVE_ITEM);
+ removeSampleButton.addActionListener(this);
+ buttonPanel.add(removeSampleButton, "wrap");
+ add(buttonPanel, "align right, span, wrap");
+
+ thresholdLabel = new JLabel();
+ thresholdLabel.setText("Counts threshold:");
+ add(thresholdLabel, "");
+
+ thresholdSpinner = new JSpinner(new SpinnerNumberModel(5, 1, 100, 1));
+ thresholdSpinner.setToolTipText("A feature is considered as detected if the corresponding number of counts is " +
+ "greater than this threshold.");
+ thresholdSpinner.setMaximumSize(new Dimension(120,100));
+ add(thresholdSpinner, "grow, wrap");
+
+ compartativeAnalysisCheckBox = new JCheckBox("Compare conditions");
+ compartativeAnalysisCheckBox.addActionListener(this);
+ add(compartativeAnalysisCheckBox, "wrap");
+
+ condition1Label = new JLabel("Condition 1 name:");
+ add(condition1Label);
+ condition1NameEdit = new JTextField(20);
+ condition1NameEdit.setText("Condition1");
+ add(condition1NameEdit, "wrap");
+
+ condition2Label = new JLabel("Condition 2 name:");
+ add(condition2Label);
+ condition2NameEdit = new JTextField(20);
+ condition2NameEdit.setText("Condition2");
+ add(condition2NameEdit, "wrap");
+
+ provideInfoFileCheckBox = new JCheckBox("Include feature classification");
+ provideInfoFileCheckBox.addActionListener(this);
+ add(provideInfoFileCheckBox, "wrap");
+
+ speciesButton = new JRadioButton("Species: ");
+ speciesButton.setSelected(true);
+ speciesButton.addActionListener(this);
+ speciesButton.setToolTipText(SPECIES_ITEM_TOOLTIP);
+ add(speciesButton);
+
+ String[] speicesComboItems = { Constants.TYPE_COMBO_SPECIES_HUMAN, Constants.TYPE_COMBO_SPECIES_MOUSE };
+ speciesCombo = new JComboBox<String>(speicesComboItems);
+ speciesCombo.setToolTipText(SPECIES_ITEM_TOOLTIP);
+ add(speciesCombo, "grow, wrap");
+
+ infoFileButton = new JRadioButton("Info file:");
+ infoFileButton.addActionListener(this);
+ infoFileButton.setToolTipText(INFO_FILE_TOOLTIP);
+ add(infoFileButton, "");
+
+ infoFileEdit = new JTextField(30);
+ infoFileEdit.setToolTipText(INFO_FILE_TOOLTIP);
+ add(infoFileEdit, "grow");
+
+ browseInfoFileButton = new JButton("...");
+ browseInfoFileButton.addActionListener( new BrowseButtonActionListener(homeFrame,
+ infoFileEdit, "Species files", "txt"));
+
+ add(browseInfoFileButton, "align center, wrap 30px");
+
+ ButtonGroup group = new ButtonGroup();
+ group.add(infoFileButton);
+ group.add(speciesButton);
+
+
+ add(new JLabel("Log"), "wrap");
+ setupLogArea();
+ add(logAreaScrollPane, "span, grow, wrap 30px");
+
+ // Action done while the statistics graphics are loaded
+ setupProgressStream();
+ add(progressStream, "align center");
+
+ setupProgressBar();
+ add(progressBar, "grow, wrap 30px");
+
+ startAnalysisButton = new JButton();
+ startAnalysisButton.addActionListener(this);
+ startAnalysisButton.setActionCommand(Constants.COMMAND_RUN_ANALYSIS);
+ startAnalysisButton.setText(">>> Run Analysis");
+
+ add(startAnalysisButton, "span, align right, wrap");
+
+ pack();
+
+ // Default data for testing
+ if (System.getenv("QUALIMAP_DEBUG") != null) {
+ CountsSampleInfo i1 = new CountsSampleInfo();
+ i1.name = "Infected1";
+ i1.path = "/home/kokonech/sample_data/counts/mb141.counts.txt";
+ i1.conditionIndex = 1;
+ i1.columnNum = 2;
+ sampleTableModel.addItem(i1);
+
+
+ CountsSampleInfo i2 = new CountsSampleInfo();
+ i2.name = "Infected2";
+ i2.path = "/home/kokonech/sample_data/counts/mb141.counts.txt";
+ i2.conditionIndex = 1;
+ i2.columnNum = 3;
+ sampleTableModel.addItem(i2);
+
+ CountsSampleInfo u1 = new CountsSampleInfo();
+ u1.name = "Uninfected1";
+ u1.path = "/home/kokonech/sample_data/counts/mb141.counts.txt";
+ u1.conditionIndex = 2;
+ u1.columnNum = 5;
+ sampleTableModel.addItem(u1);
+
+ CountsSampleInfo u2 = new CountsSampleInfo();
+ u2.name = "Uninfected2";
+ u2.path = "/home/kokonech/sample_data/counts/mb141.counts.txt";
+ u2.conditionIndex = 2;
+ u2.columnNum = 6;
+ sampleTableModel.addItem(u2);
+
+ }
+
+ updateState();
+ setResizable(false);
+
+
+
+
+ }
+
+ public int getItemCount() {
+ return sampleTableModel.getRowCount();
+ }
+
+ public CountsSampleInfo getDataItem(int index) {
+ return sampleTableModel.getItem(index);
+ }
+
+ public void addDataItem(CountsSampleInfo item) {
+ sampleTableModel.addItem(item);
+ updateState();
+ }
+
+ public void replaceDataItem(int itemIndex, CountsSampleInfo item) {
+ sampleTableModel.replaceItem(itemIndex, item);
+ updateState();
+ }
+
+ private void removeDataItem(int index) {
+ sampleTableModel.removeItem(index);
+ updateState();
+ }
+
+ public List<CountsSampleInfo> getDataItems() {
+ return sampleTableModel.getItems();
+ }
+
+ @Override
+ public void actionPerformed(ActionEvent actionEvent) {
+ String actionCommand = actionEvent.getActionCommand();
+
+ if ( actionCommand.equals(Constants.COMMAND_ADD_ITEM) ) {
+ EditCountsSampleInfoDialog dlg = new EditCountsSampleInfoDialog(this);
+ dlg.setModal(true);
+ dlg.setLocationRelativeTo(this);
+ dlg.setVisible(true);
+ } else if ( actionCommand.equals(Constants.COMMAND_REMOVE_ITEM) ) {
+ int index = inputDataTable.getSelectedRow();
+ if (index != -1 ) {
+ removeDataItem(index);
+ }
+ } else if ( actionCommand.equals(Constants.COMMAND_EDIT_ITEM) ) {
+ int index = inputDataTable.getSelectedRow();
+ if (index != -1) {
+ EditCountsSampleInfoDialog dlg = new EditCountsSampleInfoDialog(this, index);
+ dlg.setModal(true);
+ dlg.setLocationRelativeTo(this);
+ dlg.setVisible(true);
+ }
+ } else if ( actionCommand.equals(Constants.COMMAND_RUN_ANALYSIS) ) {
+
+ String errMsg = validateInput();
+ if (errMsg.isEmpty()) {
+ resetProgress();
+ TabPageController tabController = new TabPageController(AnalysisType.COUNTS_QC);
+ CountsQCAnalysisThread t = new CountsQCAnalysisThread(this, tabController );
+
+ Thread.UncaughtExceptionHandler eh = new AnalysisDialog.ExceptionHandler(this);
+ t.setUncaughtExceptionHandler(eh);
+
+ t.start();
+
+ } else {
+ JOptionPane.showMessageDialog(this, errMsg, "Validate Input", JOptionPane.ERROR_MESSAGE);
+ }
+ } else {
+ updateState();
+ }
+ }
+
+
+ String validateInput() {
+
+ if (sampleTableModel.getRowCount() == 0) {
+ return "No input data is provided!";
+ }
+
+ if (compartativeAnalysisCheckBox.isSelected()) {
+
+ if (sampleTableModel.getRowCount() == 0) {
+ return "Need at least 2 samples to compare conditions";
+ }
+ if (condition1NameEdit.getText().length() == 0) {
+ return "Condition 1 name is empty!";
+ }
+ if (condition2NameEdit.getText().length() == 0) {
+ return "Condition 2 name is empty!";
+ }
+
+ List<CountsSampleInfo> items = sampleTableModel.getItems();
+ int idx = items.get(0).conditionIndex;
+ boolean allSamplesSameIndex = true;
+ for (int i = 1; i < items.size(); ++i) {
+ if (items.get(i).conditionIndex != idx) {
+ allSamplesSameIndex = false;
+ break;
+ }
+ }
+
+ if (allSamplesSameIndex) {
+ return "All samples have the same condition!\n" +
+ "To perform comparison different conditions are required.";
+ }
+
+
+
+
+ }
+
+ if (provideInfoFileCheckBox.isSelected()) {
+ // Validation for info file
+ if (infoFileButton.isSelected() ) {
+ String infoFilePath = infoFileEdit.getText();
+ if (infoFilePath.isEmpty()) {
+ return "Info file path is empty!";
+ } else if (!validateInputFile(infoFilePath)) {
+ return "Info file does not exist!";
+ }
+
+ }
+ }
+
+ return "";
+ }
+
+ public void updateState() {
+ int numRows = inputDataTable.getRowCount();
+ removeSampleButton.setEnabled(numRows > 0);
+ editSampleButton.setEnabled(numRows > 0);
+
+ boolean provideInfoFile = provideInfoFileCheckBox.isSelected();
+
+ infoFileButton.setEnabled(provideInfoFile);
+ speciesButton.setEnabled(provideInfoFile);
+ infoFileEdit.setEnabled(infoFileButton.isSelected() && provideInfoFile);
+ browseInfoFileButton.setEnabled(infoFileButton.isSelected() && provideInfoFile);
+ speciesCombo.setEnabled(speciesButton.isSelected() && provideInfoFile);
+
+ boolean performComparison = compartativeAnalysisCheckBox.isSelected();
+ condition1NameEdit.setEnabled(performComparison);
+ condition1Label.setEnabled(performComparison);
+ condition2NameEdit.setEnabled(performComparison);
+ condition2Label.setEnabled(performComparison);
+
+ }
+
+ public Map<Integer,String> getConditionsMap() {
+ Map<Integer,String> cMap = new HashMap<Integer, String>();
+
+ cMap.put(1, condition1NameEdit.getText() );
+ cMap.put(2, condition2NameEdit.getText() );
+
+ return cMap;
+
+ }
+
+ public boolean infoFileIsProvided() {
+ return infoFileButton.isSelected();
+ }
+
+ public String getInfoFilePath() {
+ return infoFileEdit.getText();
+ }
+
+ public String getSelectedSpecies() {
+
+ String speciesName = speciesCombo.getSelectedItem().toString();
+
+ if (speciesName.equals(Constants.TYPE_COMBO_SPECIES_HUMAN)) {
+ return Constants.FILE_SPECIES_INFO_HUMAN_ENS68;
+ } else if (speciesName.equals(Constants.TYPE_COMBO_SPECIES_MOUSE)) {
+ return Constants.FILE_SPECIES_INFO_MOUSE_ENS68;
+ } else {
+ return "";
+ }
+ }
+
+ public boolean annotationIsProvided() {
+ return provideInfoFileCheckBox.isSelected();
+ }
+
+ public boolean performComparison() {
+ return compartativeAnalysisCheckBox.isSelected();
+ }
+
+ public int getCountsThreshold() {
+ return ((SpinnerNumberModel) thresholdSpinner.getModel()).getNumber().intValue();
+ }
+
+
+}
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/panels/EpigeneticAnalysisDialog.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/panels/EpigeneticAnalysisDialog.java
new file mode 100644
index 0000000..7efdab5
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/panels/EpigeneticAnalysisDialog.java
@@ -0,0 +1,409 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.gui.panels;
+
+import net.miginfocom.swing.MigLayout;
+import org.bioinfo.ngs.qc.qualimap.common.AnalysisType;
+import org.bioinfo.ngs.qc.qualimap.common.Constants;
+import org.bioinfo.ngs.qc.qualimap.gui.dialogs.AnalysisDialog;
+import org.bioinfo.ngs.qc.qualimap.gui.dialogs.BrowseButtonActionListener;
+import org.bioinfo.ngs.qc.qualimap.gui.dialogs.EditEpigeneticsInputDataDialog;
+import org.bioinfo.ngs.qc.qualimap.gui.frames.HomeFrame;
+import org.bioinfo.ngs.qc.qualimap.gui.threads.EpigeneticsAnalysisThread;
+import org.bioinfo.ngs.qc.qualimap.gui.utils.TabPageController;
+import org.bioinfo.ngs.qc.qualimap.process.EpiAnalysis;
+import org.bioinfo.ngs.qc.qualimap.process.EpiAnalysis.ReplicateItem;
+import org.bioinfo.ngs.qc.qualimap.common.DocumentUtils;
+
+
+import javax.swing.*;
+import javax.swing.table.AbstractTableModel;
+import java.awt.*;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.io.File;
+import java.util.*;
+import java.util.List;
+
+/**
+ * Created by kokonech
+ * Date: 1/3/12
+ * Time: 4:01 PM
+ */
+public class EpigeneticAnalysisDialog extends AnalysisDialog implements ActionListener{
+
+ JTextField regionsField, clustersField;
+ JSpinner leftOffsetSpinner, rightOffsetSpinner, stepSpinner, smoothingLengthSpinner;
+ JButton browseGeneSelectionButton;
+ JButton startAnalysisButton, addSampleButton, removeSampleButton, editSampleButton;
+ JTextField experimentName;
+ JComboBox vizTypeBox;
+ JTable inputDataTable;
+ JPanel buttonPanel, locationPanel;
+ SampleDataTableModel sampleTableModel;
+
+
+ static final boolean DEBUG = false;
+
+ public String getGeneSelectionPath() {
+ return regionsField.getText();
+ }
+
+ public String getLeftOffset() {
+ return leftOffsetSpinner.getValue().toString();
+ }
+
+ public String getRightOffset() {
+ return rightOffsetSpinner.getValue().toString();
+ }
+
+ public String getStep() {
+ return stepSpinner.getValue().toString();
+ }
+
+
+ public List<EpiAnalysis.ReplicateItem> getSampleItems() {
+ return sampleTableModel.getItems();
+ }
+
+ public String getClusterNumbers() {
+ return clustersField.getText().trim();
+ }
+
+ public String getInputDataName() {
+ return experimentName.getText();
+ }
+
+ public String getExperimentName() {
+ return experimentName.getText();
+ }
+
+
+ static class SampleDataTableModel extends AbstractTableModel {
+
+ List<ReplicateItem> sampleReplicateList;
+ final String[] columnNames = { "Replicate Name", "Sample BAM file", "Control BAM file"};
+
+ public SampleDataTableModel() {
+ sampleReplicateList = new ArrayList<EpiAnalysis.ReplicateItem>();
+ }
+
+ public void addItem(ReplicateItem item) {
+ sampleReplicateList.add(item);
+ fireTableDataChanged();
+ }
+
+ public void replaceItem(int index, EpiAnalysis.ReplicateItem newItem) {
+ sampleReplicateList.set(index, newItem);
+ fireTableDataChanged();
+ }
+
+ public void removeItem(int index) {
+ sampleReplicateList.remove(index);
+ fireTableDataChanged();
+ }
+
+ @Override
+ public String getColumnName(int column) {
+ return columnNames[column];
+ }
+
+ @Override
+ public int getRowCount() {
+ return sampleReplicateList.size();
+ }
+
+ @Override
+ public int getColumnCount() {
+ return columnNames.length;
+ }
+
+ @Override
+ public Object getValueAt(int i, int j) {
+ EpiAnalysis.ReplicateItem replicate = sampleReplicateList.get(i);
+
+ if (j == 0) {
+ return replicate.name;
+ } else if (j == 1) {
+ return replicate.medipPath;
+ } else if (j == 2) {
+ return replicate.inputPath;
+ } else {
+ return "";
+ }
+
+
+ }
+
+ public EpiAnalysis.ReplicateItem getItem(int index) {
+ return sampleReplicateList.get(index);
+ }
+
+ public List<EpiAnalysis.ReplicateItem> getItems() {
+ return sampleReplicateList;
+ }
+ }
+
+
+ public EpigeneticAnalysisDialog(HomeFrame homeFrame) {
+
+ super(homeFrame,"Cluster epigenomic signals") ;
+
+ getContentPane().setLayout(new MigLayout("insets 20"));
+
+ add(new JLabel("Experiment ID: "), "");
+ experimentName = new JTextField(20);
+ experimentName.setText("Experiment 1");
+ add(experimentName, "wrap");
+
+ add(new JLabel("Alignment data:"), "span 2, wrap");
+
+ sampleTableModel = new SampleDataTableModel();
+ inputDataTable = new JTable(sampleTableModel);
+ JScrollPane scroller = new JScrollPane(inputDataTable);
+ scroller.setPreferredSize(new Dimension(700, 100));
+ add(scroller, "span, wrap");
+
+ buttonPanel = new JPanel();
+ buttonPanel.setLayout(new MigLayout("insets 0"));
+
+ addSampleButton = new JButton("Add");
+ addSampleButton.setActionCommand(Constants.COMMAND_ADD_ITEM);
+ addSampleButton.addActionListener(this);
+ buttonPanel.add(addSampleButton, "");
+ editSampleButton = new JButton("Edit");
+ editSampleButton.setActionCommand(Constants.COMMAND_EDIT_ITEM);
+ editSampleButton.addActionListener(this);
+ buttonPanel.add(editSampleButton, "");
+ removeSampleButton = new JButton("Remove");
+ removeSampleButton.setActionCommand(Constants.COMMAND_REMOVE_ITEM);
+ removeSampleButton.addActionListener(this);
+ buttonPanel.add(removeSampleButton, "wrap");
+ add(buttonPanel, "align right, span, wrap");
+
+ // Gene selection
+ add(new JLabel("Regions of interest:"));
+ regionsField = new JTextField(40);
+ regionsField.setToolTipText("Path to annotation file in BED or GFF format");
+ add(regionsField, "grow");
+
+ browseGeneSelectionButton = new JButton();
+ browseGeneSelectionButton.setText("...");
+ String[] supportedExtentions = { "bed", "gff"};
+ browseGeneSelectionButton.addActionListener(
+ new BrowseButtonActionListener(this, regionsField,"Annotation files", supportedExtentions ));
+ add(browseGeneSelectionButton, "align center, wrap");
+
+ add(new JLabel("Location"), "span 2, wrap");
+
+ locationPanel = new JPanel();
+ locationPanel.setLayout(new MigLayout("insets 5"));
+
+ locationPanel.add(new JLabel("Upstream offset (bp):"));
+ leftOffsetSpinner = new JSpinner(new SpinnerNumberModel(2000, 1,1000000,1));
+ locationPanel.add(leftOffsetSpinner, "");
+ locationPanel.add(new JLabel("Downstream offset (bp):"));
+ rightOffsetSpinner = new JSpinner(new SpinnerNumberModel(500, 1,10000000,1));
+ locationPanel.add(rightOffsetSpinner, "");
+ locationPanel.add(new JLabel("Bin size (bp):"));
+ stepSpinner = new JSpinner(new SpinnerNumberModel(100, 1,10000,1));
+ locationPanel.add(stepSpinner, "wrap");
+ add(locationPanel, "span, wrap");
+
+ add(new JLabel("Number of clusters:"));
+ clustersField = new JTextField((20));
+ clustersField.setText("10,15,20,25,30");
+ add(clustersField, "wrap");
+
+ add(new JLabel("Fragment length (bp):"));
+ smoothingLengthSpinner = new JSpinner(new SpinnerNumberModel(300, 100,500,1));
+ add(smoothingLengthSpinner, "wrap");
+
+ String[] vizTypes = { "Heatmap", "Line" };
+ vizTypeBox = new JComboBox(vizTypes);
+ add(new JLabel("Visualization type:"), "");
+ add(vizTypeBox, "wrap");
+
+ add(new JLabel("Log"), "wrap");
+ setupLogArea();
+ add(logAreaScrollPane, "span, grow, wrap 30px");
+
+ setupProgressBar();
+ add(progressBar, "grow, wrap 30px");
+
+ startAnalysisButton = new JButton();
+ startAnalysisButton.setText(">>> Run Analysis");
+ startAnalysisButton.setActionCommand(Constants.COMMAND_RUN_ANALYSIS);
+ startAnalysisButton.addActionListener(this);
+ add(startAnalysisButton, "align right, span, wrap");
+
+
+ pack();
+
+ setResizable(false);
+
+ if (DEBUG) {
+
+ regionsField.setText("/home/kokonech/sample_data/clustering_sample/CpGIslandsByTakai.wihtNames.short.bed");
+
+ experimentName.setText("24h-i");
+
+ // add some preliminary data
+ EpiAnalysis.ReplicateItem item1 = new ReplicateItem();
+ item1.name = "24h-i_1";
+ item1.medipPath = "/home/kokonech/qualimapEpi/src/medip/mapping/24h-i-medip_1.uniq.sorted.noDup.bam.small";
+ item1.inputPath = "/home/kokonech/qualimapEpi/src/medip/mapping/24h-i-input.uniq.sorted.noDup.bam.small";
+ addDataItem(item1);
+
+ ReplicateItem item2 = new EpiAnalysis.ReplicateItem();
+ item2.name = "24h-i_2";
+ item2.medipPath = "/home/kokonech/qualimapEpi/src/medip/mapping/24h-i-medip_2.uniq.sorted.noDup.bam.small";
+ item2.inputPath = "/home/kokonech/qualimapEpi/src/medip/mapping/24h-i-input.uniq.sorted.noDup.bam.small";
+ addDataItem(item2);
+
+ }
+
+ updateState();
+
+
+
+ }
+
+ public void updateState() {
+
+ int numRows = inputDataTable.getRowCount();
+ removeSampleButton.setEnabled(numRows > 0);
+ editSampleButton.setEnabled(numRows > 0);
+ }
+
+ @Override
+ public void actionPerformed(ActionEvent actionEvent) {
+ String actionCommand = actionEvent.getActionCommand();
+
+ if ( actionCommand.equals(Constants.COMMAND_ADD_ITEM) ) {
+ EditEpigeneticsInputDataDialog dlg = new EditEpigeneticsInputDataDialog(this);
+ dlg.setModal(true);
+ dlg.setLocationRelativeTo(this);
+ dlg.setVisible(true);
+ } else if ( actionCommand.equals(Constants.COMMAND_REMOVE_ITEM) ) {
+ int index = inputDataTable.getSelectedRow();
+ if (index != -1 ) {
+ removeDataItem(index);
+ }
+ } else if ( actionCommand.equals(Constants.COMMAND_EDIT_ITEM) ) {
+ int index = inputDataTable.getSelectedRow();
+ if (index != -1) {
+ EditEpigeneticsInputDataDialog dlg = new EditEpigeneticsInputDataDialog(this, index);
+ dlg.setModal(true);
+ dlg.setLocationRelativeTo(this);
+ dlg.setVisible(true);
+ }
+ } else if ( actionCommand.equals(Constants.COMMAND_RUN_ANALYSIS) ) {
+
+ String errMsg = validateInput();
+ if (errMsg.isEmpty()) {
+ TabPageController tabController = new TabPageController(AnalysisType.CLUSTERING);
+ EpigeneticsAnalysisThread t = new EpigeneticsAnalysisThread(this, tabController );
+ t.start();
+ } else {
+ JOptionPane.showMessageDialog(this, errMsg, "Validate Input", JOptionPane.ERROR_MESSAGE);
+ }
+ } else {
+ updateState();
+ }
+ }
+
+ public void removeDataItem(int index) {
+ sampleTableModel.removeItem(index);
+ updateState();
+ }
+
+ public void addDataItem(ReplicateItem item) {
+ sampleTableModel.addItem(item);
+ updateState();
+ }
+
+ public void replaceDataItem(int itemIndex, ReplicateItem item) {
+ sampleTableModel.replaceItem(itemIndex, item);
+ updateState();
+ }
+
+
+ public EpiAnalysis.ReplicateItem getDataItem(int index) {
+ return sampleTableModel.getItem(index);
+ }
+
+ public HomeFrame getHomeFrame() {
+ return homeFrame;
+ }
+
+ String validateInput() {
+
+ String geneSelectionPath = getGeneSelectionPath();
+
+ if (geneSelectionPath.isEmpty()) {
+ return "Path to regions is not set!";
+ }
+
+ if ( !(new File(geneSelectionPath)).exists() ) {
+ return "Gene selection path is not valid!";
+ }
+
+ String errMsg = DocumentUtils.validateTabDelimitedFile(geneSelectionPath, 4);
+ if (!errMsg.isEmpty()) {
+ return errMsg;
+ }
+
+ String[] clusterNumbers = getClusterNumbers().split(",");
+
+ if (clusterNumbers.length == 0) {
+ return "Cluster numbers are not provided!";
+ } else {
+ for (String clusterNumber : clusterNumbers) {
+ try {
+ Integer.parseInt(clusterNumber);
+ } catch (NumberFormatException e) {
+ return "Can not parse number of clusters: " + clusterNumber;
+ }
+ }
+ }
+
+ if (sampleTableModel.getRowCount() == 0) {
+ return "No MEDIP input data is provided!";
+ }
+
+ return "";
+
+ }
+
+ public void setProgressStatus(String message) {
+ progressStream.setText(message);
+ }
+
+ public String getReadSmoothingLength() {
+ return smoothingLengthSpinner.getValue().toString();
+ }
+
+ public String getVisuzliationType() {
+ return vizTypeBox.getSelectedItem().toString().toLowerCase();
+ }
+
+}
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/panels/HtmlJPanel.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/panels/HtmlJPanel.java
new file mode 100755
index 0000000..f1c7c5f
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/panels/HtmlJPanel.java
@@ -0,0 +1,89 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+/*
+ * Blast2GO
+ * All Rights Reserved.
+ */
+package org.bioinfo.ngs.qc.qualimap.gui.panels;
+
+import java.awt.BorderLayout;
+
+import javax.swing.JEditorPane;
+import javax.swing.JPanel;
+import javax.swing.event.HyperlinkEvent;
+import javax.swing.event.HyperlinkListener;
+import javax.swing.text.html.HTMLEditorKit;
+
+//TODO: move pure HTML stuff to another class
+
+
+public class HtmlJPanel extends JPanel implements HyperlinkListener {
+
+ public static final Object BR = "<br/>";
+ public static final String COLSTARTFIX = "<tr><td width=300>";
+ public static final String COLSTART = "<tr><td>";
+ public static final String COLMID = "</td><td align=left>";
+ public static final String COLEND = "</td></tr>";
+ private JEditorPane aJEditorPane;
+ private String html;
+
+ public HtmlJPanel() {
+ this.html = getHeader()+getHeadFooter();
+ this.aJEditorPane = new JEditorPane();
+ final HTMLEditorKit eKit = new HTMLEditorKit();
+ this.aJEditorPane.setEditorKit(eKit);
+ this.aJEditorPane.setText(this.html);
+ this.aJEditorPane.setEditable(false);
+ this.setLayout(new BorderLayout());
+ this.add(this.aJEditorPane);
+ }
+
+ public void setHtmlPage(final String html) {
+ this.html = html;
+ this.aJEditorPane.setText(this.html);
+ this.revalidate();
+ this.repaint();
+ }
+
+ @Override
+ public void hyperlinkUpdate(HyperlinkEvent arg0) {
+ }
+
+ public static String getHeader() {
+ return "<HTML>\n<HEAD>\n <link rel=\"stylesheet\" href=\"css/agogo.css\" type=\"text/css\" /> " +
+ "\n<link rel=\"stylesheet\" href=\"css/pygments.css\" type=\"text/css\" />" +
+
+ "\n<TITLE>Qualimap Report</TITLE>\n</HEAD><BODY BGCOLOR=\"#EEEEEE\">";
+ }
+
+ public static String getHeadFooter() {
+ return "</BODY></HTML>";
+ }
+
+ public static Object getTableHeader(int width, String color) {
+ return "<table BGCOLOR=\"#"+color+"\" cellspacing=\"-1\" border=\"0\" " +
+ "width=\""+width+"\" align=\"center\" valign=\"top\">";
+ }
+
+ public static Object getTableFooter() {
+ return "</table>";
+ }
+}
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/panels/MultisampleBamQcDialog.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/panels/MultisampleBamQcDialog.java
new file mode 100644
index 0000000..d4046fb
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/panels/MultisampleBamQcDialog.java
@@ -0,0 +1,501 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.gui.panels;
+
+import net.miginfocom.swing.MigLayout;
+import org.apache.commons.io.FilenameUtils;
+import org.bioinfo.ngs.qc.qualimap.common.AnalysisType;
+import org.bioinfo.ngs.qc.qualimap.common.Constants;
+import org.bioinfo.ngs.qc.qualimap.gui.dialogs.AnalysisDialog;
+import org.bioinfo.ngs.qc.qualimap.gui.dialogs.EditSampleInfoDialog;
+import org.bioinfo.ngs.qc.qualimap.gui.frames.HomeFrame;
+import org.bioinfo.ngs.qc.qualimap.gui.threads.MultisampleBamQcThread;
+import org.bioinfo.ngs.qc.qualimap.gui.utils.TabPageController;
+import org.bioinfo.ngs.qc.qualimap.process.BamStatsAnalysisConfig;
+import org.bioinfo.ngs.qc.qualimap.process.MultisampleBamQcAnalysis;
+import org.bioinfo.ngs.qc.qualimap.process.SampleInfo;
+
+import javax.swing.*;
+import javax.swing.filechooser.FileFilter;
+import javax.swing.table.AbstractTableModel;
+import java.awt.*;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.io.File;
+import java.io.IOException;
+import java.util.*;
+import java.util.List;
+
+/**
+ * Created by kokonech
+ * Date: 6/6/14
+ * Time: 3:04 PM
+ */
+public class MultisampleBamQcDialog extends AnalysisDialog implements ActionListener {
+
+ static class SampleDataTableModel extends AbstractTableModel {
+
+ java.util.List<SampleInfo> sampleReplicateList;
+ final String[] columnNames = { "Sample name", "Path"};
+
+ public SampleDataTableModel() {
+ sampleReplicateList = new ArrayList<SampleInfo>();
+ }
+
+ public void addItem(SampleInfo item) {
+ sampleReplicateList.add(item);
+ fireTableDataChanged();
+ }
+
+ public void replaceItem(int index, SampleInfo newItem) {
+ sampleReplicateList.set(index, newItem);
+ fireTableDataChanged();
+ }
+
+ public void removeItem(int index) {
+ sampleReplicateList.remove(index);
+ fireTableDataChanged();
+ }
+
+ public void clearItems() {
+ sampleReplicateList.clear();
+ fireTableDataChanged();
+ }
+
+ @Override
+ public String getColumnName(int column) {
+ return columnNames[column];
+ }
+
+ @Override
+ public int getRowCount() {
+ return sampleReplicateList.size();
+ }
+
+ @Override
+ public int getColumnCount() {
+ return columnNames.length;
+ }
+ @Override
+ public Object getValueAt(int i, int j) {
+ SampleInfo sampleInfo = sampleReplicateList.get(i);
+
+ if (j == 0) {
+ return sampleInfo.name;
+ } else if (j == 1) {
+ return sampleInfo.path;
+ } else {
+ return "";
+ }
+
+ }
+
+ public SampleInfo getItem(int index) {
+ return sampleReplicateList.get(index);
+ }
+
+ public java.util.List<SampleInfo> getItems() {
+ return sampleReplicateList;
+ }
+ }
+
+ SampleDataTableModel sampleTableModel;
+ JTable inputDataTable;
+ JPanel buttonPanel;
+ JCheckBox activateBamQcMode;
+ JButton addSampleButton, editSampleButton, removeSampleButton, importConfigButton;
+
+ // BAM QC stuff
+ JPanel bamQcOptionsPanel;
+ JCheckBox analyzeRegionsCheckBox, drawChromosomeLimits;
+ JTextField pathGffFile;
+ JButton browseGffButton;
+ JLabel labelNw, labelPathToGff, labelNumReadsPerBunch, labelMinHmSize;
+ JSpinner valueNwSpinner, minHmSizeSpinner, numReadsPerBunchSpinner;
+
+
+ public MultisampleBamQcDialog(HomeFrame parent) {
+ super(parent, "Multi-sample BAM QC");
+ getContentPane().setLayout(new MigLayout("insets 20"));
+
+ add(new JLabel("Samples:"), "span 2, wrap");
+
+ sampleTableModel = new SampleDataTableModel();
+ inputDataTable = new JTable(sampleTableModel);
+
+ JScrollPane scroller = new JScrollPane(inputDataTable);
+ scroller.setPreferredSize(new Dimension(700, 100));
+ add(scroller, "span, wrap");
+
+ buttonPanel = new JPanel();
+ buttonPanel.setLayout(new MigLayout("insets 0"));
+ addSampleButton = new JButton("Add");
+ addSampleButton.setActionCommand(Constants.COMMAND_ADD_ITEM);
+ addSampleButton.setToolTipText("Add novel sample for analysis");
+ addSampleButton.addActionListener(this);
+ buttonPanel.add(addSampleButton, "");
+ editSampleButton = new JButton("Edit");
+ editSampleButton.setActionCommand(Constants.COMMAND_EDIT_ITEM);
+ editSampleButton.setToolTipText("Edit selected sample.");
+ editSampleButton.addActionListener(this);
+ buttonPanel.add(editSampleButton, "");
+ removeSampleButton = new JButton("Remove");
+ removeSampleButton.setActionCommand(Constants.COMMAND_REMOVE_ITEM);
+ removeSampleButton.addActionListener(this);
+ removeSampleButton.setToolTipText("Remove selected sample.");
+ buttonPanel.add(removeSampleButton, "");
+
+ importConfigButton = new JButton("Import configuration...");
+ importConfigButton.setActionCommand(Constants.COMMAND_IMPORT_CONFIG);
+ importConfigButton.addActionListener(this);
+ importConfigButton.setToolTipText("Import existing configuration file. Replaces all existing samples.");
+ buttonPanel.add(importConfigButton, "wrap");
+
+ add(buttonPanel, "align right, span, wrap");
+
+ activateBamQcMode = new JCheckBox("\"Raw data\" mode: run BAM QC on input samples");
+ activateBamQcMode.setSelected(false);
+ activateBamQcMode.setToolTipText("<html><body>By default precomputed BAM QC results are expected as input.<br>" +
+ "However it is possible to provide raw BAM files as input<br>" +
+ "and run BAM QC on each sample.</body></html>");
+ activateBamQcMode.addActionListener(this);
+ add(activateBamQcMode, "span 2, wrap");
+
+ setupBamQcGui();
+ add(bamQcOptionsPanel, "span 2, wrap");
+
+ add(new JLabel("Log"), "wrap");
+ setupLogArea();
+ add(logAreaScrollPane, "span, grow, wrap 30px");
+
+ // Action done while the statistics graphics are loaded
+ setupProgressStream();
+ add(progressStream, "align center");
+
+ setupProgressBar();
+ add(progressBar, "grow, wrap 30px");
+
+ startAnalysisButton = new JButton();
+ startAnalysisButton.addActionListener(this);
+ startAnalysisButton.setActionCommand(Constants.COMMAND_RUN_ANALYSIS);
+ startAnalysisButton.setText(">>> Run Analysis");
+
+ add(startAnalysisButton, "span, align right, wrap");
+
+ pack();
+
+ // Default data for testing
+ if (System.getenv("QUALIMAP_DEBUG") != null) {
+ SampleInfo s1 = new SampleInfo();
+ s1.name = "MCF7";
+ s1.path = "/data/fusions-data/breast_cancer_MCF7/tophat_out/accepted_hits_stats";
+ sampleTableModel.addItem(s1);
+
+
+ SampleInfo s2 = new SampleInfo();
+ s2.name = "Kidney";
+ s2.path = "/data/qualimap_release_data/counts/kidney_stats";
+ sampleTableModel.addItem(s2);
+
+ SampleInfo s3 = new SampleInfo();
+ s3.name = "Liver";
+ s3.path = "/data/qualimap_release_data/counts/liver_stats";
+ sampleTableModel.addItem(s3);
+
+ SampleInfo s4 = new SampleInfo();
+ s4.name = "Plasmodium DNA";
+ s4.path = "/data/qualimap_release_data/alignments/Plasmodium-falciparum-3D7_stats";
+ sampleTableModel.addItem(s4);
+
+ }
+
+ //Default data 2
+ /*if (System.getenv("QUALIMAP_DEBUG") != null) {
+
+ SampleInfo s1 = new SampleInfo();
+ s1.name = "S1";
+ s1.path = "/data/qualimap_release_data/alignments/HG00096.chrom20.bam";
+ sampleTableModel.addItem(s1);
+
+
+ SampleInfo s2 = new SampleInfo();
+ s2.name = "S2";
+ s2.path = "/home/kokonech/sample_data/example-alignment.sorted.bam";
+ sampleTableModel.addItem(s2);
+
+
+ }*/
+
+ updateState();
+ setResizable(false);
+
+ }
+
+ private void setupBamQcGui() {
+
+ bamQcOptionsPanel = new JPanel();
+ bamQcOptionsPanel.setLayout(new MigLayout("insets 10"));
+
+ analyzeRegionsCheckBox = new JCheckBox("Analyze regions");
+ analyzeRegionsCheckBox.addActionListener(this);
+ analyzeRegionsCheckBox.setToolTipText("Check to only analyze the regions defined in the features file");
+ bamQcOptionsPanel.add(analyzeRegionsCheckBox, "wrap");
+
+ labelPathToGff = new JLabel("Regions file (GFF/BED):");
+ bamQcOptionsPanel.add(labelPathToGff, "");
+
+ pathGffFile = new JTextField(40);
+ pathGffFile.setToolTipText("Path to GFF/GTF or BED file containing regions of interest");
+ bamQcOptionsPanel.add(pathGffFile, "grow");
+
+ browseGffButton = new JButton();
+ browseGffButton.setText("...");
+ browseGffButton.setActionCommand(Constants.COMMAND_BROWSE_GFF);
+ browseGffButton.addActionListener(this);
+ bamQcOptionsPanel.add(browseGffButton, "align center, wrap");
+
+ drawChromosomeLimits = new JCheckBox("Chromosome limits");
+ drawChromosomeLimits.setCursor(Cursor.getPredefinedCursor(Cursor.HAND_CURSOR));
+ drawChromosomeLimits.setToolTipText("Check to draw the chromosome limits");
+ drawChromosomeLimits.setSelected(true);
+ bamQcOptionsPanel.add(drawChromosomeLimits, "wrap");
+
+ labelNw = new JLabel("Number of windows:");
+ bamQcOptionsPanel.add(labelNw);
+
+ valueNwSpinner = new JSpinner(new SpinnerNumberModel(Constants.DEFAULT_NUMBER_OF_WINDOWS, 100, 4000, 50));
+ valueNwSpinner.setToolTipText("Number of sampling windows across the reference");
+ bamQcOptionsPanel.add(valueNwSpinner, "wrap");
+
+ labelMinHmSize = new JLabel("Homopolymer size:");
+ bamQcOptionsPanel.add(labelMinHmSize);
+ minHmSizeSpinner = new JSpinner(new SpinnerNumberModel(Constants.DEFAULT_HOMOPOLYMER_SIZE, 2, 7, 1));
+ minHmSizeSpinner.setToolTipText("<html>Only homopolymers of this size or larger will be considered " +
+ "<br>when estimating number of homopolymer indels.</html>" );
+ bamQcOptionsPanel.add(minHmSizeSpinner, "wrap");
+
+ labelNumReadsPerBunch = new JLabel("Size of the chunk:");
+ bamQcOptionsPanel.add(labelNumReadsPerBunch, "gapleft 20");
+ numReadsPerBunchSpinner = new JSpinner(new SpinnerNumberModel(Constants.DEFAULT_CHUNK_SIZE, 100, 5000, 1));
+ numReadsPerBunchSpinner.setToolTipText("<html>To speed up the computation reads are analyzed in chunks. " +
+ "Each bunch is analyzed by single thread. <br>This option controls the number of reads in the chunk." +
+ "<br>Smaller number may result in lower performance, " +
+ "but also the memory consumption will be reduced.</html>");
+ bamQcOptionsPanel.add(numReadsPerBunchSpinner, "wrap 20px");
+
+
+
+
+ }
+
+ @Override
+ public void actionPerformed(ActionEvent actionEvent) {
+ String actionCommand = actionEvent.getActionCommand();
+
+ if ( actionCommand.equals(Constants.COMMAND_ADD_ITEM) ) {
+ EditSampleInfoDialog dlg = new EditSampleInfoDialog(this);
+ dlg.setModal(true);
+ dlg.setLocationRelativeTo(this);
+ dlg.setVisible(true);
+ } else if ( actionCommand.equals(Constants.COMMAND_REMOVE_ITEM) ) {
+ int index = inputDataTable.getSelectedRow();
+ if (index != -1 ) {
+ removeDataItem(index);
+ }
+ } else if ( actionCommand.equals(Constants.COMMAND_EDIT_ITEM) ) {
+ int index = inputDataTable.getSelectedRow();
+ if (index != -1) {
+ EditSampleInfoDialog dlg = new EditSampleInfoDialog(this, index);
+ dlg.setModal(true);
+ dlg.setLocationRelativeTo(this);
+ dlg.setVisible(true);
+ }
+ } else if (actionCommand.equals(Constants.COMMAND_IMPORT_CONFIG)) {
+ importConfiguration();
+ } else if (actionCommand.equals(Constants.COMMAND_BROWSE_GFF)) {
+ browseGffFile();
+ } else if ( actionCommand.equals(Constants.COMMAND_RUN_ANALYSIS) ) {
+
+ String errMsg = validateInput();
+ if (errMsg.isEmpty()) {
+ resetProgress();
+ TabPageController tabController = new TabPageController(AnalysisType.MULTISAMPLE_BAM_QC);
+
+ MultisampleBamQcThread t = new MultisampleBamQcThread(this, tabController );
+
+ Thread.UncaughtExceptionHandler eh = new AnalysisDialog.ExceptionHandler(this);
+ t.setUncaughtExceptionHandler(eh);
+
+ t.start();
+ } else {
+ JOptionPane.showMessageDialog(this, errMsg, "Validate Input", JOptionPane.ERROR_MESSAGE);
+ }
+ } else {
+ updateState();
+ }
+ }
+
+ private void importConfiguration() {
+
+ JFileChooser fileChooser = HomeFrame.getFileChooser();
+
+ int valor = fileChooser.showOpenDialog(homeFrame.getCurrentInstance());
+ if (valor == JFileChooser.APPROVE_OPTION) {
+ String inputFile = fileChooser.getSelectedFile().getPath();
+
+ try {
+ List<SampleInfo> bamQcResults = MultisampleBamQcAnalysis.parseInputFile(inputFile);
+ if (bamQcResults.size() == 0) {
+
+ JOptionPane.showMessageDialog(this,
+ "The input file " + inputFile + " does not contain any samples. " +
+ "Please check file format.", "Import configuration file", JOptionPane.ERROR_MESSAGE);
+ return;
+ }
+
+ sampleTableModel.clearItems();
+ for (SampleInfo item : bamQcResults) {
+ sampleTableModel.addItem(item);
+ }
+
+
+ } catch (IOException e) {
+ JOptionPane.showMessageDialog(this, "Failed to load configuration file " + inputFile +
+ ". Please check file format", "Import configuration file", JOptionPane.ERROR_MESSAGE);
+ }
+
+ }
+
+ }
+
+ private void browseGffFile() {
+
+ JFileChooser fileChooser = HomeFrame.getFileChooser();
+
+ FileFilter filter = new FileFilter() {
+ public boolean accept(File fileShown) {
+ boolean result = true;
+
+ String ext = FilenameUtils.getExtension(fileShown.getName());
+
+ if (!fileShown.isDirectory() && !Constants.FILE_EXTENSION_REGION.containsKey(ext.toUpperCase())) {
+ result = false;
+ }
+
+ return result;
+ }
+
+ public String getDescription() {
+ return ("Region Files (*.gff *.gtf *.bed)");
+ }
+ };
+ fileChooser.setFileFilter(filter);
+ int valor = fileChooser.showOpenDialog(homeFrame.getCurrentInstance());
+
+ if (valor == JFileChooser.APPROVE_OPTION) {
+ pathGffFile.setText(fileChooser.getSelectedFile().getPath());
+ }
+ }
+
+
+ public void updateState() {
+ boolean runBamQc = activateBamQcMode.isSelected();
+ bamQcOptionsPanel.setEnabled(runBamQc);
+ analyzeRegionsCheckBox.setEnabled(runBamQc);
+ boolean regionsAvailable = analyzeRegionsCheckBox.isSelected();
+ browseGffButton.setEnabled(runBamQc && regionsAvailable);
+ pathGffFile.setEnabled(runBamQc && regionsAvailable);
+ labelPathToGff.setEnabled(runBamQc && regionsAvailable);
+ drawChromosomeLimits.setEnabled(runBamQc);
+ labelMinHmSize.setEnabled(runBamQc);
+ minHmSizeSpinner.setEnabled(runBamQc);
+ labelNumReadsPerBunch.setEnabled(runBamQc);
+ numReadsPerBunchSpinner.setEnabled(runBamQc);
+ labelNw.setEnabled(runBamQc);
+ valueNwSpinner.setEnabled(runBamQc);
+ }
+
+ String validateInput() {
+
+ if (sampleTableModel.getRowCount() == 0) {
+ return "No input samples are provided!";
+ } else if (sampleTableModel.getRowCount() == 1) {
+ return "Only one sample is provided! Please include more samples.";
+ }
+
+ if (analyzeRegionsCheckBox.isSelected()) {
+ if (pathGffFile.getText().isEmpty()) {
+ return "Path to GFF file is not set!";
+ }
+ }
+
+ return "";
+ }
+
+ public int getItemCount() {
+ return sampleTableModel.getRowCount();
+ }
+
+ public SampleInfo getDataItem(int index) {
+ return sampleTableModel.getItem(index);
+ }
+
+ public void addDataItem(SampleInfo item) {
+ sampleTableModel.addItem(item);
+ updateState();
+ }
+
+ public void replaceDataItem(int itemIndex, SampleInfo item) {
+ sampleTableModel.replaceItem(itemIndex, item);
+ updateState();
+ }
+
+ private void removeDataItem(int index) {
+ sampleTableModel.removeItem(index);
+ updateState();
+ }
+
+ public java.util.List<SampleInfo> getDataItems() {
+ return sampleTableModel.getItems();
+ }
+
+ public boolean runBamQcFirst() {
+ return activateBamQcMode.isSelected();
+ }
+
+ public BamStatsAnalysisConfig getBamQcConfig() {
+
+ BamStatsAnalysisConfig cfg = new BamStatsAnalysisConfig();
+ if (analyzeRegionsCheckBox.isSelected()) {
+ cfg.gffFile = pathGffFile.getText();
+ }
+
+ cfg.drawChromosomeLimits = drawChromosomeLimits.isSelected();
+ cfg.numberOfWindows = (Integer) valueNwSpinner.getValue();
+ cfg.minHomopolymerSize = (Integer) minHmSizeSpinner.getValue();
+ cfg.bunchSize = (Integer) numReadsPerBunchSpinner.getValue();
+
+ return cfg;
+ }
+
+
+
+}
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/panels/OpenLoadedStatistics.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/panels/OpenLoadedStatistics.java
new file mode 100644
index 0000000..a23bdf1
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/panels/OpenLoadedStatistics.java
@@ -0,0 +1,574 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.gui.panels;
+
+import java.awt.*;
+import java.awt.event.*;
+import java.awt.image.BufferedImage;
+import java.io.File;
+import java.io.IOException;
+import java.util.List;
+
+import javax.imageio.ImageIO;
+import javax.swing.*;
+import javax.swing.filechooser.FileFilter;
+
+import org.bioinfo.commons.log.Logger;
+import org.bioinfo.ngs.qc.qualimap.beans.ChartRawDataWriter;
+import org.bioinfo.ngs.qc.qualimap.beans.QChart;
+import org.bioinfo.ngs.qc.qualimap.beans.StatsReporter;
+import org.bioinfo.ngs.qc.qualimap.common.AnalysisType;
+import org.bioinfo.ngs.qc.qualimap.common.Constants;
+import org.bioinfo.ngs.qc.qualimap.gui.frames.HomeFrame;
+import org.bioinfo.ngs.qc.qualimap.gui.utils.*;
+
+import org.jfree.chart.ChartPanel;
+import org.jfree.chart.JFreeChart;
+
+/**
+ * Class to manage the statistics loaded from a determinate file
+ *
+ * @author Luis Miguel Cruz
+ */
+public class OpenLoadedStatistics extends JPanel implements ComponentListener {
+ private static final long serialVersionUID = -6408484044729636203L;
+ HomeFrame homeFrame;
+ protected Logger logger;
+
+ private ImageIcon treeMinusIcon, treePlusIcon;
+ /** Panels that contains the dynamic structures */
+ private JScrollPane leftScrollPane, rightScrollPane;
+
+ /** Variable to manage the left panel that contains the links to the results */
+ public JPanel leftPanel;
+ private JLabel initialLabel;
+ private TabPageController tabPageController;
+
+ static class RightPanelListener extends MouseAdapter {
+
+ TabPageController tabPageController;
+ JComponent parent;
+
+ public RightPanelListener(JComponent parent, TabPageController tabProperties) {
+ this.parent = parent;
+ this.tabPageController = tabProperties;
+ }
+
+ public void mousePressed(MouseEvent e) {
+ maybeShowPopup(e);
+ }
+
+ public void mouseReleased(MouseEvent e) {
+ maybeShowPopup(e);
+ }
+
+ private void maybeShowPopup(MouseEvent e) {
+ if (e.isPopupTrigger()) {
+ JPopupMenu popup = new JPopupMenu();
+ final String graphicName = tabPageController.getLoadedGraphicName();
+ StatsReporter reporter = tabPageController.getActiveReporter();
+ if (!graphicName.isEmpty()) {
+ JMenuItem savePictureItem = createSaveGraphicMenuItem(reporter, graphicName);
+ popup.add(savePictureItem);
+
+ QChart chart = tabPageController.getActiveReporter().findChartByName(graphicName);
+ if (chart != null && chart.canExportRawData()) {
+ JMenuItem exportDataMenuItem = createExportRawDataMenuItem(chart, parent);
+ popup.addSeparator();
+ popup.add(exportDataMenuItem);
+ }
+
+ // TODO: Each reporter should add own items to the popup menu.
+ if (tabPageController.getTypeAnalysis() == AnalysisType.CLUSTERING) {
+ JMenuItem exportGeneListItem = new JMenuItem("Export feature list...");
+ exportGeneListItem.addActionListener(new ActionListener() {
+ @Override
+ public void actionPerformed(ActionEvent actionEvent) {
+ HomeFrame.showExportGenesDialog(parent, tabPageController);
+ }
+ });
+ popup.addSeparator();
+ popup.add(exportGeneListItem);
+ }
+ }
+
+ popup.show(e.getComponent(),
+ e.getX(), e.getY());
+ }
+ }
+
+ private JMenuItem createSaveGraphicMenuItem(final StatsReporter reporter, final String graphicName) {
+ JMenuItem savePictureItem = new JMenuItem("Save picture...");
+ savePictureItem.addActionListener(new ActionListener() {
+ @Override
+ public void actionPerformed(ActionEvent actionEvent) {
+ JFileChooser fileChooser = HomeFrame.getFileChooser();
+ fileChooser.setFileFilter( new FileFilter() {
+ @Override
+ public boolean accept(File file) {
+ return true;
+ }
+
+ @Override
+ public String getDescription() {
+ return "PNG images";
+ }
+ });
+ int res = fileChooser.showDialog(parent, "Save");
+ if (res == JFileChooser.APPROVE_OPTION) {
+ String path = fileChooser.getSelectedFile().getAbsolutePath();
+ if (path.endsWith(".png")) {
+ path = path + ".png";
+ }
+ BufferedImage image = reporter.findChartByName(graphicName).getBufferedImage();
+ try {
+ ImageIO.write(image, "png", new File(path));
+ } catch (IOException e1) {
+ JOptionPane.showMessageDialog(parent, "Failed to save image!",
+ "Save image", JOptionPane.ERROR_MESSAGE);
+ }
+
+ }
+ }
+ });
+ return savePictureItem;
+ }
+
+
+ }
+
+ public OpenLoadedStatistics(HomeFrame homeFrame, TabPageController tabProperties) {
+ super();
+ this.homeFrame = homeFrame;
+ this.tabPageController = tabProperties;
+ treeMinusIcon = new ImageIcon(homeFrame.getClass().getResource(Constants.pathImages + "minus_blue.png"));
+ treePlusIcon = new ImageIcon(homeFrame.getClass().getResource(Constants.pathImages + "add.png"));
+ }
+
+
+ /**
+ * Show the statistics loaded into the tab selected
+ *
+ * @return JSplitPane, User Interface with the data loaded.
+ */
+ public JSplitPane getLoadedStatistics() {
+ JSplitPane statisticsContainer = new JSplitPane(JSplitPane.HORIZONTAL_SPLIT);
+ statisticsContainer.setDividerSize(2);
+ int leftPanelWidth = 250;
+
+ leftPanel = new JPanel();
+ leftPanel.setLayout(new BoxLayout(leftPanel, BoxLayout.Y_AXIS));
+ leftScrollPane = new JScrollPane(leftPanel);
+ leftScrollPane.setHorizontalScrollBarPolicy(ScrollPaneConstants.HORIZONTAL_SCROLLBAR_NEVER);
+ leftScrollPane.setVerticalScrollBarPolicy(ScrollPaneConstants.VERTICAL_SCROLLBAR_AS_NEEDED);
+ leftScrollPane.setMinimumSize(new Dimension(leftPanelWidth, 500));
+ leftScrollPane.setPreferredSize(new Dimension(leftPanelWidth, 2000));
+ leftScrollPane.setViewportView(leftPanel);
+
+ rightScrollPane = new JScrollPane();
+ rightScrollPane.setHorizontalScrollBarPolicy(ScrollPaneConstants.HORIZONTAL_SCROLLBAR_AS_NEEDED);
+ rightScrollPane.setVerticalScrollBarPolicy(ScrollPaneConstants.VERTICAL_SCROLLBAR_AS_NEEDED);
+
+ tabPageController.getGraphicImage().addComponentListener(this);
+
+ /*
+ Done by constructor
+ tabPageController.setLastLinkSelected(null);
+ tabPageController.setLoadedGraphicName("");*/
+
+
+ prepareLeftPanel();
+
+ JPanel rightPanel = new JPanel();
+ rightPanel.setLayout(new GroupLayout(rightPanel));
+ rightScrollPane.setViewportView(rightPanel);
+ rightScrollPane.addMouseListener(new RightPanelListener(rightPanel,tabPageController));
+
+ statisticsContainer.setLeftComponent(leftScrollPane);
+ statisticsContainer.setRightComponent(rightScrollPane);
+ statisticsContainer.validate();
+ leftScrollPane.validate();
+
+ validate();
+
+ return statisticsContainer;
+ }
+
+ private void prepareLeftPanel() {
+
+ List<StatsReporter> reporters = tabPageController.getReporters();
+
+
+ int idx = 0;
+ for (StatsReporter reporter : reporters) {
+ String sectionName = reporter.getName() + reporter.getNamePostfix();
+ JCheckBox checkFirstSection = createResultsCheckBox(sectionName);
+ leftPanel.add(checkFirstSection);
+
+ if (reporter.hasInputDescription()) {
+ JLabel inputLabel = createInputDescriptionLinkLabel("Input data & parameters", idx);
+ inputLabel.setToolTipText("Input data description");
+ inputLabel.setIcon(new ImageIcon(getClass().getResource(Constants.pathImages + "bullet_blue.png")));
+ leftPanel.add(inputLabel);
+ }
+
+ if (reporter.hasSummary() ) {
+ JLabel summaryLabel = createSummaryLinkLabel("Summary", idx);
+ summaryLabel.setIcon(new ImageIcon(getClass().getResource(Constants.pathImages + "bullet_green.png")));
+ leftPanel.add(summaryLabel);
+ if (initialLabel == null) {
+ initialLabel = summaryLabel;
+ }
+ }
+
+ List<QChart> charts = reporter.getCharts();
+
+ for (QChart chart : charts) {
+ JLabel linkLabel = createImageLinkLabel(chart.getTitle(), chart.getName(), idx);
+ linkLabel.setToolTipText(chart.getToolTip());
+ leftPanel.add(linkLabel);
+ }
+ ++idx;
+ }
+ }
+
+
+ public void showInitialPage()
+ {
+ if(AnalysisType.BAM_QC == tabPageController.getTypeAnalysis() && initialLabel != null){
+ showLeftSideSummaryInformation(0, initialLabel);
+ } else {
+
+ JPanel centerPanel = new JPanel();
+ centerPanel.setLayout(new FlowLayout(FlowLayout.CENTER,0, 50));
+ centerPanel.add(new JLabel("To start browsing statistics please select an item" +
+ " from the list to the left."));
+ rightScrollPane.setViewportView( centerPanel);
+ }
+
+ }
+
+ /**
+ * Refresh the left menu showing or hiding the elements depends on the user
+ * selection.
+ *
+ * @param evt
+ * ActionEvent that contains the JCheckbox selected by the user.
+ */
+ private void refreshLeftMenu(ActionEvent evt) {
+
+
+ JCheckBox checkBoxSelected = (JCheckBox) evt.getSource();
+ boolean showItem = (checkBoxSelected).isSelected();
+
+
+ int i = 0;
+ boolean afterSubmenuChanged = false;
+ Component elem;
+
+ while (i < leftPanel.getComponentCount()) {
+ elem = leftPanel.getComponent(i);
+
+ // We have to get the last checkbox selected to change the
+ // location of the elements of its submenu.
+ if (elem instanceof JCheckBox) {
+ afterSubmenuChanged = checkBoxSelected.equals(elem);
+ } else if (elem instanceof JLabel && afterSubmenuChanged) {
+ // If the element is into the submenu of the checkbox selected
+ // and this checkbox have to show the elements, we show this
+ // element.
+ if (showItem) {
+ elem.setVisible(true);
+ } else {
+ elem.setVisible(false);
+ }
+ }
+
+ i++;
+ }
+
+ leftPanel.validate();
+ }
+
+ /**
+ * Fill the commons properties for the graphic and text links
+ *
+ * @param labelText
+ * Name displayed of the label
+ * @return JLabel label set
+ */
+
+ JLabel createLinkLabel(final String labelText) {
+ JLabel label = new JLabel(labelText);
+ label.setFont(new Font(label.getFont().getFontName(), label.getFont().getStyle(), 11));
+ label.setIcon(new ImageIcon(getClass().getResource(Constants.pathImages + "bullet_green.png")));
+ label.setOpaque(true);
+ label.setCursor(Cursor.getPredefinedCursor(Cursor.HAND_CURSOR));
+ label.setIconTextGap(0);
+ label.setToolTipText(labelText);
+
+ return label;
+ }
+
+ JLabel createSummaryLinkLabel(final String labelText, final int reporterIndex) {
+ final JLabel label = createLinkLabel(labelText);
+ label.addMouseListener(new JLabelMouseListener() {
+ public void mouseClicked(MouseEvent arg0) {
+ showLeftSideSummaryInformation(reporterIndex, label);
+ }
+ });
+
+ return label;
+ }
+
+ JLabel createInputDescriptionLinkLabel(final String labelText, final int reporterIndex) {
+ final JLabel label = createLinkLabel(labelText);
+ label.addMouseListener(new JLabelMouseListener() {
+ public void mouseClicked(MouseEvent arg0) {
+ showLeftSideInputDescription(reporterIndex, label);
+ }
+ });
+
+ return label;
+ }
+
+
+ JLabel createImageLinkLabel(final String labelText, final String graphicName, final int reporterIndex) {
+ final JLabel label = createLinkLabel(labelText);
+ label.addMouseListener(new JLabelMouseListener() {
+ public void mouseClicked(MouseEvent arg0) {
+ showLeftSideInformation(graphicName, label, reporterIndex);
+ }
+ });
+
+ return label;
+ }
+
+
+ JCheckBox createResultsCheckBox(String text) {
+ JCheckBox checkBox = new JCheckBox(text);
+ checkBox.setSelected(true);
+ checkBox.setIcon(treePlusIcon);
+ checkBox.setSelectedIcon(treeMinusIcon);
+ checkBox.setCursor(Cursor.getPredefinedCursor(Cursor.HAND_CURSOR));
+ checkBox.setAction(getActionShowSubMenu(text));
+
+ return checkBox;
+ }
+
+ public void showLeftSideSummaryInformation(int reporterIndex, JLabel label) {
+ tabPageController.setLoadedGraphicName("");
+ prepareHtmlSummary(getReporter(reporterIndex));
+ tabPageController.setSelectedReporterIndex(reporterIndex);
+ fillColorLink(label);
+ }
+
+ public void showLeftSideInputDescription(int reporterIndex, JLabel label) {
+ tabPageController.setLoadedGraphicName("");
+ prepareHtmlInputDescription(getReporter(reporterIndex));
+ tabPageController.setSelectedReporterIndex(reporterIndex);
+ fillColorLink(label);
+ }
+
+ private void showLeftSideInformation(String graphicName, JLabel label, int reporterIndex) {
+ if (graphicName != null) {
+ showGraphic(graphicName, getReporter(reporterIndex));
+ tabPageController.setSelectedReporterIndex(reporterIndex);
+ }
+ fillColorLink(label);
+ }
+
+ private StatsReporter getReporter(int reporterIndex){
+ return tabPageController.getReporters().get(reporterIndex);
+ }
+
+ /**
+ * Fill the color of the link pressed by the user in the left menu
+ *
+ * @param label
+ * label to set the colors
+ */
+ private void fillColorLink(JLabel label) {
+ //TabPropertiesVO tabProperties = homeFrame.getListTabsProperties().get(homeFrame.getTabbedPane().getSelectedIndex());
+
+ if (tabPageController.getLastLinkSelected() != null) {
+ tabPageController.getLastLinkSelected().setBackground(null);
+ tabPageController.getLastLinkSelected().setFont(new Font(label.getFont().getFontName(), label.getFont().getStyle(), label.getFont().getSize()));
+ }
+ if (label != null) {
+ label.setBackground(new Color(240, 230, 140));
+ label.setFont(HomeFrame.defaultFontItalic);
+ label.setSize(label.getPreferredSize());
+ label.validate();
+ tabPageController.setLastLinkSelected(label);
+ }
+ }
+
+ /**
+ * Show into the split of the selected tab the selected graphic data.
+ *
+ * @param name
+ * Name of the file loaded (if its a graphic file).
+ * @param reporter
+ * BamQCRegionReporter graphic input values
+ */
+ private void showGraphic(String name, StatsReporter reporter) {
+
+
+
+ QChart chart = reporter.findChartByName(name);
+ if (chart == null) {
+ logger.error("Can not find chart " + name);
+ return;
+ }
+
+ if (chart.isBufferedImage()) {
+
+ // Get a Singleton to manage the image to display
+ GraphicImagePanel panelImage = tabPageController.getGraphicImage();
+ BufferedImage imageToDisplay = chart.getBufferedImage();
+ // Set the image with the file image get
+ panelImage.setImage(imageToDisplay);
+ // Scale the image
+ if (tabPageController.getTypeAnalysis() == AnalysisType.CLUSTERING ) {
+ int width = imageToDisplay.getWidth();
+ int height = imageToDisplay.getHeight();
+ panelImage.setPreferredSize(new Dimension(width, height));
+ panelImage.resizeImage(width, height);
+ } else {
+ panelImage.resizeImage(rightScrollPane.getWidth(), rightScrollPane.getHeight());
+ }
+ rightScrollPane.setViewportView(panelImage);
+
+ } else {
+
+ JFreeChart jFreeChart = chart.getJFreeChart();
+ ChartPanel panelImage = new ChartPanel( jFreeChart );
+
+ if (chart.canExportRawData()) {
+ JMenuItem exportDataItem = createExportRawDataMenuItem(chart, this);
+ panelImage.getPopupMenu().addSeparator();
+ panelImage.getPopupMenu().add( exportDataItem );
+ }
+ panelImage.setSize(rightScrollPane.getSize());
+ rightScrollPane.setViewportView(panelImage);
+
+ }
+
+ tabPageController.setLoadedGraphicName(name);
+
+
+
+
+ homeFrame.updateMenuBar();
+
+ }
+
+ private static JMenuItem createExportRawDataMenuItem(QChart chart, JComponent parent) {
+ ChartRawDataWriter dataWriter = chart.getDataWriter();
+ JMenuItem exportDataItem = new JMenuItem("Export plot data");
+ exportDataItem.addActionListener( new ExportChartDataActionListener(parent, dataWriter, chart.getTitle()));
+ return exportDataItem;
+ }
+
+
+ /**
+ * Show into the split of the selected tab the text values selected.
+ *
+ * @param reporter
+ * BamQCRegionReporter data input values
+ */
+ private void prepareHtmlSummary(StatsReporter reporter) {
+ HtmlJPanel panelDerecha = new HtmlJPanel();
+ panelDerecha.setSize(rightScrollPane.getWidth(), rightScrollPane.getHeight());
+ panelDerecha.setFont(HomeFrame.defaultFont);
+ int width = rightScrollPane.getWidth() - 100;
+
+ StringBuilder summaryHtml = new StringBuilder();
+
+ summaryHtml.append( HtmlJPanel.getHeader() );
+ summaryHtml.append(reporter.getSummary(width));
+ summaryHtml.append( HtmlJPanel.getHeadFooter() );
+
+ panelDerecha.setHtmlPage(summaryHtml.toString());
+ rightScrollPane.setViewportView(panelDerecha);
+ }
+
+ private void prepareHtmlInputDescription(StatsReporter reporter) {
+ int width = rightScrollPane.getWidth() - 100;
+ String inputDescText = reporter.getInputDescription(width);
+
+ if (inputDescText != null) {
+ HtmlJPanel htmlPanel = new HtmlJPanel();
+ htmlPanel.setSize(rightScrollPane.getWidth(), rightScrollPane.getHeight());
+ htmlPanel.setFont(HomeFrame.defaultFont);
+
+ StringBuilder inputDesc = new StringBuilder();
+ inputDesc.append( HtmlJPanel.getHeader() );
+ inputDesc.append( inputDescText );
+ inputDesc.append( HtmlJPanel.getHeadFooter() );
+ htmlPanel.setHtmlPage(inputDesc.toString());
+
+ rightScrollPane.setViewportView(htmlPanel);
+ }
+ }
+
+ /**
+ * Action to show or hide the submenu of graphics images
+ *
+ * @param name Action name
+ * @return AbstractAction with the event selected
+ */
+ private AbstractAction getActionShowSubMenu(String name) {
+ return new AbstractAction(name, null) {
+ private static final long serialVersionUID = -6311968455290159751L;
+
+ public void actionPerformed(ActionEvent evt) {
+ refreshLeftMenu(evt);
+ }
+ };
+}
+
+ @Override
+ public void componentResized(ComponentEvent componentEvent) {
+ Component c = componentEvent.getComponent();
+ GraphicImagePanel imagePanel = tabPageController.getGraphicImage();
+ if (c == imagePanel && tabPageController.getTypeAnalysis() != AnalysisType.CLUSTERING) {
+ imagePanel.resizeImage(c.getWidth(), c.getHeight());
+ rightScrollPane.setViewportView(imagePanel);
+ }
+ }
+
+ @Override
+ public void componentMoved(ComponentEvent componentEvent) {
+ //Do nothing
+ }
+
+ @Override
+ public void componentShown(ComponentEvent componentEvent) {
+ //Do nothing
+ }
+
+ @Override
+ public void componentHidden(ComponentEvent componentEvent) {
+ //Do nothing
+ }
+}
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/panels/OpenLoadedStatistics.java~ b/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/panels/OpenLoadedStatistics.java~
new file mode 100644
index 0000000..908d04f
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/panels/OpenLoadedStatistics.java~
@@ -0,0 +1,879 @@
+package org.bioinfo.ngs.qc.qualimap.gui.panels;
+
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Cursor;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.event.ActionEvent;
+import java.awt.event.MouseEvent;
+import java.awt.image.BufferedImage;
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileReader;
+import java.io.IOException;
+import java.util.Iterator;
+import java.util.Map;
+
+import javax.swing.AbstractAction;
+import javax.swing.GroupLayout;
+import javax.swing.ImageIcon;
+import javax.swing.JCheckBox;
+import javax.swing.JComponent;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JSplitPane;
+import javax.swing.JTextField;
+import javax.swing.JViewport;
+import javax.swing.ScrollPaneConstants;
+
+import org.bioinfo.commons.log.Logger;
+import org.bioinfo.ngs.qc.qualimap.beans.BamQCRegionReporter;
+import org.bioinfo.ngs.qc.qualimap.gui.frames.HomeFrame;
+import org.bioinfo.ngs.qc.qualimap.gui.utils.Constants;
+import org.bioinfo.ngs.qc.qualimap.gui.utils.GraphicImagePanel;
+import org.bioinfo.ngs.qc.qualimap.gui.utils.JLabelMouseListener;
+import org.bioinfo.ngs.qc.qualimap.gui.utils.ReferencePosition;
+import org.bioinfo.ngs.qc.qualimap.gui.utils.StringUtilsSwing;
+import org.bioinfo.ngs.qc.qualimap.gui.utils.TabPropertiesVO;
+import org.jfree.chart.ChartPanel;
+import org.jfree.chart.JFreeChart;
+
+/**
+ * Class to manage the statistics loaded from a determinate file
+ *
+ * @author Luis Miguel Cruz
+ */
+public class OpenLoadedStatistics extends JPanel {
+ private static final long serialVersionUID = -6408484044729636203L;
+ HomeFrame homeFrame;
+ protected Logger logger;
+
+ private static final ImageIcon TREEMINUSICON = new ImageIcon(Class.class.getResource(Constants.pathImages + "minus_blue.png"));
+
+ /** Panels that contains the dynamic structures */
+ private JScrollPane scrollPaneIzquierda, scrollPaneDerecha;
+
+ /** Variable to manage the left panel that contains the links to the results */
+ private JPanel panelIzquierda;
+
+ /**
+ * Variable to store the last component inserted visible inserted into the
+ * left menu, to know the position in the screen for the next element that
+ * the user can see.
+ */
+ private Component lastComponentVisible;
+
+ /**
+ * Variable to store the vertical position to set the next element of a
+ * fieldset into the right panel at each moment
+ */
+ private int heightValue;
+ private JLabel summaryLable;
+
+ public OpenLoadedStatistics() {
+ super();
+ }
+
+ /**
+ * Show the statistics loaded into the tab selected
+ *
+ * @param homeFrame
+ * HomeFrame reference that contains the reference to the wrapper
+ * @return JSplitPane, User Interface with the data loaded.
+ */
+ public JSplitPane getLoadedStatistics(HomeFrame homeFrame) {
+ this.homeFrame = homeFrame;
+
+ JSplitPane statisticsContainer = new JSplitPane(JSplitPane.HORIZONTAL_SPLIT);
+ statisticsContainer.setDividerSize(2);
+ int leftPanelWidth = 250;
+
+ panelIzquierda = new JPanel();
+ panelIzquierda.setLayout(new GroupLayout((JComponent) panelIzquierda));
+ scrollPaneIzquierda = new JScrollPane(panelIzquierda);
+ scrollPaneIzquierda.setHorizontalScrollBarPolicy(ScrollPaneConstants.HORIZONTAL_SCROLLBAR_NEVER);
+ scrollPaneIzquierda.setVerticalScrollBarPolicy(ScrollPaneConstants.VERTICAL_SCROLLBAR_AS_NEEDED);
+ scrollPaneIzquierda.setMinimumSize(new Dimension(leftPanelWidth, 500));
+ scrollPaneIzquierda.setPreferredSize(new Dimension(leftPanelWidth, 2000));
+ scrollPaneIzquierda.setViewportView(panelIzquierda);
+
+ scrollPaneDerecha = new JScrollPane();
+ scrollPaneDerecha.setHorizontalScrollBarPolicy(ScrollPaneConstants.HORIZONTAL_SCROLLBAR_AS_NEEDED);
+ scrollPaneDerecha.setVerticalScrollBarPolicy(ScrollPaneConstants.VERTICAL_SCROLLBAR_AS_NEEDED);
+
+ TabPropertiesVO tabProperties = homeFrame.getListTabsProperties().get(homeFrame.getTabbedPane().getSelectedIndex());
+
+ if (tabProperties.getTypeAnalysis().compareTo(Constants.TYPE_BAM_ANALYSIS_RNA) == 0) {
+ fillLeftRnaSplit();
+ fillRightSplit();
+ } else {
+ fillLeftSplit();
+ fillRightSplit();
+ }
+
+ statisticsContainer.setLeftComponent(scrollPaneIzquierda);
+ statisticsContainer.setRightComponent(scrollPaneDerecha);
+ statisticsContainer.validate();
+ scrollPaneIzquierda.validate();
+ return statisticsContainer;
+ }
+
+
+
+ /**
+ * Function that load the left panel with the statistics links
+ */
+ private void fillLeftSplit() {
+ boolean showAditionalGraphicsInfo = homeFrame.getListTabsProperties().get(homeFrame.getTabbedPane().getSelectedIndex()).isGffSelected();
+
+ TabPropertiesVO tabProperties = homeFrame.getListTabsProperties().get(homeFrame.getTabbedPane().getSelectedIndex());
+ tabProperties.setLastLinkSelected(null);
+
+ if (!showAditionalGraphicsInfo) {
+ JCheckBox checkFirstSection = new JCheckBox("Results");
+ checkFirstSection.setSelected(true);
+ checkFirstSection.setIcon(new ImageIcon(getClass().getResource(Constants.pathImages + "add.png")));
+ checkFirstSection.setSelectedIcon(TREEMINUSICON);
+ checkFirstSection.setCursor(Cursor.getPredefinedCursor(Cursor.HAND_CURSOR));
+ checkFirstSection.setSize(checkFirstSection.getPreferredSize());
+ checkFirstSection.setLocation(0, 3);
+ checkFirstSection.setAction(getActionShowSubMenu("Results"));
+ panelIzquierda.add(checkFirstSection);
+
+ Integer marginSubMenu = checkFirstSection.getX() + Constants.marginLeftForElementSubMenu;
+
+ summaryLable = fillLabelSubMenuText("Summary", checkFirstSection, marginSubMenu, null, Constants.REPORT_INPUT_BAM_FILE);
+ summaryLable.setIcon(new ImageIcon(getClass().getResource(Constants.pathImages + "bullet_yellow.png")));
+ summaryLable.setToolTipText("Basic information and statistics for the alignment sequencing input");
+ panelIzquierda.add(summaryLable);
+
+ JLabel j1_1 = fillLabelSubMenuGraphic("Coverage Across Reference", summaryLable, marginSubMenu, Constants.GRAPHIC_NAME_GENOME_COVERAGE_ACROSS_REFERENCE);
+ panelIzquierda.add(j1_1);
+
+ JLabel j1_2 = fillLabelSubMenuGraphic("Coverage Histogram", j1_1, marginSubMenu, Constants.GRAPHIC_NAME_GENOME_COVERAGE_HISTOGRAM);
+ j1_2.setToolTipText("Frequency histogram of the coverage");
+ panelIzquierda.add(j1_2);
+
+ JLabel j1_3 = fillLabelSubMenuGraphic("Coverage Histogram (0-50x)", j1_2, marginSubMenu, Constants.GRAPHIC_NAME_GENOME_COVERAGE_HISTOGRAM_0_50);
+ j1_3.setToolTipText("There is often big picks of coverage across the reference " + "and the scale of the Coverage Histogram graph scale may not be adequate. " + "In order to solve this, in this graph genome locations with a coverage greater " + "than 50X are groped into the last bin");
+
+ panelIzquierda.add(j1_3);
+
+ JLabel j1_4 = fillLabelSubMenuGraphic("Coverage Quota", j1_3, marginSubMenu, Constants.GRAPHIC_NAME_GENOME_COVERAGE_QUOTA);
+ j1_4.setToolTipText("Provides an easy way of viewing how much reference has been " + "sequenced with a coverage higher than a selected level");
+ panelIzquierda.add(j1_4);
+
+ JLabel j1_5 = fillLabelSubMenuGraphic("Mapping Quality Across Ref.", j1_4, marginSubMenu, Constants.GRAPHIC_NAME_GENOME_MAPPING_QUALITY_ACROSS_REFERENCE);
+ j1_5.setIcon(new ImageIcon(getClass().getResource(Constants.pathImages + "bullet_blue.png")));
+ j1_5.setToolTipText("Mapping Quality Across Reference");
+ panelIzquierda.add(j1_5);
+
+ JLabel j1_6 = fillLabelSubMenuGraphic("Mapping Quality Histogram", j1_5, marginSubMenu, Constants.GRAPHIC_NAME_GENOME_MAPPING_QUALITY_HISTOGRAM);
+ j1_6.setIcon(new ImageIcon(getClass().getResource(Constants.pathImages + "bullet_blue.png")));
+ j1_6.setToolTipText("Frequency histogram of the mapping quality");
+ panelIzquierda.add(j1_6);
+
+ // JLabel j1_7 =
+ // fillLabelSubMenuGraphic("Nucleotide Rel. Content", j1_6,
+ // marginSubMenu,
+ // Constants.GRAPHIC_NAME_GENOME_NUCLEOTIDE_RELATIVE_CONTENT);
+ // j1_7.setIcon(new
+ // ImageIcon(getClass().getResource(Constants.pathImages +
+ // "bullet_purple.png")));
+ // j1_7.setToolTipText("Nucleotide Relative Content");
+ // panelIzquierda.add(j1_7);
+ //
+ // JLabel j1_8 =
+ // fillLabelSubMenuGraphic("GC/AT Relative Content", j1_7,
+ // marginSubMenu,
+ // Constants.GRAPHIC_NAME_GENOME_GC_AT_RELATIVE_CONTENT);
+ // j1_8.setIcon(new
+ // ImageIcon(getClass().getResource(Constants.pathImages +
+ // "bullet_purple.png")));
+ // panelIzquierda.add(j1_8);
+
+ lastComponentVisible = panelIzquierda.getComponent(panelIzquierda.getComponentCount() - 1);
+
+ } else if (showAditionalGraphicsInfo) {
+ JCheckBox checkFirstSection = new JCheckBox("Reads inside region");
+ checkFirstSection.setSelected(true);
+ checkFirstSection.setIcon(new ImageIcon(getClass().getResource(Constants.pathImages + "add.png")));
+ checkFirstSection.setSelectedIcon(TREEMINUSICON);
+ checkFirstSection.setCursor(Cursor.getPredefinedCursor(Cursor.HAND_CURSOR));
+ checkFirstSection.setSize(checkFirstSection.getPreferredSize());
+ checkFirstSection.setLocation(0, 3);
+ checkFirstSection.setAction(getActionShowSubMenu("Reads inside region"));
+ panelIzquierda.add(checkFirstSection);
+
+ Integer marginSubMenu = checkFirstSection.getX() + Constants.marginLeftForElementSubMenu;
+
+ lastComponentVisible = panelIzquierda.getComponent(panelIzquierda.getComponentCount() - 1);
+ summaryLable = fillLabelSubMenuText("Summary", checkFirstSection, marginSubMenu, null, Constants.REPORT_INSIDE_BAM_FILE);
+ summaryLable.setIcon(new ImageIcon(getClass().getResource(Constants.pathImages + "bullet_yellow.png")));
+ summaryLable.setToolTipText("Basic information and statistics for the alignment sequencing input");
+ panelIzquierda.add(summaryLable);
+
+ JLabel j2_1 = fillLabelSubMenuGraphic("Coverage Across Reference", summaryLable, marginSubMenu, Constants.GRAPHIC_NAME_GENOME_INSIDE_COVERAGE_ACROSS_REFERENCE);
+ panelIzquierda.add(j2_1);
+
+ JLabel j2_2 = fillLabelSubMenuGraphic("Coverage Histogram", j2_1, marginSubMenu, Constants.GRAPHIC_NAME_GENOME_INSIDE_COVERAGE_HISTOGRAM);
+ j2_2.setToolTipText("Frequency histogram of the coverage");
+ panelIzquierda.add(j2_2);
+
+ JLabel j2_3 = fillLabelSubMenuGraphic("Coverage Histogram (0-50x)", j2_2, marginSubMenu, Constants.GRAPHIC_NAME_GENOME_INSIDE_COVERAGE_HISTOGRAM_0_50);
+ j2_3.setToolTipText("There is often big picks of coverage across the reference " + "and the scale of the Coverage Histogram graph scale may not be adequate. " + "In order to solve this, in this graph genome locations with a coverage greater " + "than 50X are groped into the last bin");
+ panelIzquierda.add(j2_3);
+
+ JLabel j2_4 = fillLabelSubMenuGraphic("Coverage Quota", j2_3, marginSubMenu, Constants.GRAPHIC_NAME_GENOME_INSIDE_COVERAGE_QUOTA);
+ j2_4.setToolTipText("Provides an easy way of viewing how much reference has been " + "sequenced with a coverage higher than a selected level");
+ panelIzquierda.add(j2_4);
+
+ JLabel j2_5 = fillLabelSubMenuGraphic("Mapping Quality Across Ref.", j2_4, marginSubMenu, Constants.GRAPHIC_NAME_GENOME_INSIDE_MAPPING_QUALITY_ACROSS_REFERENCE);
+ j2_5.setIcon(new ImageIcon(getClass().getResource(Constants.pathImages + "bullet_blue.png")));
+ j2_5.setToolTipText("Mapping Quality Across Reference");
+ panelIzquierda.add(j2_5);
+
+ JLabel j2_6 = fillLabelSubMenuGraphic("Mapping Quality Histogram", j2_5, marginSubMenu, Constants.GRAPHIC_NAME_GENOME_INSIDE_MAPPING_QUALITY_HISTOGRAM);
+ j2_6.setIcon(new ImageIcon(getClass().getResource(Constants.pathImages + "bullet_blue.png")));
+ j2_6.setToolTipText("Frequency histogram of the mapping quality");
+ panelIzquierda.add(j2_6);
+
+ // JLabel j2_7 =
+ // fillLabelSubMenuGraphic("Nucleotide Rel. Content", j2_6,
+ // marginSubMenu,
+ // Constants.GRAPHIC_NAME_GENOME_INSIDE_NUCLEOTIDE_RELATIVE_CONTENT,
+ // false);
+ // j2_7.setToolTipText("Nucleotide Relative Content");
+ // j2_7.setIcon(new
+ // ImageIcon(getClass().getResource(Constants.pathImages +
+ // "bullet_purple.png")));
+ // panelIzquierda.add(j2_7);
+ //
+ // JLabel j2_8 =
+ // fillLabelSubMenuGraphic("GC/AT Relative Content", j2_7,
+ // marginSubMenu,
+ // Constants.GRAPHIC_NAME_GENOME_INSIDE_GC_AT_RELATIVE_CONTENT,
+ // false);
+ // j2_8.setIcon(new
+ // ImageIcon(getClass().getResource(Constants.pathImages +
+ // "bullet_purple.png")));
+ // panelIzquierda.add(j2_8);
+
+ lastComponentVisible = panelIzquierda.getComponent(panelIzquierda.getComponentCount() - 1);
+
+ JCheckBox checkSecondSection = new JCheckBox("Reads outside region");
+ checkSecondSection.setSelected(true);
+ checkSecondSection.setIcon(new ImageIcon(getClass().getResource(Constants.pathImages + "add.png")));
+ checkSecondSection.setSelectedIcon(TREEMINUSICON);
+ checkSecondSection.setCursor(Cursor.getPredefinedCursor(Cursor.HAND_CURSOR));
+ checkSecondSection.setSize(checkSecondSection.getPreferredSize());
+ checkSecondSection.setLocation(0, lastComponentVisible.getY() + lastComponentVisible.getHeight() + Constants.marginTopForElementSubMenu);
+ checkSecondSection.setAction(getActionShowSubMenu("Reads outside region"));
+ panelIzquierda.add(checkSecondSection);
+
+ lastComponentVisible = panelIzquierda.getComponent(panelIzquierda.getComponentCount() - 1);
+
+ // General Summary
+ JLabel summary = fillLabelSubMenuText("Summary", checkFirstSection, marginSubMenu, null, Constants.REPORT_OUTSIDE_BAM_FILE);
+ summary.setIcon(new ImageIcon(getClass().getResource(Constants.pathImages + "bullet_yellow.png")));
+ summary.setToolTipText("Basic information and statistics for the alignment sequencing input");
+ panelIzquierda.add(summary);
+
+ JLabel j3_1 = fillLabelSubMenuGraphic("Coverage Across Reference", checkSecondSection, marginSubMenu, Constants.GRAPHIC_NAME_GENOME_OUTSIDE_COVERAGE_ACROSS_REFERENCE, false);
+ panelIzquierda.add(j3_1);
+
+ JLabel j3_2 = fillLabelSubMenuGraphic("Coverage Histogram", j3_1, marginSubMenu, Constants.GRAPHIC_NAME_GENOME_OUTSIDE_COVERAGE_HISTOGRAM, false);
+ j3_2.setToolTipText("Frequency histogram of the coverage");
+ panelIzquierda.add(j3_2);
+
+ JLabel j3_3 = fillLabelSubMenuGraphic("Coverage Histogram (0-50x)", j3_2, marginSubMenu, Constants.GRAPHIC_NAME_GENOME_OUTSIDE_COVERAGE_HISTOGRAM_0_50, false);
+ j3_3.setToolTipText("There is often big picks of coverage across the reference " + "and the scale of the Coverage Histogram graph scale may not be adequate. " + "In order to solve this, in this graph genome locations with a coverage greater " + "than 50X are groped into the last bin");
+ panelIzquierda.add(j3_3);
+
+ JLabel j3_4 = fillLabelSubMenuGraphic("Coverage Quota", j3_3, marginSubMenu, Constants.GRAPHIC_NAME_GENOME_OUTSIDE_COVERAGE_QUOTA, false);
+ j3_4.setToolTipText("Provides an easy way of viewing how much reference has been " + "sequenced with a coverage higher than a selected level");
+ panelIzquierda.add(j3_4);
+
+ JLabel j3_5 = fillLabelSubMenuGraphic("Mapping Quality Across Ref.", j3_4, marginSubMenu, Constants.GRAPHIC_NAME_GENOME_OUTSIDE_MAPPING_QUALITY_ACROSS_REFERENCE, false);
+ j3_5.setIcon(new ImageIcon(getClass().getResource(Constants.pathImages + "bullet_blue.png")));
+ j3_5.setToolTipText("Mapping Quality Across Reference");
+ panelIzquierda.add(j3_5);
+
+ JLabel j3_6 = fillLabelSubMenuGraphic("Mapping Quality Histogram", j3_5, marginSubMenu, Constants.GRAPHIC_NAME_GENOME_OUTSIDE_MAPPING_QUALITY_HISTOGRAM, false);
+ j3_6.setIcon(new ImageIcon(getClass().getResource(Constants.pathImages + "bullet_blue.png")));
+ j3_6.setToolTipText("Frequency histogram of the mapping quality");
+ panelIzquierda.add(j3_6);
+
+ // JLabel j3_7 =
+ // fillLabelSubMenuGraphic("Nucleotide Rel. Content", j3_6,
+ // marginSubMenu,
+ // Constants.GRAPHIC_NAME_GENOME_OUTSIDE_NUCLEOTIDE_RELATIVE_CONTENT,
+ // false);
+ // j3_7.setIcon(new
+ // ImageIcon(getClass().getResource(Constants.pathImages +
+ // "bullet_purple.png")));
+ // j3_7.setToolTipText("Nucleotide Relative Content");
+ // panelIzquierda.add(j3_7);
+ //
+ // JLabel j3_8 =
+ // fillLabelSubMenuGraphic("GC/AT Relative Content", j3_7,
+ // marginSubMenu,
+ // Constants.GRAPHIC_NAME_GENOME_OUTSIDE_GC_AT_RELATIVE_CONTENT,
+ // false);
+ // j3_8.setIcon(new
+ // ImageIcon(getClass().getResource(Constants.pathImages +
+ // "bullet_purple.png")));
+ // panelIzquierda.add(j3_8);
+ }
+
+ // Set the last component showed at the left split
+ tabProperties.setLeftSplitLastElement((JComponent) lastComponentVisible);
+ }
+
+ /**
+ * Function that load the left panel with the statistics links for the
+ * RNA-sqe
+ */
+ private void fillLeftRnaSplit() {
+ TabPropertiesVO tabProperties = homeFrame.getListTabsProperties().get(homeFrame.getTabbedPane().getSelectedIndex());
+ boolean infoFileSelected = tabProperties.getRnaAnalysisVO().getInfoFileIsSet();
+ boolean speciesFileSelected = tabProperties.getRnaAnalysisVO().getSpecieFileIsSet();
+ tabProperties.setLastLinkSelected(null);
+
+ JCheckBox checkFirstSection = new JCheckBox("Results");
+ checkFirstSection.setSelected(true);
+ checkFirstSection.setIcon(new ImageIcon(getClass().getResource(Constants.pathImages + "add.png")));
+ checkFirstSection.setSelectedIcon(TREEMINUSICON);
+ checkFirstSection.setCursor(Cursor.getPredefinedCursor(Cursor.HAND_CURSOR));
+ checkFirstSection.setSize(checkFirstSection.getPreferredSize());
+ checkFirstSection.setLocation(0, 3);
+ checkFirstSection.setAction(getActionShowSubMenu("Results"));
+ ReferencePosition referencePosition = new ReferencePosition(checkFirstSection);
+ panelIzquierda.add(checkFirstSection);
+
+ Integer marginSubMenu = referencePosition.getX() + Constants.marginLeftForElementSubMenu;
+
+ summaryLable = fillLabelSubMenuGraphic("Global Saturation", referencePosition, marginSubMenu, Constants.GRAPHIC_NAME_RNA_GLOBAL_SATURATION);
+ summaryLable.setIcon(new ImageIcon(getClass().getResource(Constants.pathImages + "bullet_yellow.png")));
+ summaryLable.setToolTipText("Basic information and statistics for the alignment sequencing input");
+ referencePosition.setComponent(summaryLable);
+ panelIzquierda.add(summaryLable);
+
+ if (infoFileSelected || speciesFileSelected) {
+
+ Map<String, Object> mapGenotypes = tabProperties.getRnaAnalysisVO().getMapClassesInfoFile();
+ JLabel j1_1 = fillLabelSubMenuGraphic("Saturation per class", referencePosition, marginSubMenu, Constants.GRAPHIC_NAME_RNA_SATURATION_PER_CLASS, true);
+ referencePosition.setComponent(j1_1);
+ panelIzquierda.add(j1_1);
+
+ JLabel j1_2 = fillLabelSubMenuGraphic("Counts per class", referencePosition, marginSubMenu, Constants.GRAPHIC_NAME_RNA_COUNTS_PER_CLASS, true);
+ j1_2.setToolTipText("Frequency histogram of the coverage");
+ referencePosition.setComponent(j1_2);
+ panelIzquierda.add(j1_2);
+
+
+ JCheckBox checkSaturationSection = new JCheckBox("Saturations per class");
+ checkSaturationSection.setIcon(new ImageIcon(getClass().getResource(Constants.pathImages + "add.png")));
+ checkSaturationSection.setSelectedIcon(TREEMINUSICON);
+ checkSaturationSection.setCursor(Cursor.getPredefinedCursor(Cursor.HAND_CURSOR));
+ checkSaturationSection.setSize(checkSaturationSection.getPreferredSize());
+ checkSaturationSection.setLocation(0, referencePosition.getY() + referencePosition.getHeight() + Constants.marginTopForElementSubMenu);
+ checkSaturationSection.setAction(getActionShowSubMenu("Saturations per class"));
+ checkSaturationSection.setSelected(true);
+ checkSaturationSection.setVisible(true);
+ referencePosition.setComponent(checkSaturationSection);
+ panelIzquierda.add(checkSaturationSection);
+
+
+ JLabel j = null;
+ Iterator it = mapGenotypes.entrySet().iterator();
+ while (it.hasNext()) {
+ Map.Entry<String, String> entry = (Map.Entry<String, String>) it.next();
+ j = fillLabelSubMenuGraphic(entry.getKey().toString(), referencePosition, marginSubMenu, entry.getValue().toString(), true);
+ referencePosition.setComponent(j);
+ panelIzquierda.add(j);
+ }
+
+ JCheckBox checkCountsSection = new JCheckBox("Counts per class");
+ checkCountsSection.setIcon(new ImageIcon(getClass().getResource(Constants.pathImages + "add.png")));
+ checkCountsSection.setSelectedIcon(TREEMINUSICON);
+ checkCountsSection.setCursor(Cursor.getPredefinedCursor(Cursor.HAND_CURSOR));
+ checkCountsSection.setSize(checkCountsSection.getPreferredSize());
+ checkCountsSection.setLocation(0, referencePosition.getY() + referencePosition.getHeight() + Constants.marginTopForElementSubMenu);
+ checkCountsSection.setAction(getActionShowSubMenu("Counts per class"));
+ checkCountsSection.setVisible(true);
+ checkCountsSection.setSelected(true);
+ referencePosition.setComponent(checkCountsSection);
+ panelIzquierda.add(checkCountsSection);
+
+
+ it = mapGenotypes.entrySet().iterator();
+ while (it.hasNext()) {
+ Map.Entry<String, String> entry = (Map.Entry<String, String>) it.next();
+ j = fillLabelSubMenuGraphic(entry.getKey().toString(), referencePosition, marginSubMenu, entry.getKey().toString() + "_boxplot.png", true);
+ referencePosition.setComponent(j);
+ panelIzquierda.add(j);
+ }
+ }
+
+ // Set the last component showed at the left split
+ lastComponentVisible = panelIzquierda.getComponent(panelIzquierda.getComponentCount() - 1);
+ tabProperties.setLeftSplitLastElement((JComponent) lastComponentVisible);
+ }
+
+ /**
+ * Function that load the right panel with the statistics data
+ */
+ private void fillRightSplit() {
+ JPanel panelDerecha = new JPanel();
+ panelDerecha.setLayout(new GroupLayout((JComponent) panelDerecha));
+ // panelDerecha.setSize(scrollPaneDerecha.getWidth(),
+ // scrollPaneDerecha.getHeight());
+
+ scrollPaneDerecha.setViewportView(panelDerecha);
+ }
+
+ /**
+ * Refresh the left menu showing or hiding the elements depends on the user
+ * selection.
+ *
+ * @param evt
+ * ActionEvent that contains the JCheckbox selected by the user.
+ */
+ private void refreshLeftMenu(ActionEvent evt) {
+ int i = 0;
+ boolean afterSubmenuChanged = false;
+ Component elem;
+ JCheckBox checkBoxSelected = (JCheckBox) evt.getSource();
+ boolean showItem = (checkBoxSelected).isSelected();
+
+ lastComponentVisible = panelIzquierda.getComponent(0);
+ while (i < panelIzquierda.getComponentCount()) {
+ elem = panelIzquierda.getComponent(i);
+
+ // We have to get the last checkbox selected to change the
+ // location of the elements of its submenu.
+ if (elem instanceof JCheckBox) {
+ if (checkBoxSelected.equals(elem)) {
+ afterSubmenuChanged = true;
+ } else {
+ afterSubmenuChanged = false;
+ }
+ } else if (elem instanceof JLabel && afterSubmenuChanged) {
+ // If the element is into the submenu of the checkbox selected
+ // and this checkbox have to show the elements, we show this
+ // element.
+ if (showItem) {
+ elem.setVisible(true);
+ } else {
+ elem.setVisible(false);
+ }
+ }
+
+ if (i > 0) {
+ elem.setLocation(elem.getLocation().x, lastComponentVisible.getY() + lastComponentVisible.getHeight() + Constants.marginTopForElementSubMenu);
+ resizeLeftPanel(elem);
+ }
+
+ if (elem.isVisible()) {
+ lastComponentVisible = elem;
+ }
+
+ i++;
+ }
+ }
+
+
+
+ /**
+ * Function to resize the left panel if the content is bigger than the
+ * reserved space adding scroll bars.
+ *
+ * @param elem
+ * Component that contains the element with the size and position
+ * of the last element to draw
+ */
+ private void resizeLeftPanel(Component elem) {
+ JViewport panelIzquierda = (JViewport) scrollPaneIzquierda.getViewport();
+ Component subElementIzquierda = panelIzquierda.getComponent(0);
+ TabPropertiesVO tabProperties = homeFrame.getListTabsProperties().get(homeFrame.getTabbedPane().getSelectedIndex());
+
+ if (subElementIzquierda instanceof JPanel) {
+ tabProperties.setLeftSplitLastElement((JComponent) lastComponentVisible);
+ if (lastComponentVisible.getX() + lastComponentVisible.getWidth() <= scrollPaneIzquierda.getHeight() && lastComponentVisible.getY() + lastComponentVisible.getHeight() <= scrollPaneIzquierda.getWidth()) {
+ this.panelIzquierda.setSize(this.panelIzquierda.getWidth(), lastComponentVisible.getY() + lastComponentVisible.getHeight());
+ this.panelIzquierda.setPreferredSize(this.panelIzquierda.getSize());
+ } else if (lastComponentVisible.getY() + lastComponentVisible.getHeight() > scrollPaneIzquierda.getWidth()) {
+ this.panelIzquierda.setSize(this.panelIzquierda.getWidth(), elem.getY() + elem.getHeight());
+ this.panelIzquierda.setPreferredSize(this.panelIzquierda.getSize());
+ }
+ }
+ panelIzquierda.validate();
+ }
+
+ /**
+ * Creates a label for the submenu with the necessary properties for the
+ * graphics links
+ *
+ * @param labelName
+ * Name displayed of the label
+ * @param locationRef
+ * position in the screen to refer
+ * @param marginSubMenu
+ * margin respect the element before
+ * @param graphicName
+ * name of the graphic to show if necessary
+ * @return JLabel label created
+ */
+ private JLabel fillLabelSubMenuGraphic(String labelName, Component locationRef, Integer marginSubMenu, String graphicName) {
+ return fillLabelSubMenuGraphic(labelName, locationRef, marginSubMenu, graphicName, true);
+ }
+
+ /**
+ * Creates a label for the submenu with the necessary properties for the
+ * graphic links.
+ *
+ * @param labelName
+ * Name displayed of the label
+ * @param locationRef
+ * position in the screen to refer
+ * @param marginSubMenu
+ * margin respect the element before
+ * @param graphicName
+ * name of the graphic to show if necessary
+ * @param boolean visibility of the label
+ * @return JLabel label created
+ */
+
+ private JLabel fillLabelSubMenuGraphic(String labelName, Component locationRef, Integer marginSubMenu, final String graphicName, boolean visible) {
+ final JLabel label = fillLabelLink(labelName, locationRef, marginSubMenu, visible);
+ label.addMouseListener(new JLabelMouseListener() {
+ public void mouseClicked(MouseEvent arg0) {
+ showLeftSideInformation(graphicName, label);
+ }
+ });
+ if (!visible) {
+ label.setVisible(false);
+ }
+
+ return label;
+ }
+
+ private JLabel fillLabelSubMenuText(String labelName, Component locationRef, Integer marginSubMenu, String textFileName, int typeReport) {
+ return fillLabelSubMenuText(labelName, locationRef, marginSubMenu, textFileName, true, typeReport);
+ }
+
+ private JLabel fillLabelSubMenuText(String labelName, Component locationRef, Integer marginSubMenu, final String textFileName, boolean visible, final int typeReport) {
+ final JLabel label = fillLabelLink(labelName, locationRef, marginSubMenu, visible);
+ label.addMouseListener(new JLabelMouseListener() {
+ public void mouseClicked(MouseEvent arg0) {
+ showLeftSideSummeryInformation(typeReport, label);
+ }
+ });
+ return label;
+ }
+
+ public void showLeftSideSummeryInformation(int typeReport, JLabel label) {
+ BamQCRegionReporter reporter = null;
+ // Select the reporter that contains the data
+ if (typeReport == Constants.REPORT_INPUT_BAM_FILE) {
+ reporter = homeFrame.getListTabsProperties().get(homeFrame.getTabbedPane().getSelectedIndex()).getReporter();
+ } else if (typeReport == Constants.REPORT_INSIDE_BAM_FILE) {
+ reporter = homeFrame.getListTabsProperties().get(homeFrame.getTabbedPane().getSelectedIndex()).getInsideReporter();
+ } else {
+ reporter = homeFrame.getListTabsProperties().get(homeFrame.getTabbedPane().getSelectedIndex()).getOutsideReporter();
+ }
+ openTextLink(reporter);
+ fillColorLink(label);
+ }
+
+ public void showSummary() {
+ if(this.summaryLable!=null){
+ BamQCRegionReporter reporter = null;
+ // Select the reporter that contains the data
+ if (homeFrame.getTypeAnalysis() == Constants.REPORT_INPUT_BAM_FILE) {
+ reporter = homeFrame.getListTabsProperties().get(homeFrame.getTabbedPane().getSelectedIndex()).getReporter();
+ } else if (homeFrame.getTypeAnalysis() == Constants.REPORT_INSIDE_BAM_FILE) {
+ reporter = homeFrame.getListTabsProperties().get(homeFrame.getTabbedPane().getSelectedIndex()).getInsideReporter();
+ } else {
+ reporter = homeFrame.getListTabsProperties().get(homeFrame.getTabbedPane().getSelectedIndex()).getOutsideReporter();
+ }
+ openTextLink(reporter);
+ fillColorLink(summaryLable);
+ }
+ }
+
+ private void showLeftSideInformation(String graphicName, JLabel label) {
+ // If we have a name of the graphic, we display it
+ TabPropertiesVO tabProperties = homeFrame.getListTabsProperties().get(homeFrame.getTabbedPane().getSelectedIndex());
+
+ if (graphicName != null) {
+ BamQCRegionReporter reporter = null;
+
+ if (tabProperties.getTypeAnalysis().compareTo(Constants.TYPE_BAM_ANALYSIS_DNA) == 0 || tabProperties.getTypeAnalysis().compareTo(Constants.TYPE_BAM_ANALYSIS_EXOME) == 0) {
+
+ // Select the reporter that contains the graphics
+ if (graphicName.startsWith("inside")) {
+ reporter = homeFrame.getListTabsProperties().get(homeFrame.getTabbedPane().getSelectedIndex()).getInsideReporter();
+ } else if (graphicName.startsWith("outside")) {
+ reporter = homeFrame.getListTabsProperties().get(homeFrame.getTabbedPane().getSelectedIndex()).getOutsideReporter();
+ } else {
+ reporter = homeFrame.getListTabsProperties().get(homeFrame.getTabbedPane().getSelectedIndex()).getReporter();
+ }
+
+ openGraphic(graphicName, reporter);
+ } else {
+ reporter = homeFrame.getListTabsProperties().get(homeFrame.getTabbedPane().getSelectedIndex()).getReporter();
+ openGraphic(graphicName, reporter);
+ }
+ }
+ fillColorLink(label);
+ }
+
+ /**
+ * Fill the commons properties for the graphic and text links
+ *
+ * @param labelName
+ * Name displayed of the label
+ * @param locationRef
+ * position in the screen to refer
+ * @param marginSubMenu
+ * margin respect the element before
+ * @param boolean visibility of the label
+ * @return JLabel label set
+ */
+ private JLabel fillLabelLink(String labelName, Component locationRef, Integer marginSubMenu, boolean visible) {
+ JLabel label = new JLabel(labelName);
+ label.setFont(new Font(label.getFont().getFontName(), label.getFont().getStyle(), 11));
+ label.setIcon(new ImageIcon(getClass().getResource(Constants.pathImages + "bullet_green.png")));
+ label.setSize(label.getPreferredSize());
+ label.setOpaque(true);
+ label.setLocation(marginSubMenu, locationRef.getY() + locationRef.getHeight() + Constants.marginTopForElementSubMenu);
+ label.setCursor(Cursor.getPredefinedCursor(Cursor.HAND_CURSOR));
+ label.setIconTextGap(0);
+ label.setToolTipText(labelName);
+
+ if (!visible) {
+ label.setVisible(false);
+ }
+ return label;
+ }
+
+ /**
+ * Fill the color of the link pressed by the user in the left menu
+ *
+ * @param label
+ * label to set the colors
+ */
+ private void fillColorLink(JLabel label) {
+ TabPropertiesVO tabProperties = homeFrame.getListTabsProperties().get(homeFrame.getTabbedPane().getSelectedIndex());
+
+ if (tabProperties.getLastLinkSelected() != null) {
+ tabProperties.getLastLinkSelected().setBackground(null);
+ tabProperties.getLastLinkSelected().setFont(new Font(label.getFont().getFontName(), label.getFont().getStyle(), label.getFont().getSize()));
+ }
+ if (label != null) {
+ label.setBackground(new Color(240, 230, 140));
+ label.setFont(HomeFrame.defaultFontItalic);
+ tabProperties.setLastLinkSelected(label);
+ }
+ }
+
+ /**
+ * Show into the split of the selected tab the selected graphic data.
+ *
+ * @param name
+ * Name of the file loaded (if its a graphic file).
+ * @param reporter
+ * BamQCRegionReporter graphic input values
+ */
+ private void openGraphic(String name, BamQCRegionReporter reporter) {
+ Object imageToDisplay = reporter.getMapCharts().get(name);
+
+ // The image can be a JFreeChart generated of come from a file like a
+ // BufferedImage
+ if (imageToDisplay instanceof JFreeChart) {
+ // Create the ChartPanel that contains the chart
+ ChartPanel panelImage = new ChartPanel((JFreeChart) imageToDisplay);
+ panelImage.setSize(scrollPaneDerecha.getSize());
+
+ scrollPaneDerecha.setViewportView(panelImage);
+ } else if (imageToDisplay instanceof BufferedImage) {
+ // Get a Singleton to manage the image to display
+ TabPropertiesVO tabProperties = homeFrame.getListTabsProperties().get(homeFrame.getTabbedPane().getSelectedIndex());
+
+ GraphicImagePanel panelImage = tabProperties.getGraphicImage();
+
+ // Set the image with the file image get
+ panelImage.setImage((BufferedImage) imageToDisplay);
+
+ // Scale the image
+ panelImage.resizeImage(scrollPaneDerecha.getWidth(), scrollPaneDerecha.getHeight());
+
+ scrollPaneDerecha.setViewportView(panelImage);
+ }
+ }
+
+ /**
+ * Show into the split of the selected tab the text values selected.
+ *
+ * @param reporter
+ * BamQCRegionReporter data input values
+ */
+ private void openTextLink(BamQCRegionReporter reporter) {
+ HtmlJPanel panelDerecha = new HtmlJPanel();
+ panelDerecha.setSize(scrollPaneDerecha.getWidth(), scrollPaneDerecha.getHeight());
+ panelDerecha.setFont(HomeFrame.defaultFont);
+ StringUtilsSwing sdf = new StringUtilsSwing();
+
+ StringBuffer summaryHtml = new StringBuffer("");
+ int width = scrollPaneDerecha.getWidth() - 100;
+
+ summaryHtml.append(HtmlJPanel.getHeader());
+ summaryHtml.append("<p align=center><b>Summary of: " + new File(reporter.getBamFileName()).getName() + "</b></p>" + HtmlJPanel.BR);
+ summaryHtml.append(HtmlJPanel.getTableHeader(width, "EEEEEE"));
+ summaryHtml.append(HtmlJPanel.COLSTART + "<b>Globals:</b>");
+ summaryHtml.append(HtmlJPanel.getTableHeader(width, "FFFFFF"));
+ summaryHtml.append(HtmlJPanel.COLSTARTFIX + "Number of bases" + HtmlJPanel.COLMID + sdf.formatLong(reporter.getBasesNumber()) + HtmlJPanel.COLEND);
+ summaryHtml.append(HtmlJPanel.COLSTARTFIX + "Number of reads" + HtmlJPanel.COLMID + sdf.formatLong(reporter.getNumReads()) + HtmlJPanel.COLEND);
+ summaryHtml.append(HtmlJPanel.COLSTARTFIX + "Number of mapped reads" + HtmlJPanel.COLMID + sdf.formatInteger(reporter.getNumMappedReads()) + HtmlJPanel.COLEND);
+ summaryHtml.append(HtmlJPanel.COLSTARTFIX + "Number of mapped bases" + HtmlJPanel.COLMID + sdf.formatLong(reporter.getNumMappedBases()) + HtmlJPanel.COLEND);
+ summaryHtml.append(HtmlJPanel.COLSTARTFIX + "Number of sequenced bases" + HtmlJPanel.COLMID + sdf.formatLong(reporter.getNumSequencedBases()) + HtmlJPanel.COLEND);
+ summaryHtml.append(HtmlJPanel.COLSTARTFIX + "Number of aligned bases" + HtmlJPanel.COLMID + sdf.formatLong(reporter.getNumAlignedBases()) + HtmlJPanel.COLEND);
+ summaryHtml.append(HtmlJPanel.getTableFooter());
+
+ summaryHtml.append(HtmlJPanel.BR);
+ summaryHtml.append("<b>ACGT Content:</b>" + HtmlJPanel.BR);
+ summaryHtml.append(HtmlJPanel.getTableHeader(width, "FFFFFF"));
+ summaryHtml.append(HtmlJPanel.COLSTARTFIX + "Number of A's" + HtmlJPanel.COLMID + sdf.formatLong(reporter.getaNumber()) + HtmlJPanel.COLEND);
+ summaryHtml.append(HtmlJPanel.COLSTARTFIX + "Number of C's" + HtmlJPanel.COLMID + sdf.formatLong(reporter.getcNumber()) + HtmlJPanel.COLEND);
+ summaryHtml.append(HtmlJPanel.COLSTARTFIX + "Number of T's" + HtmlJPanel.COLMID + sdf.formatLong(reporter.gettNumber()) + HtmlJPanel.COLEND);
+ summaryHtml.append(HtmlJPanel.COLSTARTFIX + "Number of G's" + HtmlJPanel.COLMID + sdf.formatLong(reporter.getgNumber()) + HtmlJPanel.COLEND);
+ summaryHtml.append(HtmlJPanel.COLSTARTFIX + "Number of N's" + HtmlJPanel.COLMID + sdf.formatLong(reporter.getnNumber()) + HtmlJPanel.COLEND);
+ summaryHtml.append(HtmlJPanel.COLSTARTFIX + "GC Percentage" + HtmlJPanel.COLMID + sdf.formatPercentage(reporter.getGcPercent()) + HtmlJPanel.COLEND);
+ summaryHtml.append(HtmlJPanel.COLSTARTFIX + "AT Percentage" + HtmlJPanel.COLMID + sdf.formatPercentage(reporter.getAtPercent()) + HtmlJPanel.COLEND);
+ summaryHtml.append(HtmlJPanel.getTableFooter());
+
+ summaryHtml.append(HtmlJPanel.BR);
+ summaryHtml.append("<b>Coverage:</b>" + HtmlJPanel.BR);
+ summaryHtml.append(HtmlJPanel.getTableHeader(width, "FFFFFF"));
+ summaryHtml.append(HtmlJPanel.COLSTARTFIX + "Mean Coverage" + HtmlJPanel.COLMID + sdf.formatDecimal(reporter.getMeanCoverage()) + HtmlJPanel.COLEND);
+ summaryHtml.append(HtmlJPanel.COLSTARTFIX + "Std Percentage" + HtmlJPanel.COLMID + sdf.formatDecimal(reporter.getStdCoverage()) + HtmlJPanel.COLEND);
+ summaryHtml.append(HtmlJPanel.getTableFooter());
+
+ summaryHtml.append(HtmlJPanel.BR);
+ summaryHtml.append("<b>Mapping Quality:</b>");
+ summaryHtml.append(HtmlJPanel.getTableHeader(width, "FFFFFF"));
+ summaryHtml.append(HtmlJPanel.COLSTARTFIX + "Mean Mapping Quality:" + HtmlJPanel.COLMID + sdf.formatDecimal(reporter.getMeanMappingQuality()) + HtmlJPanel.COLEND);
+ summaryHtml.append(HtmlJPanel.getTableFooter());
+
+ if (homeFrame.getListTabsProperties().get(homeFrame.getTabbedPane().getSelectedIndex()).getTypeAnalysis().compareTo(Constants.TYPE_BAM_ANALYSIS_DNA) == 0) {
+ summaryHtml.append(HtmlJPanel.BR);
+ summaryHtml.append("<b>Chromosomes:</b>" + HtmlJPanel.BR);
+ summaryHtml.append(HtmlJPanel.getTableHeader(width, "FFFFFF"));
+ summaryHtml.append(fillHtmlTableFromFile(Constants.NAME_OF_FILE_CHROMOSOMES));
+ summaryHtml.append(HtmlJPanel.getTableFooter());
+ }
+ summaryHtml.append(HtmlJPanel.COLEND);
+ summaryHtml.append(HtmlJPanel.getTableFooter());
+ panelDerecha.setHtmlPage(summaryHtml.toString());
+ scrollPaneDerecha.setViewportView(panelDerecha);
+ }
+
+ private String fillHtmlTableFromFile(String fileName) {
+ StringBuffer htmlTable = new StringBuffer("");
+ TabPropertiesVO tabPropertiesVO = homeFrame.getListTabsProperties().get(homeFrame.getTabbedPane().getSelectedIndex());
+ BufferedReader br = null;
+ try {
+ br = new BufferedReader(new FileReader(new File("/tmp/outputs/" + tabPropertiesVO.getOutputFolder() + fileName)));
+ String strLine;
+ // Iterate the file reading the lines
+ while ((strLine = br.readLine()) != null) {
+ // Test if the read is the header of the table or not
+ if (strLine.startsWith("#")) {
+ strLine = strLine.substring(1);
+ String[] tableTitles = strLine.split("\t");
+ for (String s : tableTitles) {
+ htmlTable.append("<th align='left'>" + s + "</th>");
+ }
+ } else {
+ String[] tableValues = strLine.split("\t");
+ htmlTable.append(HtmlJPanel.COLSTART);
+ int i = 0;
+ for (String s : tableValues) {
+ i++;
+ htmlTable.append(s);
+ if (i < tableValues.length) {
+ htmlTable.append(HtmlJPanel.COLMID);
+ }
+ }
+ htmlTable.append(HtmlJPanel.COLEND);
+ }
+ }
+ } catch (FileNotFoundException e) {
+ System.out.println(e.getMessage());
+ } catch (IOException e) {
+ System.out.println(e.getMessage());
+ } finally {
+ if (br != null) {
+ try {
+ br.close();
+ } catch (IOException e) {
+ }
+ }
+ }
+ return htmlTable.toString();
+ }
+
+ /**
+ * Function to fill a row of the fieldset with the specific information
+ *
+ * @param labelName
+ * Name of the label for this line
+ * @param firstElement
+ * boolean to know if the element is in the first line in the
+ * fieldset
+ * @param fieldset
+ * Fieldset where we have to put the line
+ * @param value
+ * String with the value of the field
+ */
+ private void fillRowOfFieldsetDataInfo(String labelName, boolean firstElement, JLabel fieldset, String value) {
+ int hPosition = (firstElement ? Constants.marginTopForFirstElement : heightValue);
+
+ JLabel titleElemFieldset = new JLabel(labelName);
+ titleElemFieldset.setSize(Constants.labelInputElementWidthLong, Constants.elementHeight);
+ titleElemFieldset.setLocation(Constants.marginLeftForElement + 20, hPosition);
+ fieldset.add(titleElemFieldset);
+
+ JTextField valueElemFieldset = new JTextField();
+ valueElemFieldset.setSize(Constants.widthInputNumber, Constants.elementHeight);
+ valueElemFieldset.setLocation(titleElemFieldset.getX() + titleElemFieldset.getWidth() + Constants.marginLeftForElement, titleElemFieldset.getY());
+ valueElemFieldset.setEditable(false);
+ valueElemFieldset.setHorizontalAlignment(JTextField.RIGHT);
+ valueElemFieldset.setText(value);
+ fieldset.add(valueElemFieldset);
+
+ heightValue = valueElemFieldset.getY() + valueElemFieldset.getHeight() + Constants.marginTopForElementSubMenu;
+ }
+
+ /**
+ * Action to show or hide the submenu of graphics images
+ *
+ * @return AbstractAction with the event selected
+ */
+ private AbstractAction getActionShowSubMenu(String name) {
+ AbstractAction action = new AbstractAction(name, null) {
+ private static final long serialVersionUID = -6311968455290159751L;
+
+ public void actionPerformed(ActionEvent evt) {
+ refreshLeftMenu(evt);
+ }
+ };
+
+ return action;
+ }
+}
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/panels/RNASeqQCDialog.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/panels/RNASeqQCDialog.java
new file mode 100644
index 0000000..7077301
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/panels/RNASeqQCDialog.java
@@ -0,0 +1,335 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.gui.panels;
+
+import net.miginfocom.swing.MigLayout;
+import org.bioinfo.ngs.qc.qualimap.common.*;
+import org.bioinfo.ngs.qc.qualimap.gui.dialogs.AnalysisDialog;
+import org.bioinfo.ngs.qc.qualimap.gui.dialogs.BrowseButtonActionListener;
+import org.bioinfo.ngs.qc.qualimap.gui.frames.HomeFrame;
+import org.bioinfo.ngs.qc.qualimap.gui.threads.RNASeqQCAnalysisThread;
+import org.bioinfo.ngs.qc.qualimap.common.AnalysisType;
+import org.bioinfo.ngs.qc.qualimap.gui.utils.TabPageController;
+import org.bioinfo.ngs.qc.qualimap.process.ComputeCountsTask;
+
+import javax.swing.*;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.io.File;
+import java.util.*;
+
+/**
+ * Created by kokonech
+ * Date: 7/13/13
+ * Time: 11:19 AM
+ */
+public class RNASeqQCDialog extends AnalysisDialog implements ActionListener {
+
+ JTextField bamPathEdit, gffPathEdit, countsPathEdit;
+ JButton browseBamButton, browseGffButton, browseCountsFileButton;
+ JComboBox strandTypeCombo, countingAlgoCombo;
+ JCheckBox advancedOptions, outputCountsBox, pairedAnalysisBox, alreadySortedBox;
+ JLabel countingMethodLabel, countsPathLabel;
+
+ static class BrowseGffButtonListener extends BrowseButtonActionListener {
+
+ RNASeqQCDialog dlg;
+ Set<String> featuresTypes, featureNames;
+ static final int NUM_LINES = 100000;
+ static final String[] extentions = { "gtf" };
+
+ public BrowseGffButtonListener(RNASeqQCDialog parent, JTextField textField) {
+ super(parent, textField, "Annotation files", extentions );
+ this.dlg = parent;
+ featuresTypes = new HashSet<String>();
+ featureNames = new HashSet<String>();
+ }
+
+ @Override
+ public void validateInput() {
+
+ String filePath = pathEdit.getText();
+ try {
+ preloadGff(filePath);
+ } catch (Exception e) {
+ JOptionPane.showMessageDialog(parent,
+ "File is not a valid GTF.",
+ dlg.getTitle(), JOptionPane.ERROR_MESSAGE);
+ return;
+ }
+
+ if (featuresTypes.isEmpty()) {
+ JOptionPane.showMessageDialog(parent,
+ "No features are found in GTF file, please make sure the file is not empty.",
+ dlg.getTitle(), JOptionPane.ERROR_MESSAGE);
+ }
+
+ }
+
+ void preloadGff(String filePath) throws Exception {
+ GenomicFeatureStreamReader parser = new GenomicFeatureStreamReader(filePath, FeatureFileFormat.GTF);
+ for (int i = 0; i < NUM_LINES; ++i) {
+ GenomicFeature rec = parser.readNextRecord();
+ if (rec == null) {
+ break;
+ }
+ String featureType = rec.getFeatureName();
+ featuresTypes.add(featureType);
+ Collection<String> fNames = rec.getAttributeNames();
+ for (String name : fNames) {
+ featureNames.add(name);
+ }
+ }
+
+ }
+ }
+
+ public RNASeqQCDialog(HomeFrame homeFrame) {
+
+ super(homeFrame, "RNASeq QC");
+
+ getContentPane().setLayout(new MigLayout("insets 20"));
+
+ add(new JLabel("BAM file:"), "");
+
+ bamPathEdit = new JTextField(40);
+ bamPathEdit.setToolTipText("Path to BAM alignment file");
+ add(bamPathEdit, "grow");
+
+ browseBamButton = new JButton("...");
+ browseBamButton.addActionListener( new BrowseButtonActionListener(this,
+ bamPathEdit, "BAM files", "bam"));
+ add(browseBamButton, "align center, wrap");
+
+ add(new JLabel("Annotation file:"), "");
+
+ gffPathEdit = new JTextField(40);
+ gffPathEdit.setToolTipText("File with the definition of the regions for the features in Ensembl GTF format).");
+ add(gffPathEdit, "grow");
+
+ browseGffButton = new JButton();
+ browseGffButton.setText("...");
+ browseGffButton.addActionListener(new BrowseGffButtonListener(this, gffPathEdit));
+ browseBamButton.addActionListener(this);
+ add(browseGffButton, "align center, wrap");
+
+
+ add(new JLabel("Protocol:"));
+ String[] protocolComboItems = LibraryProtocol.getProtocolNames();
+ strandTypeCombo = new JComboBox<String>(protocolComboItems);
+ strandTypeCombo.setToolTipText("Select the corresponding sequencing protocol");
+ strandTypeCombo.addActionListener(this);
+ add(strandTypeCombo, "wrap");
+
+ pairedAnalysisBox = new JCheckBox("Paired-end analysis");
+ pairedAnalysisBox.setToolTipText("<html>This option activates counting of fragments instead of counting of reads. " +
+ "<br>Only valid for paired-end sequencing experiments.</html>");
+ pairedAnalysisBox.addActionListener(this);
+ add(pairedAnalysisBox);
+
+ alreadySortedBox = new JCheckBox("Alignment is sorted by name");
+ alreadySortedBox.setToolTipText("<html>The paired-end analysis requires the BAM file to be sorted by name. " +
+ "<br>Check this box if it is the case, otherwise temporary BAM sorted by name" +
+ "<br>will be created.</html>");
+ add(alreadySortedBox, "wrap");
+
+
+ outputCountsBox = new JCheckBox("Output gene counts");
+ outputCountsBox.addActionListener(this);
+ add(outputCountsBox, "wrap");
+
+
+ countsPathLabel = new JLabel("Path:");
+ add( countsPathLabel );
+
+ countsPathEdit = new JTextField(40);
+ countsPathEdit.setToolTipText("Path to the file which will contain output gene counts");
+ add(countsPathEdit, "grow");
+ browseCountsFileButton = new JButton("...");
+ browseCountsFileButton.addActionListener(new BrowseButtonActionListener(this,
+ countsPathEdit, "Counts file", false));
+ add(browseCountsFileButton, "align center, wrap");
+
+ advancedOptions = new JCheckBox("Advanced options:");
+ advancedOptions.addActionListener(this);
+ add(advancedOptions, "wrap");
+
+ countingMethodLabel = new JLabel("Multi-mapped reads:");
+ countingMethodLabel.setToolTipText("Select method to count reads that map to several genome locations");
+ add(countingMethodLabel);
+ String[] algoComboItems = {ComputeCountsTask.COUNTING_ALGORITHM_ONLY_UNIQUELY_MAPPED,
+ ComputeCountsTask.COUNTING_ALGORITHM_PROPORTIONAL
+ };
+ countingAlgoCombo = new JComboBox<String>(algoComboItems);
+ countingAlgoCombo.addActionListener(this);
+ add(countingAlgoCombo, "wrap");
+
+
+
+ add(new JLabel("Log:"), "wrap");
+ setupLogArea();
+ add(logAreaScrollPane, "span, grow, wrap 30px");
+
+ JPanel buttonPanel = new JPanel();
+ buttonPanel.setLayout(new MigLayout("insets 20"));
+
+ startAnalysisButton = new JButton();
+ startAnalysisButton.setActionCommand(Constants.OK_COMMAND);
+ startAnalysisButton.addActionListener(this);
+ startAnalysisButton.setText(">>> Run Analysis");
+
+ add(new JLabel(""), "span 2");
+ add(startAnalysisButton, "wrap");
+
+ if (System.getenv("QUALIMAP_DEBUG") != null) {
+ bamPathEdit.setText("/home/kokonech/sample_data/paired_rna_seq/pe_nssp_hg19.chr20.bam");
+ gffPathEdit.setText("/data/annotations/Homo_sapiens.GRCh37.68.chr20.gtf");
+
+ }
+
+ pack();
+ updateState();
+
+
+ }
+
+ @Override
+ public void actionPerformed(ActionEvent actionEvent) {
+ if (actionEvent.getActionCommand().equals(Constants.OK_COMMAND)) {
+ String errMsg = validateInput();
+ if (!errMsg.isEmpty()) {
+ JOptionPane.showMessageDialog(this, errMsg, getTitle(), JOptionPane.ERROR_MESSAGE);
+ return;
+ }
+
+ TabPageController tabPageController = new TabPageController(AnalysisType.RNA_SEQ_QC);
+ RNASeqQCAnalysisThread t = new RNASeqQCAnalysisThread(this, tabPageController);
+
+ Thread.UncaughtExceptionHandler eh = new AnalysisDialog.ExceptionHandler(this);
+ t.setUncaughtExceptionHandler(eh);
+
+ t.start();
+
+
+ } else if (actionEvent.getActionCommand().equals(Constants.CANCEL_COMMAND)) {
+ setVisible(false);
+ } else {
+ updateState();
+ }
+
+
+ }
+
+ public void updateState() {
+
+ alreadySortedBox.setEnabled(pairedAnalysisBox.isSelected());
+
+ countingAlgoCombo.setEnabled(advancedOptions.isSelected());
+ countingMethodLabel.setEnabled(advancedOptions.isSelected());
+
+ String countingMethod = countingAlgoCombo.getSelectedItem().toString();
+ String algorithmHint = countingMethod.equals(ComputeCountsTask.COUNTING_ALGORITHM_ONLY_UNIQUELY_MAPPED) ?
+ "Only uniquely mapped reads will be consider" :
+ "<html>Each read will be weighted according to its number" +
+ " of mapped locations. <br>For example, a read with 4 mapping locations will " +
+ "<br>add 0.25 to the counts on each location.</html>";
+
+ countingAlgoCombo.setToolTipText(algorithmHint);
+
+
+ String protocol = strandTypeCombo.getSelectedItem().toString();
+ if (protocol.equals(LibraryProtocol.PROTOCOL_NON_STRAND_SPECIFIC)) {
+ strandTypeCombo.setToolTipText("Reads are counted if mapped to a feature independent of strand");
+ } else if (protocol.equals(LibraryProtocol.PROTOCOL_FORWARD_STRAND)) {
+ strandTypeCombo.setToolTipText("<html>The single-end reads must have the same strand as the feature." +
+ "<br>For paired-end reads first of a pair must have the same strand as the feature," +
+ "<br>while the second read must be on the opposite strand</html>");
+ } else {
+ strandTypeCombo.setToolTipText("<html>The single-end reads must have the strand opposite to the feature." +
+ "<br>For paired-end reads first of a pair must have on the opposite strand," +
+ "<br>while the second read must be on the same strand as the feature.</html>");
+ }
+
+
+ boolean countsEnabled = outputCountsBox.isSelected();
+
+ countsPathLabel.setEnabled(countsEnabled);
+ countsPathEdit.setEnabled(countsEnabled);
+ browseCountsFileButton.setEnabled(countsEnabled);
+
+
+ }
+
+ public String getBamFilePath() {
+ return bamPathEdit.getText();
+ }
+
+ public String getGtfFilePath() {
+ return gffPathEdit.getText();
+ }
+
+ public String getProtocol() {
+ return strandTypeCombo.getSelectedItem().toString();
+ }
+
+ public String getCountingAlgorithm() {
+ return countingAlgoCombo.getSelectedItem().toString();
+ }
+
+
+ private String validateInput() {
+
+ File bamFile = new File(bamPathEdit.getText());
+ if (!bamFile.exists()) {
+ return "BAM file is not found!";
+ }
+
+ File gffFile = new File(gffPathEdit.getText());
+ if (!gffFile.exists()) {
+ return "Annotations file is not found!";
+ }
+
+ if (outputCountsBox.isSelected()) {
+ if (countsPathEdit.getText().isEmpty()) {
+ return "Path to counts file is not set!";
+ }
+ }
+
+ return "";
+ }
+
+ public boolean outputCounts() {
+ return outputCountsBox.isSelected();
+ }
+
+ public String getCountsOutputPath() {
+ return countsPathEdit.getText();
+ }
+
+ public boolean pairedAnalysisBoxIsSelected() {
+ return pairedAnalysisBox.isSelected();
+ }
+
+ public boolean sortedAlignmentBoxIsSelected() {
+ return alreadySortedBox.isSelected();
+ }
+
+}
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/panels/SavePanel.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/panels/SavePanel.java
new file mode 100644
index 0000000..b115971
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/panels/SavePanel.java
@@ -0,0 +1,357 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.gui.panels;
+
+import java.awt.*;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.KeyListener;
+import java.io.File;
+
+import javax.swing.AbstractAction;
+import javax.swing.JButton;
+import javax.swing.JDialog;
+import javax.swing.JFileChooser;
+import javax.swing.JLabel;
+import javax.swing.JOptionPane;
+import javax.swing.JProgressBar;
+import javax.swing.JTextField;
+import javax.swing.UIManager;
+import javax.swing.filechooser.FileNameExtensionFilter;
+
+import net.miginfocom.swing.MigLayout;
+import org.bioinfo.commons.log.Logger;
+import org.bioinfo.ngs.qc.qualimap.common.Constants;
+import org.bioinfo.ngs.qc.qualimap.gui.frames.HomeFrame;
+import org.bioinfo.ngs.qc.qualimap.gui.threads.ExportHtmlThread;
+import org.bioinfo.ngs.qc.qualimap.gui.threads.ExportPdfThread;
+import org.bioinfo.ngs.qc.qualimap.gui.utils.PopupKeyListener;
+import org.bioinfo.ngs.qc.qualimap.gui.utils.TabPageController;
+
+/**
+ * Class to generate the save panel to control the save options
+ * for a file.
+ * @author Luis Miguel Cruz
+ * @author kokonech
+ */
+public class SavePanel extends javax.swing.JPanel {
+ /** Serial Version ID */
+ private static final long serialVersionUID = -5164084147407879120L;
+
+ /** Object that contains the frame to wrap this panel */
+ HomeFrame homeFrame;
+
+ /** Logger to print information */
+ protected Logger logger;
+
+ /** JDialog that contains the panel to save a file */
+ JDialog resultContainer;
+
+ /** Progress bar to show the process state */
+ JProgressBar progressBar;
+
+ /** Variable to show the status progress while we are saving */
+ JLabel progressStream;
+
+ /** Variable that contains the path to saved file */
+ JTextField pathDataDir;
+
+ /** Variable to manage the message to show if any process fails */
+ StringBuffer stringValidation;
+
+
+ public SavePanel() {
+ super();
+ logger = new Logger(this.getClass().getName());
+ }
+
+
+ static class SaveFileButtonActionListener implements ActionListener {
+
+ JTextField pathTextField;
+ String fileType;
+ String ext;
+ Component parent;
+
+ public SaveFileButtonActionListener(Component parent, JTextField pathTextField, String fileType, String ext) {
+ this.pathTextField = pathTextField;
+ this.parent = parent;
+ this.fileType = fileType;
+ this.ext = ext;
+ }
+
+ @Override
+ public void actionPerformed(ActionEvent actionEvent) {
+ JFileChooser fileChooser = HomeFrame.getFileChooser();
+ fileChooser.setFileFilter( new FileNameExtensionFilter(fileType, ext));
+
+ int res = fileChooser.showSaveDialog(parent);
+
+ if (res == JFileChooser.APPROVE_OPTION) {
+ pathTextField.setText(fileChooser.getSelectedFile()
+ .getPath());
+ }
+
+ }
+
+ }
+
+ public JDialog getExportToPdfDialog(HomeFrame homeFrame) {
+ this.homeFrame = homeFrame;
+
+ resultContainer = new JDialog();
+ resultContainer.setLayout( new MigLayout("insets 20"));
+
+ KeyListener keyListener = new PopupKeyListener(homeFrame, resultContainer, progressBar);
+ resultContainer.add(new JLabel("Path:"));
+
+ final String fileType = Constants.FILE_EXTENSION_PDF_FILE;
+
+ pathDataDir = new JTextField(40);
+ pathDataDir.addKeyListener(keyListener);
+ pathDataDir.setText(new File("").getAbsolutePath() + File.separator +
+ "qualimapReport." + fileType.toLowerCase() );
+ resultContainer.add(pathDataDir, "grow");
+
+ JButton pathDirButton = new JButton();
+ pathDirButton.setText("...");
+ pathDirButton.addActionListener(
+ new SaveFileButtonActionListener(this,pathDataDir, fileType, fileType));
+ pathDirButton.addKeyListener(keyListener);
+ resultContainer.add(pathDirButton, "wrap");
+
+ // Progress Bar to show while the statistics graphics are loaded
+ UIManager.put("ProgressBar.selectionBackground", Color.black);
+ UIManager.put("ProgressBar.selectionForeground", Color.black);
+ progressBar = new JProgressBar(0, 100);
+ progressBar.setVisible(false);
+ progressBar.setStringPainted(true);
+ progressBar.setBorderPainted(true);
+ progressBar.setForeground(new Color(244, 200, 120));
+
+ // Action done while the statistics graphics are loaded
+ progressStream = new JLabel();
+ progressStream.setVisible(false);
+
+ resultContainer.add(progressStream);
+ resultContainer.add(progressBar, "span 2, wrap");
+
+ JButton saveButton = new JButton();
+ saveButton.setText("Save");
+ saveButton.setAction(getActionSavePdf());
+ saveButton.addKeyListener(keyListener);
+ resultContainer.add(saveButton, "span, align right");
+ resultContainer.setTitle("Export to PDF");
+ resultContainer.setResizable(false);
+
+ resultContainer.pack();
+
+ return resultContainer;
+ }
+
+
+
+ public JDialog getExportToHtmlFilePanel(final HomeFrame homeFrame) {
+
+ this.homeFrame = homeFrame;
+
+ resultContainer = new JDialog();
+
+ KeyListener keyListener = new PopupKeyListener(homeFrame, resultContainer, progressBar);
+
+ resultContainer.getContentPane().setLayout( new MigLayout("insets 20") );
+
+ // Input folder
+ JLabel label = new JLabel();
+ label.setText("Output folder");
+ resultContainer.add(label);
+
+ pathDataDir = new JTextField(40);
+ pathDataDir.addKeyListener(keyListener);
+ resultContainer.add(pathDataDir, "grow");
+
+ JButton pathDirButton = new JButton();
+ pathDirButton.setText("...");
+ pathDirButton.addActionListener(new ActionListener() {
+ @Override
+ public void actionPerformed(ActionEvent actionEvent) {
+ JFileChooser fileChooser = HomeFrame.getFileChooser();
+ fileChooser.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY);
+
+
+ int valor = fileChooser.showOpenDialog(homeFrame
+ .getCurrentInstance());
+
+ if (valor == JFileChooser.APPROVE_OPTION) {
+ pathDataDir.setText(fileChooser.getSelectedFile()
+ .getPath());
+ }
+ }
+ });
+ pathDirButton.addKeyListener(keyListener);
+ resultContainer.add(pathDirButton, "wrap");
+
+ // Action done while the statistics graphics are loaded
+ progressStream = new JLabel();
+ progressStream.setVisible(false);
+ resultContainer.add(progressStream);
+
+ // Progress Bar to show while the statistics graphics are loaded
+ UIManager.put("ProgressBar.selectionBackground", Color.black);
+ UIManager.put("ProgressBar.selectionForeground", Color.black);
+ progressBar = new JProgressBar(0, 100);
+ progressBar.setVisible(false);
+ progressBar.setStringPainted(true);
+ progressBar.setBorderPainted(true);
+ progressBar.setForeground(new Color(244, 200, 120));
+ resultContainer.add(progressBar, "span 2, align center, wrap");
+
+ JButton saveButton = new JButton();
+ saveButton.setText("Save");
+
+ saveButton.addActionListener( new ActionListener() {
+ @Override
+ public void actionPerformed(ActionEvent actionEvent) {
+
+ if (pathDataDir.getText().isEmpty()) {
+ JOptionPane.showMessageDialog(resultContainer,
+ "Output folder is not set!", "Error", JOptionPane.ERROR_MESSAGE);
+ return;
+ }
+
+ // Try if the file exists
+ File file = new File(pathDataDir.getText());
+
+ if (file.exists() && !file.isDirectory()) {
+ JOptionPane.showMessageDialog(resultContainer,
+ "Invalid output folder path: target is not a directory!", "Error", JOptionPane.ERROR_MESSAGE);
+ return;
+ }
+
+ // If the file doesn't exists or exits and the user want to replace it
+ exportToHtml(file.getAbsolutePath());
+ }
+ });
+
+ saveButton.addKeyListener(keyListener);
+ resultContainer.add(saveButton, "span, align right, wrap");
+
+ resultContainer.setTitle("Export to html");
+ resultContainer.pack();
+ resultContainer.setResizable(false);
+
+ return resultContainer;
+ }
+
+
+ /**
+ * Test if the input date are correct or not.
+ * @return boolean, true if the input data are correct.
+ */
+ private boolean validateInput() {
+
+ stringValidation = new StringBuffer();
+
+ // Check the directory where we want to write
+ if (pathDataDir.getText().isEmpty()) {
+ stringValidation.append(" • The output path is required \n");
+ }
+
+ return stringValidation.length() == 0;
+ }
+
+
+ /**
+ * Function that calls a thread that create the pdf file with the data read in the selected tab
+ * and save it into the disk.
+ * @param path Output PDF path
+ */
+ private void exportToPdf(String path){
+ TabPageController tabController = homeFrame.getSelectedTabPageController();
+
+ ExportPdfThread t =
+ new ExportPdfThread(this, tabController, path);
+
+ t.start();
+ }
+
+
+ private void exportToHtml(String dirPath) {
+ TabPageController tabController = homeFrame.getSelectedTabPageController();
+
+ ExportHtmlThread t =
+ new ExportHtmlThread(this, tabController, dirPath);
+
+ t.start();
+ }
+
+
+
+ /**
+ * Action to save all the loaded data into a pdf file.
+ * @return AbstractAction with the event
+ */
+ private AbstractAction getActionSavePdf() {
+ return new AbstractAction("Save", null) {
+ private static final long serialVersionUID = -6901271560142385333L;
+
+ public void actionPerformed(ActionEvent evt) {
+ if (validateInput()) {
+ // Add the extension if necessary
+ if(!pathDataDir.getText().endsWith(".pdf")){
+ pathDataDir.setText(pathDataDir.getText() + ".pdf");
+ }
+
+ // Try if the file exists
+ File file = new File(pathDataDir.getText());
+
+ // If the file doesn't exists or exits and the user want to replace it
+ if (!file.exists() || (file.exists() && JOptionPane.showConfirmDialog(null,
+ "The file " + file.getPath() + " already exists." +
+ "Do you want to replace the existing file?",
+ "Confirm", JOptionPane.OK_OPTION) == 0)) {
+ //createPdfFile(file.getAbsolutePath());
+ exportToPdf(file.getAbsolutePath());
+ }
+ } else {
+ JOptionPane.showMessageDialog(null,
+ stringValidation.toString(), "Error", 0);
+ }
+ }
+ };
+
+ }
+
+ public HomeFrame getHomeFrame() {
+ return homeFrame;
+ }
+
+ public JProgressBar getProgressBar() {
+ return progressBar;
+ }
+
+ public JLabel getProgressStream() {
+ return progressStream;
+ }
+
+
+
+}
\ No newline at end of file
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/threads/BamAnalysisThread.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/threads/BamAnalysisThread.java
new file mode 100644
index 0000000..5ad8433
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/threads/BamAnalysisThread.java
@@ -0,0 +1,195 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.gui.threads;
+
+import net.sf.samtools.SAMFormatException;
+import org.bioinfo.commons.log.Logger;
+import org.bioinfo.ngs.qc.qualimap.beans.BamQCRegionReporter;
+import org.bioinfo.ngs.qc.qualimap.gui.panels.BamAnalysisDialog;
+import org.bioinfo.ngs.qc.qualimap.gui.utils.AnalysisDialogLoggerThread;
+import org.bioinfo.ngs.qc.qualimap.gui.utils.TabPageController;
+import org.bioinfo.ngs.qc.qualimap.main.NgsSmartMain;
+import org.bioinfo.ngs.qc.qualimap.process.BamStatsAnalysis;
+
+import javax.swing.*;
+import java.io.PrintWriter;
+import java.io.StringWriter;
+
+/**
+ * Class to manage a thread to do the Bam analysis to the input bam files and
+ * calculate resulting charts
+ *
+ * @author kokonech
+ */
+public class BamAnalysisThread extends Thread {
+
+ /** Logger to print information */
+ protected Logger logger;
+
+ /** Variable to manage the panel with the progressbar at the init */
+ private BamAnalysisDialog bamDialog;
+
+ /** Variables that contains the tab properties loaded in the thread */
+ TabPageController resultManager;
+
+ public BamAnalysisThread(String str, BamAnalysisDialog bamDialog, TabPageController tabProperties) {
+ super(str);
+ this.bamDialog = bamDialog;
+ this.resultManager = tabProperties;
+ logger = new Logger(this.getClass().getName());
+ }
+
+ /**
+ * Public method to run this thread. Its executed when an user call to
+ * method start over this thread.
+ */
+ public void run() {
+
+ // Create the outputDir directory
+ StringBuilder outputDirPath = resultManager.createDirectory();
+
+ BamStatsAnalysis bamQC = new BamStatsAnalysis(bamDialog.getInputFile().getAbsolutePath());
+
+ bamQC.setNumberOfWindows(bamDialog.getNumberOfWindows());
+ bamQC.setNumberOfThreads(bamDialog.getNumThreads());
+ bamQC.setNumberOfReadsInBunch(bamDialog.getBunchSize());
+ bamQC.setProtocol( bamDialog.getLibraryProtocol() );
+ bamQC.setMinHomopolymerSize( bamDialog.getMinHomopolymerSize());
+ bamQC.setSkipDuplicatedReads(bamDialog.getSkipDuplicatesStatus());
+ if (bamDialog.getOverlappingReadPairAlignmentStatus()) {
+ bamQC.activateIntersectingPairedEndReadsStats();
+ }
+
+ // Set the region file
+ boolean regionsAvailable = false;
+ if (bamDialog.getRegionFile() != null) {
+ bamQC.setSelectedRegions(bamDialog.getRegionFile().getAbsolutePath());
+ bamQC.setComputeOutsideStats(bamDialog.getComputeOutsideRegions());
+ regionsAvailable = true;
+ }
+
+ // reporting
+ bamQC.activeReporting(outputDirPath.toString());
+
+ // setup logging
+ AnalysisDialogLoggerThread loggerThread = new AnalysisDialogLoggerThread(bamDialog);
+ bamQC.setLoggerThread(loggerThread);
+
+ bamDialog.setUiEnabled(false);
+ bamDialog.getProgressStream().setText("Running BAM file analysis...");
+
+ try {
+
+ bamQC.run();
+ //timer.cancel();
+
+ bamDialog.getProgressStream().setText("End of bam qc");
+ bamDialog.getProgressBar().setValue(100);
+
+ // report
+ bamDialog.getProgressStream().setText("Computing report...");
+ BamQCRegionReporter reporter = new BamQCRegionReporter(regionsAvailable, true);
+ bamQC.prepareInputDescription(reporter, bamDialog.getDrawChromosomeLimits());
+
+ // Draw the Chromosome Limits or not
+ reporter.setPaintChromosomeLimits( bamDialog.getDrawChromosomeLimits() );
+ if (bamDialog.compareGcContentToPrecalculated()) {
+ String genomeName = bamDialog.getGenomeName();
+ reporter.setGenomeGCContentName(genomeName);
+ }
+
+ bamDialog.getProgressStream().setText(" text report...");
+ reporter.loadReportData(bamQC.getBamStats());
+ bamDialog.getProgressStream().setText("OK");
+
+ bamDialog.getProgressStream().setText(" charts...");
+ reporter.computeChartsBuffers(bamQC.getBamStats(), bamQC.getLocator(), bamQC.isPairedData());
+ bamDialog.getProgressStream().setText("OK");
+
+
+ // Set the reporter into the created tab
+ resultManager.addReporter(reporter);
+
+ if (bamDialog.getRegionFile() != null && bamDialog.getComputeOutsideRegions() ) {
+
+ BamQCRegionReporter outsideReporter = new BamQCRegionReporter(regionsAvailable, false);
+
+ bamQC.prepareInputDescription(outsideReporter, bamDialog.getDrawChromosomeLimits());
+ // Draw the Chromosome Limits or not
+ outsideReporter.setPaintChromosomeLimits(bamDialog.getDrawChromosomeLimits());
+
+ if (bamDialog.compareGcContentToPrecalculated()) {
+ String genomeName = bamDialog.getGenomeName();
+ outsideReporter.setGenomeGCContentName(genomeName);
+ }
+
+ // save stats
+ bamDialog.getProgressStream().setText(" outside text report...");
+ outsideReporter.loadReportData(bamQC.getOutsideBamStats());
+ bamDialog.getProgressStream().setText("OK");
+
+ // save charts
+ bamDialog.getProgressStream().setText(" outside charts...");
+ outsideReporter.computeChartsBuffers(bamQC.getOutsideBamStats(), bamQC.getLocator(), bamQC.isPairedData());
+ bamDialog.getProgressStream().setText("OK");
+
+ // Set the reporters into the created tab
+ resultManager.addReporter(outsideReporter);
+ }
+
+ // Increment the progress bar
+ bamDialog.getProgressStream().setText("OK");
+ bamDialog.getProgressBar().setValue(100);
+
+ } catch (SAMFormatException se) {
+ System.out.print(se.getMessage());
+ JOptionPane.showMessageDialog(null, "Error parsing BAM file! See log for details.",
+ bamDialog.getTitle(), JOptionPane.ERROR_MESSAGE);
+ se.printStackTrace();
+ bamDialog.resetProgress();
+ bamDialog.setUiEnabled(true);
+ bamDialog.updateState();
+ return;
+ } catch (Exception e) {
+
+ String message = "Analysis is failed.\n" + e.getMessage();
+
+ StringWriter errorsWriter = new StringWriter();
+ e.printStackTrace(new PrintWriter(errorsWriter));
+ String errorReport = errorsWriter.toString();
+
+ if (errorReport.contains("java.lang.OutOfMemoryError") ) {
+ message = NgsSmartMain.OUT_OF_MEMORY_REPORT;
+ }
+
+ JOptionPane.showMessageDialog(bamDialog, message, bamDialog.getTitle(), JOptionPane.ERROR_MESSAGE);
+ bamDialog.resetProgress();
+ bamDialog.setUiEnabled(true);
+ bamDialog.updateState();
+ return;
+ }
+
+ bamDialog.addNewPane(resultManager);
+
+ }
+
+
+}
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/threads/CountsQCAnalysisThread.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/threads/CountsQCAnalysisThread.java
new file mode 100644
index 0000000..a27771e
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/threads/CountsQCAnalysisThread.java
@@ -0,0 +1,113 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+/**
+ * Created by kokonech
+ * Date: 5/15/14
+ * Time: 5:30 PM
+ */
+package org.bioinfo.ngs.qc.qualimap.gui.threads;
+
+import java.io.*;
+
+import org.bioinfo.commons.log.Logger;
+import org.bioinfo.ngs.qc.qualimap.gui.panels.CountsQcDialog;
+import org.bioinfo.ngs.qc.qualimap.gui.utils.AnalysisDialogLoggerThread;
+import org.bioinfo.ngs.qc.qualimap.gui.utils.TabPageController;
+import org.bioinfo.ngs.qc.qualimap.process.CountsQcAnalysis;
+
+import javax.swing.*;
+
+/**
+ * Class to manage a thread that performs the analysis from counts of the input files
+ *
+ * @author kokonech
+ */
+
+public class CountsQCAnalysisThread extends Thread {
+
+
+ /** Logger to print information */
+ protected Logger logger;
+
+ /** Variable to manage the panel with the progressbar at the init */
+ private CountsQcDialog settingsDlg;
+
+ /** Variables that contains the tab properties loaded in the thread */
+ TabPageController tabProperties;
+
+ public CountsQCAnalysisThread(CountsQcDialog countsQcDialog, TabPageController tabProperties) {
+ super("MultisampleCountsQcThread");
+ this.settingsDlg = countsQcDialog;
+ this.tabProperties = tabProperties;
+ logger = new Logger(this.getClass().getName());
+ }
+
+ /**
+ * Public method to run this thread. Its executed when an user call to
+ * method start over this thread.
+ */
+ public void run() {
+
+ settingsDlg.setUiEnabled(false);
+
+ String homePath = settingsDlg.getHomeFrame().getQualimapFolder() + File.separator;
+
+ CountsQcAnalysis countsAnalysis = new CountsQcAnalysis(tabProperties, homePath,
+ settingsDlg.getDataItems());
+
+ countsAnalysis.setThreshold( settingsDlg.getCountsThreshold() );
+ countsAnalysis.setConditionNames( settingsDlg.getConditionsMap() );
+
+ if (settingsDlg.performComparison()) {
+ countsAnalysis.activateComparison();
+ }
+
+ boolean includeInfoFile = settingsDlg.annotationIsProvided();
+ if (includeInfoFile) {
+ String infoFilePath;
+ if (settingsDlg.infoFileIsProvided()) {
+ infoFilePath = settingsDlg.getInfoFilePath();
+ } else {
+ infoFilePath = homePath + "species" + File.separator + settingsDlg.getSelectedSpecies();
+ }
+ countsAnalysis.setInfoFilePath(infoFilePath);
+ }
+
+ AnalysisDialogLoggerThread outputParsingThread= new AnalysisDialogLoggerThread( settingsDlg ) ;
+ countsAnalysis.setOutputParsingThread(outputParsingThread);
+
+ try {
+ countsAnalysis.run();
+ } catch (Exception e) {
+ JOptionPane.showMessageDialog(settingsDlg, "Failed to analyze counts data. " + e.getMessage(),
+ settingsDlg.getTitle(), JOptionPane.ERROR_MESSAGE);
+ settingsDlg.setUiEnabled(true);
+ //settingsDlg.resetUi();
+ return;
+ }
+
+ String paneTitle = "" + settingsDlg.getItemCount();
+ settingsDlg.getHomeFrame().addNewPane(paneTitle, tabProperties);
+ }
+
+
+
+}
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/threads/EpigeneticsAnalysisThread.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/threads/EpigeneticsAnalysisThread.java
new file mode 100644
index 0000000..046c9ca
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/threads/EpigeneticsAnalysisThread.java
@@ -0,0 +1,120 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.gui.threads;
+
+import org.bioinfo.ngs.qc.qualimap.gui.panels.EpigeneticAnalysisDialog;
+import org.bioinfo.ngs.qc.qualimap.gui.utils.TabPageController;
+import org.bioinfo.ngs.qc.qualimap.process.EpiAnalysis;
+import org.bioinfo.ngs.qc.qualimap.process.EpiAnalysis.Config;
+import org.bioinfo.ngs.qc.qualimap.common.LoggerThread;
+
+
+import javax.swing.*;
+
+/**
+ * Created by kokonech
+ * Date: 1/4/12
+ * Time: 3:00 PM
+ */
+
+public class EpigeneticsAnalysisThread extends Thread {
+
+ EpigeneticAnalysisDialog settingsDialog;
+ TabPageController tabProperties;
+
+ static class OutputParsingThread extends LoggerThread {
+
+ EpigeneticAnalysisDialog parentDialog;
+
+
+ OutputParsingThread(EpigeneticAnalysisDialog parentDialog) {
+ this.parentDialog = parentDialog;
+
+ }
+
+ @Override
+ public void logLine(String msg) {
+ System.out.println(msg);
+ if (msg.contains("STATUS:")) {
+ parentDialog.setProgressStatus(msg.split(":")[1]);
+ }
+ JTextArea logArea = parentDialog.getLogArea();
+ logArea.append(msg + "\n");
+ logArea.setCaretPosition(logArea.getText().length());
+ }
+
+ }
+
+ public EpigeneticsAnalysisThread(EpigeneticAnalysisDialog settingsDialog, TabPageController tabProperties) {
+ super("EpigeneticsAnalysisThread");
+ this.settingsDialog = settingsDialog;
+ this.tabProperties = tabProperties;
+
+ }
+
+ public void run() {
+
+ settingsDialog.setUiEnabled(false);
+ settingsDialog.getLogArea().setText("");
+
+ Config cfg = new Config();
+
+ cfg.replicates = settingsDialog.getSampleItems();
+ cfg.experimentName = settingsDialog.getExperimentName();
+ cfg.pathToRegions = settingsDialog.getGeneSelectionPath();
+ cfg.leftOffset = Integer.parseInt(settingsDialog.getLeftOffset());
+ cfg.rightOffset = Integer.parseInt(settingsDialog.getRightOffset());
+ cfg.binSize = Integer.parseInt(settingsDialog.getStep());
+ cfg.fragmentLength = Integer.parseInt(settingsDialog.getReadSmoothingLength());
+ cfg.clusters = settingsDialog.getClusterNumbers();
+ cfg.vizType = settingsDialog.getVisuzliationType();
+
+ String homePath = settingsDialog.getHomeFrame().getQualimapFolder();
+ EpiAnalysis epiAnalysis = new EpiAnalysis(tabProperties, homePath, cfg);
+
+ OutputParsingThread outputParsingThread= new OutputParsingThread( settingsDialog ) ;
+ epiAnalysis.setOutputParsingThread(outputParsingThread);
+
+ epiAnalysis.setProgressStream(settingsDialog.getProgressStream());
+
+
+ try {
+
+ epiAnalysis.run();
+
+ } catch (Exception e) {
+ JOptionPane.showMessageDialog(settingsDialog, e.getMessage(),
+ "Epigenetics analysis", JOptionPane.ERROR_MESSAGE );
+ e.printStackTrace();
+ settingsDialog.setUiEnabled(true);
+ return;
+ }
+
+
+ String inputFileName = settingsDialog.getInputDataName();
+ settingsDialog.getHomeFrame().addNewPane(inputFileName, tabProperties);
+
+ settingsDialog.setVisible(false);
+
+ }
+
+
+}
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/threads/ExportHtmlThread.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/threads/ExportHtmlThread.java
new file mode 100644
index 0000000..f204cb7
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/threads/ExportHtmlThread.java
@@ -0,0 +1,332 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.gui.threads;
+
+/**
+ * Created by kokonech
+ * Date: 1/16/12
+ * Time: 2:22 PM
+ */
+
+import java.awt.Component;
+import java.awt.image.BufferedImage;
+import java.io.*;
+import java.util.Iterator;
+import java.util.List;
+import java.util.zip.ZipEntry;
+import java.util.zip.ZipInputStream;
+
+import javax.imageio.ImageIO;
+import javax.swing.JOptionPane;
+
+import org.bioinfo.commons.log.Logger;
+import org.bioinfo.ngs.qc.qualimap.beans.AnalysisResultManager;
+import org.bioinfo.ngs.qc.qualimap.beans.ChartRawDataWriter;
+import org.bioinfo.ngs.qc.qualimap.beans.QChart;
+import org.bioinfo.ngs.qc.qualimap.beans.StatsReporter;
+import org.bioinfo.ngs.qc.qualimap.common.AnalysisType;
+import org.bioinfo.ngs.qc.qualimap.common.Constants;
+import org.bioinfo.ngs.qc.qualimap.gui.panels.SavePanel;
+import org.bioinfo.ngs.qc.qualimap.common.HtmlReportGenerator;
+
+
+public class ExportHtmlThread extends Thread{
+ /** Logger to print information */
+ protected Logger logger;
+
+ /** Variable to manage the panel with the progress bar to increase */
+ private SavePanel savePanel;
+
+ /** Variable to control that all the files are saved */
+ private int numSavedFiles;
+
+ /** Variable to control the percent of each iteration of the progress bar */
+ private double percentLoad;
+
+ /** Variable to manage the dirPath of the file that we are going to save*/
+ private String dirPath;
+
+ /** Variables that contains the tab properties loaded in the thread*/
+ AnalysisResultManager resultManager;
+
+ boolean guiAvailable, saveRawData;
+
+
+ public ExportHtmlThread(Component component, AnalysisResultManager resultManager, String dirPath) {
+ super("ExportHtmlThread_Gui");
+ if (component instanceof SavePanel) {
+ this.savePanel = (SavePanel)component;
+ }
+ this.resultManager = resultManager;
+ this.dirPath = dirPath;
+ this.guiAvailable = true;
+ this.saveRawData = true;
+ }
+
+ public ExportHtmlThread(AnalysisResultManager resultManager, String dirPath) {
+ super("ExportHtmlThread");
+ this.resultManager = resultManager;
+ this.dirPath = dirPath;
+ this.guiAvailable = false;
+ this.saveRawData = true;
+ }
+
+ void setGuiVisible(boolean enable) {
+ if (guiAvailable) {
+ savePanel.getProgressStream().setVisible(enable);
+ savePanel.getProgressBar().setVisible(enable);
+ }
+ }
+
+ void reportFailure(String msg) {
+ if (guiAvailable) {
+ setGuiVisible(false);
+ JOptionPane.showMessageDialog(null,
+ msg, "Error", JOptionPane.ERROR_MESSAGE);
+ } else {
+ System.err.println(msg);
+ }
+ }
+
+
+ void reportSuccess(String msg) {
+ if (guiAvailable) {
+ // Close the window and show an info message
+ savePanel.getHomeFrame().getPopUpDialog().setVisible(false);
+ savePanel.getHomeFrame().remove(savePanel.getHomeFrame().getPopUpDialog());
+ JOptionPane.showMessageDialog(null,
+ msg, "Success", JOptionPane.INFORMATION_MESSAGE);
+ } else {
+ System.out.println(msg);
+ }
+ }
+
+ /**
+ * Public method to run this thread. Its executed when an user call to method start
+ * over this thread. */
+ public void run() {
+
+
+ try {
+
+ File dir = new File(dirPath);
+ if (!dir.exists()) {
+ boolean ok = (new File(dirPath)).mkdirs();
+ if (!ok) {
+ reportFailure("Unable to create the output directory for html report\n");
+ return;
+ }
+ }
+
+ // Show the ProgressBar and the Text Description
+ setGuiVisible(true);
+
+ // Set the number of files saved to initial value
+ numSavedFiles = 0;
+
+ int numItemsToSave = 0;
+ List<StatsReporter> reporters = resultManager.getReporters();
+ AnalysisType analysisType = resultManager.getTypeAnalysis();
+ for (StatsReporter reporter : reporters) {
+ numItemsToSave += reporter.getCharts().size();
+ }
+
+ percentLoad = (100.0/numItemsToSave);
+
+ // Add the first file of the reporter
+ boolean success = true;
+ for ( StatsReporter reporter : reporters) {
+ String htmlReportFilePath = dirPath + File.separator + reporter.getFileName() + ".html";
+ success = generateAndSaveReport(reporter, htmlReportFilePath, analysisType);
+ if (!success) {
+ break;
+ }
+ }
+
+ prepareCss();
+
+ if (saveRawData) {
+ for ( StatsReporter reporter : reporters) {
+ saveRawData(reporter, "raw_data_" + reporter.getFileName() );
+ }
+ }
+
+ if(success){
+ reportSuccess("Html report created successfully\n");
+ } else {
+ reportFailure("Failed to create the HTML file\n");
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ reportFailure("Unable to create the html file \n" + e.getMessage());
+ }
+ }
+
+
+ private boolean generateAndSaveReport(StatsReporter reporter, String path, AnalysisType genomicAnalysis) throws IOException {
+
+ HtmlReportGenerator generator = new HtmlReportGenerator(reporter, dirPath, genomicAnalysis);
+ StringBuffer htmlReport = generator.getReport();
+ saveReport(htmlReport, path);
+ return saveImages(reporter);
+
+ }
+
+ private void prepareCss() throws IOException {
+ String newPath = dirPath + "/css";
+ int BUFFER = 2048;
+
+ File destinationParent = new File(newPath);
+ if (!destinationParent.exists()) {
+ if (!destinationParent.mkdirs()) {
+ throw new IOException("Failed to create sub directory " + destinationParent.getAbsolutePath());
+ }
+ }
+
+ InputStream is = getClass().getResourceAsStream(Constants.pathResources + "css.zip");
+ ZipInputStream zis = new ZipInputStream(is);
+ ZipEntry entry;
+ BufferedInputStream source = new BufferedInputStream(zis);
+
+ while ((entry = zis.getNextEntry()) != null) {
+ String currentEntryName = entry.getName();
+ File destFile = new File(newPath,currentEntryName);
+
+ if (destFile.exists()) {
+ continue;
+ }
+
+ int currentByte;
+
+ byte data[] = new byte[BUFFER];
+
+ BufferedOutputStream dest = new BufferedOutputStream(new FileOutputStream(destFile), BUFFER);
+ while ((currentByte = source.read(data, 0, BUFFER)) != -1) {
+ dest.write(data, 0, currentByte);
+ }
+
+ dest.flush();
+ dest.close();
+
+ }
+
+ source.close();
+
+
+
+ }
+
+
+ private void saveReport(StringBuffer htmlReport, String path) throws FileNotFoundException {
+ PrintStream outStream = new PrintStream( new BufferedOutputStream(new FileOutputStream(path)));
+ outStream.print(htmlReport.toString());
+
+ outStream.close();
+
+ }
+
+
+ public boolean saveImages(StatsReporter reporter) throws IOException {
+
+ boolean success = true;
+
+ Iterator<QChart> it = reporter.getCharts().iterator();
+
+ // Generate the Graphics images
+
+ while(it.hasNext() && success){
+
+ QChart chart = it.next();
+ BufferedImage bufImage;
+
+ if(chart.isBufferedImage()){
+ bufImage = chart.getBufferedImage();
+ } else {
+ bufImage = chart.getJFreeChart().createBufferedImage(
+ Constants.GRAPHIC_TO_SAVE_WIDTH,
+ Constants.GRAPHIC_TO_SAVE_HEIGHT);
+ }
+
+ String imagePath = HtmlReportGenerator.getImagePath(reporter, chart.getName());
+ imagePath = dirPath + File.separator + imagePath;
+
+
+
+ File imageFile = new File(imagePath);
+ if (!imageFile.getParentFile().exists()) {
+ boolean ok = imageFile.getParentFile().mkdirs();
+ if (!ok) {
+ return false;
+ }
+ }
+
+ success = ImageIO.write(bufImage, "PNG", imageFile);
+
+ increaseProgressBar(chart.getTitle());
+
+ }
+
+
+ return success;
+
+ }
+
+
+ private void increaseProgressBar(String fileName){
+
+ if (!guiAvailable) {
+ return;
+ }
+
+ // Increase the number of files loaded
+ numSavedFiles++;
+ // Increase the progress bar value
+ int result = (int)Math.ceil(numSavedFiles * percentLoad);
+ savePanel.getProgressBar().setValue(result);
+
+ if(fileName != null){
+ savePanel.getProgressStream().setText("Saving graphics: "+ fileName);
+ }
+ }
+
+ void saveRawData(StatsReporter reporter, String subFolderName) throws IOException{
+ List<QChart> charts = reporter.getCharts();
+ String newPath = dirPath + File.separator + subFolderName;
+
+ File destinationParent = new File(newPath);
+ if (!destinationParent.exists()) {
+ if (!destinationParent.mkdirs()) {
+ throw new IOException("Failed to create sub directory " + destinationParent.getAbsolutePath());
+ }
+ }
+
+ for (QChart chart : charts) {
+ if (chart.canExportRawData()) {
+ ChartRawDataWriter dataWriter = chart.getDataWriter();
+ String fileName = chart.getTitle().replace(" ", "_").toLowerCase() + ".txt";
+ dataWriter.exportDataToFile(newPath + "/" + fileName);
+ }
+ }
+
+ }
+
+
+}
\ No newline at end of file
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/threads/ExportPdfThread.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/threads/ExportPdfThread.java
new file mode 100644
index 0000000..935ce47
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/threads/ExportPdfThread.java
@@ -0,0 +1,485 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.gui.threads;
+
+import com.lowagie.text.*;
+import com.lowagie.text.Document;
+import com.lowagie.text.pdf.PdfWriter;
+import org.bioinfo.ngs.qc.qualimap.beans.AnalysisResultManager;
+import org.bioinfo.ngs.qc.qualimap.beans.QChart;
+import org.bioinfo.ngs.qc.qualimap.beans.StatsReporter;
+import org.bioinfo.ngs.qc.qualimap.common.Constants;
+import org.bioinfo.ngs.qc.qualimap.gui.panels.SavePanel;
+import org.bioinfo.ngs.qc.qualimap.gui.utils.StatsKeeper;
+import org.bioinfo.ngs.qc.qualimap.main.NgsSmartMain;
+import com.lowagie.text.Font;
+
+import javax.swing.*;
+import java.awt.*;
+import java.awt.Image;
+import java.awt.image.BufferedImage;
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.OutputStream;
+import java.text.DateFormat;
+import java.text.SimpleDateFormat;
+import java.util.Date;
+import java.util.List;
+
+/**
+ * Created by kokonech
+ * Date: 3/20/12
+ * Time: 2:25 PM
+ */
+public class ExportPdfThread extends Thread {
+
+
+ //TODO: remove GUI?
+ SavePanel savePanel;
+ String path;
+ boolean guiAvailable;
+ double percentLoad;
+ int curChapterNum;
+ int numSavedItems;
+ AnalysisResultManager resultManager;
+
+
+ public ExportPdfThread(Component component, AnalysisResultManager resultManager, String path) {
+ super("ExportPDFThread_Gui");
+ if (component instanceof SavePanel) {
+ this.savePanel = (SavePanel)component;
+ }
+ this.resultManager = resultManager;
+ this.path = path;
+ this.guiAvailable = true;
+ }
+
+ public ExportPdfThread(AnalysisResultManager resultManager, String path) {
+ super("ExportPdfThread");
+ this.resultManager = resultManager;
+ this.path = path;
+ this.guiAvailable = false;
+ }
+
+ void setGuiVisible(boolean enable) {
+ if (guiAvailable) {
+ savePanel.getProgressStream().setVisible(enable);
+ savePanel.getProgressBar().setVisible(enable);
+ }
+ }
+
+ void reportFailure(String msg) {
+ if (guiAvailable) {
+ setGuiVisible(false);
+ JOptionPane.showMessageDialog(null,
+ msg, "Error", JOptionPane.ERROR_MESSAGE);
+ } else {
+ System.err.println(msg);
+ }
+ }
+
+
+ void reportSuccess(String msg) {
+ if (guiAvailable) {
+ // Close the window and show an info message
+ savePanel.getHomeFrame().getPopUpDialog().setVisible(false);
+ savePanel.getHomeFrame().remove(savePanel.getHomeFrame().getPopUpDialog());
+ JOptionPane.showMessageDialog(null,
+ msg, "Success", JOptionPane.INFORMATION_MESSAGE);
+ } else {
+ System.out.println(msg);
+ }
+ }
+
+ public void run() {
+ try {
+ OutputStream file = new FileOutputStream(path);
+
+ Document document = new Document(PageSize.A4);
+ PdfWriter.getInstance(document, file);
+
+ document.open();
+
+ numSavedItems = 0;
+
+ setGuiVisible(true);
+ initDocument(document);
+
+ // Number of items to save into the PDF file (graphics + 3 files of properties + Header + Footer)
+
+ int numItemsToSave = 0;
+ List<StatsReporter> reporters = resultManager.getReporters();
+ for (StatsReporter reporter : reporters ) {
+ numItemsToSave += reporter.getCharts().size();
+ }
+
+ percentLoad = (100.0/numItemsToSave);
+
+ curChapterNum = 1;
+
+ for (StatsReporter reporter : reporters ) {
+ addReporterData(document, reporter);
+ }
+
+ document.close();
+ file.close();
+
+ reportSuccess("Pdf File Created Successfully \n");
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ // If the file could not generate correctly
+ File f = new File(path);
+ if (!f.delete()) {
+ System.err.print("Failed to delete " + path);
+ }
+ reportFailure("Unable to create the pdf file \n" + e.getMessage());
+ }
+
+ }
+
+
+ private void addReporterData(Document document, StatsReporter reporter) throws Exception{
+
+ if (reporter.hasInputDescription()) {
+ addInputDesc( document, reporter );
+ }
+ if (reporter.hasSummary()) {
+ addSummary( document, reporter );
+ }
+
+ addPlots( document, reporter );
+ }
+
+
+ private void initDocument(Document document) throws Exception{
+
+ com.lowagie.text.Image bioInfoLogo =
+ com.lowagie.text.Image.getInstance(
+ getClass().getResource(Constants.pathImages + "logo.png"));
+ bioInfoLogo.scaleAbsolute(
+ 250,
+ 25);
+ HeaderFooter header = new HeaderFooter(new Phrase(new Chunk(bioInfoLogo, 0, -15)), false);
+ header.setBorder(0);
+
+ com.lowagie.text.Image cipfLogo =
+ com.lowagie.text.Image.getInstance(
+ getClass().getResource(Constants.pathImages + "cipf_alpha.gif"));
+ cipfLogo.scaleAbsolute(50, 25);
+ header.getBefore().add(
+ new Phrase(new Chunk(
+ cipfLogo,
+ document.getPageSize().getWidth() - bioInfoLogo.getScaledWidth() -
+ document.rightMargin() - cipfLogo.getWidth(),
+ -17)));
+ document.setHeader(header);
+
+ // *********************************************
+ // Add the footer on the PDF document
+ // *********************************************
+
+ DateFormat dateFormat = new SimpleDateFormat("yyyy/MM/dd HH:mm:ss");
+ Date date = new Date();
+ String dateLabel = dateFormat.format(date);
+
+ HeaderFooter footer = new HeaderFooter(new Phrase(""), true);
+ footer.setAlignment(Element.ALIGN_RIGHT);
+ footer.setBorder(0);
+ footer.getBefore().add("Page ");
+ footer.setPageNumber(document.getPageNumber());
+
+
+ document.setFooter(footer);
+
+
+ // *********************************************
+ // Create the first page in the PDF report
+ // *********************************************
+ Font font = new Font(Font.COURIER, 36, Font.BOLD);
+ font.setColor(new Color(85, 107, 47));
+ Paragraph title = new Paragraph("");
+ title.setAlignment(Element.ALIGN_CENTER);
+ //addEmptyLine(paragraph, 12);
+ com.lowagie.text.Image pdfTitle =
+ com.lowagie.text.Image.getInstance(
+ getClass().getResource(Constants.pathImages + "pdf_title.png"));
+ pdfTitle.scaleAbsolute(400, 70);
+ pdfTitle.setAlignment(Element.ALIGN_MIDDLE);
+ title.add(pdfTitle);
+
+
+ Paragraph analysisTitle = new Paragraph(resultManager.getTypeAnalysis().toString() + " analysis",
+ FontFactory.getFont(FontFactory.HELVETICA , 18,
+ Font.ITALIC));
+ analysisTitle.setAlignment(Element.ALIGN_CENTER);
+
+ Paragraph subTitle = new Paragraph("Generated by Qualimap " + NgsSmartMain.APP_VERSION,
+ FontFactory.getFont(FontFactory.HELVETICA , 18,
+ Font.ITALIC));
+ subTitle.setAlignment(Element.ALIGN_CENTER);
+
+ Paragraph subTitle2 = new Paragraph(dateLabel,
+ FontFactory.getFont(FontFactory.HELVETICA , 18,
+ Font.ITALIC));
+ subTitle2.setAlignment(Element.ALIGN_CENTER);
+
+ document.add(title);
+ document.add(analysisTitle);
+ document.add(subTitle);
+ document.add(subTitle2);
+
+
+ }
+
+ private void addPlots(Document document, StatsReporter reporter) throws Exception {
+ for (QChart chart : reporter.getCharts() ){
+
+ String chartTitle = chart.getTitle();
+
+ BufferedImage bufImage;
+ if (chart.isBufferedImage()) {
+ bufImage = chart.getBufferedImage();
+ } else {
+ bufImage = chart.getJFreeChart().createBufferedImage(
+ Constants.GRAPHIC_TO_SAVE_WIDTH,
+ Constants.GRAPHIC_TO_SAVE_HEIGHT);
+ }
+
+ String reporterName = reporter.getName();
+ if (reporterName.length() > 0) {
+ reporterName += " : ";
+ }
+ Paragraph chartsTitle = createChapterTitle(reporterName + chartTitle + reporter.getNamePostfix());
+ Chapter chapter = new Chapter(chartsTitle, curChapterNum);
+
+
+ com.lowagie.text.Image image =
+ com.lowagie.text.Image.getInstance(
+ bufImage.getScaledInstance(
+ bufImage.getWidth() /*Constants.GRAPHIC_TO_SAVE_WIDTH*/,
+ bufImage.getHeight() /*(Constants.GRAPHIC_TO_SAVE_HEIGHT*/,
+ Image.SCALE_REPLICATE), null);
+
+
+ float scaledWidth = 400;
+ float scaledHeight = 600;
+
+ if (bufImage.getWidth() < bufImage.getHeight()) {
+ scaledWidth = scaledHeight * ( (float) bufImage.getWidth() / bufImage.getHeight() );
+ } else {
+ scaledHeight = scaledWidth * ( (float) bufImage.getHeight() / bufImage.getTileWidth() );
+ }
+
+ image.scaleToFit(scaledWidth,scaledHeight);
+ image.setAlignment(com.lowagie.text.Image.MIDDLE);
+ chapter.add(image);
+
+ document.add(chapter);
+ curChapterNum++;
+ increaseProgressBar(chartTitle);
+ }
+
+ }
+
+ private void addInputDesc(Document doc, StatsReporter reporter) throws Exception {
+
+ String reporterName = reporter.getName();
+ if (reporterName.length() > 0) {
+ reporterName += " : ";
+ }
+
+ Paragraph chapterTitle = createChapterTitle( "Input data & parameters"
+ + reporter.getNamePostfix());
+
+ Chapter inputChapter = new Chapter(chapterTitle, curChapterNum);
+
+ List<StatsKeeper.Section> inputSections = reporter.getInputDataSections();
+
+ for (StatsKeeper.Section s : inputSections ) {
+
+ Paragraph title11 = createSectionTitle(s.getName());
+
+ Section section = inputChapter.addSection(title11);
+
+ Table table;
+ if (s.getName().equals(Constants.TABLE_SECTION_QUALIMAP_CMDLINE)) {
+ table = new Table(1);
+ } else {
+ table = new Table(2);
+ }
+
+ table.setPadding(2);
+ table.setSpacing(2);
+
+ for (String[] row : s.getRows()) {
+ for (String item : row) {
+ table.addCell(item);
+ }
+ }
+
+ section.add(table);
+ }
+
+ doc.add(inputChapter);
+ curChapterNum++;
+
+ }
+
+
+ /*private void addReporterHeader(Document doc, StatsReporter reporter) throws Exception {
+ Paragraph chapterTitle = new Paragraph();
+ // We add one empty line
+ //addEmptyLine(chapterTitle, 1);
+ com.lowagie.text.Font titleFont = new com.lowagie.text.Font(com.lowagie.text.Font.COURIER, 24,
+ com.lowagie.text.Font.BOLD);
+ chapterTitle.add(new Paragraph(reporter.getName(), titleFont));
+ doc.add(chapterTitle);
+
+
+ }*/
+
+
+ private void addSummary(Document doc, StatsReporter reporter) throws Exception {
+
+
+ Paragraph chapterTitle = createChapterTitle("Summary" + reporter.getNamePostfix());
+
+ Chapter summaryChapter = new Chapter(chapterTitle, curChapterNum);
+
+ List<StatsKeeper.Section> summarySections = reporter.getSummaryDataSections();
+
+ for (StatsKeeper.Section s : summarySections ) {
+
+ Paragraph title11 = createSectionTitle(s.getName());
+
+ Section section = summaryChapter.addSection(title11);
+ Table table = new Table(2);
+ table.setPadding(2);
+ table.setSpacing(2);
+
+ for (String[] row : s.getRows()) {
+ table.addCell(row[0]);
+ table.addCell(row[1]);
+ }
+
+ section.add(table);
+ }
+
+ if (reporter.hasTableData()) {
+
+ StatsKeeper dataStatsKeeper = reporter.getTableDataStatsKeeper();
+ List<StatsKeeper.Section> dataSections = dataStatsKeeper.getSections();
+
+ int numColumns = 0;
+
+ for (StatsKeeper.Section s : dataSections) {
+ if (s.getName().equals(Constants.TABLE_STATS_HEADER)) {
+ numColumns = s.getRows().get(0).length;
+ }
+ }
+
+
+ if (numColumns > 0) {
+ Paragraph dataTitle = createSectionTitle(dataStatsKeeper.getName());
+ Section chrSection = summaryChapter.addSection(dataTitle);
+
+ Table chrTable = new Table(numColumns);
+ chrTable.setPadding(2);
+ chrTable.setSpacing(2);
+
+
+ for (StatsKeeper.Section s : dataSections) {
+
+ if (s.getName().equals(Constants.TABLE_STATS_HEADER)) {
+
+ String row[] = s.getRows().get(0);
+ for (String item : row) {
+ Cell c = new Cell(item);
+ c.setHeader(true);
+ chrTable.addCell(c);
+ }
+
+ } else {
+
+ List<String[]> rows = s.getRows();
+ for (String[] row : rows) {
+ for (String item : row) {
+ chrTable.addCell(item);
+ }
+ }
+ }
+ }
+
+ chrSection.add(chrTable);
+ }
+ }
+
+ doc.add(summaryChapter);
+ curChapterNum++;
+
+ }
+
+
+ private Paragraph createChapterTitle(String text) {
+ return new Paragraph(text,
+ FontFactory.getFont(FontFactory.HELVETICA , 18,
+ Font.BOLD ));
+
+
+ }
+
+ private Paragraph createSectionTitle(String text) {
+ return new Paragraph(text,
+ FontFactory.getFont(FontFactory.HELVETICA , 16,
+ Font.BOLD ));
+
+
+ }
+
+
+ /*
+ * Increase the progress bar in the percent depends on the
+ * number of the element computed.
+ */
+ private void increaseProgressBar(String fileName){
+
+ if (!guiAvailable) {
+ return;
+ }
+
+ double numElem = numSavedItems;
+
+ // Increase the number of files loaded
+ numSavedItems++;
+ // Increase the progress bar value
+ int result = (int)Math.ceil(numElem * percentLoad);
+ savePanel.getProgressBar().setValue(result);
+
+ if(fileName != null){
+ savePanel.getProgressStream().setText("Adding Graphic: "+ fileName);
+ }
+ }
+
+
+
+
+}
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/threads/MultisampleBamQcThread.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/threads/MultisampleBamQcThread.java
new file mode 100644
index 0000000..1d0ef45
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/threads/MultisampleBamQcThread.java
@@ -0,0 +1,83 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.gui.threads;
+
+import org.bioinfo.ngs.qc.qualimap.gui.panels.MultisampleBamQcDialog;
+import org.bioinfo.ngs.qc.qualimap.gui.utils.AnalysisDialogLoggerThread;
+import org.bioinfo.ngs.qc.qualimap.gui.utils.TabPageController;
+import org.bioinfo.ngs.qc.qualimap.process.MultisampleBamQcAnalysis;
+
+import javax.swing.*;
+import java.io.File;
+
+/**
+ * Created by kokonech
+ * Date: 6/6/14
+ * Time: 3:42 PM
+ */
+public class MultisampleBamQcThread extends Thread {
+
+ MultisampleBamQcDialog settingsDlg;
+
+ TabPageController tabProperties;
+
+
+ public MultisampleBamQcThread(MultisampleBamQcDialog multiBamQcDialog, TabPageController tabProperties) {
+ super("MultisampleBamQcThread");
+ this.settingsDlg = multiBamQcDialog;
+ this.tabProperties = tabProperties;
+
+ }
+
+ public void run() {
+
+ settingsDlg.setUiEnabled(false);
+ settingsDlg.getProgressBar().setValue(0);
+
+ String homePath = settingsDlg.getHomeFrame().getQualimapFolder() + File.separator;
+
+ MultisampleBamQcAnalysis multiBamQcAnalysis = new MultisampleBamQcAnalysis(tabProperties, homePath,
+ settingsDlg.getDataItems());
+ AnalysisDialogLoggerThread outputParsingThread= new AnalysisDialogLoggerThread( settingsDlg ) ;
+ multiBamQcAnalysis.setOutputParsingThread(outputParsingThread);
+
+ if (settingsDlg.runBamQcFirst()) {
+ multiBamQcAnalysis.setRunBamQcFirst( settingsDlg.getBamQcConfig() );
+ }
+
+ try {
+ multiBamQcAnalysis.run();
+ } catch (Exception e) {
+ JOptionPane.showMessageDialog(settingsDlg, "Failed to run multi-sample BAM QC!\n" + e.getMessage(),
+ settingsDlg.getTitle(), JOptionPane.ERROR_MESSAGE);
+ settingsDlg.setUiEnabled(true);
+ //settingsDlg.resetUi();
+ return;
+ }
+ settingsDlg.getProgressBar().setValue(100);
+
+ String paneTitle = "" + settingsDlg.getItemCount();
+ settingsDlg.getHomeFrame().addNewPane(paneTitle, tabProperties);
+ }
+
+
+
+}
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/threads/RNASeqQCAnalysisThread.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/threads/RNASeqQCAnalysisThread.java
new file mode 100644
index 0000000..5f504c7
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/threads/RNASeqQCAnalysisThread.java
@@ -0,0 +1,115 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.gui.threads;
+
+import org.bioinfo.commons.log.Logger;
+import org.bioinfo.ngs.qc.qualimap.common.LibraryProtocol;
+import org.bioinfo.ngs.qc.qualimap.common.LoggerThread;
+import org.bioinfo.ngs.qc.qualimap.gui.panels.RNASeqQCDialog;
+
+import org.bioinfo.ngs.qc.qualimap.gui.utils.TabPageController;
+import org.bioinfo.ngs.qc.qualimap.process.ComputeCountsTask;
+import org.bioinfo.ngs.qc.qualimap.process.RNASeqQCAnalysis;
+
+import javax.swing.*;
+
+/**
+ * Created by kokonech
+ * Date: 7/13/13
+ * Time: 12:44 PM
+ */
+public class RNASeqQCAnalysisThread extends Thread {
+
+ /** Logger to print information */
+ protected Logger logger;
+
+ /** Variable to manage the panel with the progressbar at the init */
+ private RNASeqQCDialog settingsDlg;
+
+ /** Variables that contains the tab properties loaded in the thread */
+ TabPageController resultManager;
+
+ public RNASeqQCAnalysisThread(RNASeqQCDialog rnaSeqQCDialog,TabPageController resultManager) {
+
+ super("RNASeqQCAnalysisThread");
+ this.settingsDlg = rnaSeqQCDialog;
+ this.resultManager = resultManager;
+ logger = new Logger(this.getClass().getName());
+ }
+
+ /**
+ * Public method to run this thread. Its executed when an user call to
+ * method start over this thread.
+ */
+ public void run() {
+
+ settingsDlg.setUiEnabled(false);
+
+ String bamPath = settingsDlg.getBamFilePath();
+ String gffPath = settingsDlg.getGtfFilePath();
+
+ ComputeCountsTask computeCountsTask = new ComputeCountsTask(bamPath, gffPath);
+ LibraryProtocol p = LibraryProtocol.getProtocolByName(settingsDlg.getProtocol());
+ computeCountsTask.setProtocol(p);
+ computeCountsTask.setCountingAlgorithm(settingsDlg.getCountingAlgorithm());
+ computeCountsTask.addSupportedFeatureType(ComputeCountsTask.EXON_TYPE_ATTR);
+ computeCountsTask.setAttrName(ComputeCountsTask.GENE_ID_ATTR);
+
+ if (settingsDlg.pairedAnalysisBoxIsSelected()) {
+ computeCountsTask.setPairedEndAnalysis();
+ if (!settingsDlg.sortedAlignmentBoxIsSelected()) {
+ computeCountsTask.setSortingRequired();
+ }
+ }
+
+ final JTextArea logArea = settingsDlg.getLogArea();
+ logArea.setText("");
+
+ computeCountsTask.setLogger( new LoggerThread() {
+ @Override
+ public void logLine(String msg) {
+ logArea.append(msg + "\n");
+ logArea.setCaretPosition(logArea.getText().length());
+ }
+ });
+
+ RNASeqQCAnalysis rnaSeqQCAnalysis = new RNASeqQCAnalysis(resultManager, computeCountsTask );
+
+ if (settingsDlg.outputCounts()) {
+ String countsPath = settingsDlg.getCountsOutputPath();
+ rnaSeqQCAnalysis.setCountsFilePath(countsPath);
+ }
+
+
+
+ try {
+ rnaSeqQCAnalysis.run();
+ } catch (Exception e) {
+ JOptionPane.showMessageDialog(settingsDlg, "Failed to analyze RNA-seq data. " + e.getMessage(),
+ settingsDlg.getTitle(), JOptionPane.ERROR_MESSAGE);
+ settingsDlg.setUiEnabled(true);
+ return;
+ }
+
+ settingsDlg.getHomeFrame().addNewPane(bamPath, resultManager);
+ }
+
+}
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/utils/AnalysisDialogLoggerThread.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/utils/AnalysisDialogLoggerThread.java
new file mode 100644
index 0000000..a6076d8
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/utils/AnalysisDialogLoggerThread.java
@@ -0,0 +1,58 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.gui.utils;
+
+import org.bioinfo.ngs.qc.qualimap.common.LoggerThread;
+import org.bioinfo.ngs.qc.qualimap.gui.dialogs.AnalysisDialog;
+
+import javax.swing.*;
+
+/**
+ * Created by kokonech
+ * Date: 8/21/14
+ * Time: 11:22 AM
+ */
+public class AnalysisDialogLoggerThread extends LoggerThread {
+
+ AnalysisDialog parentDialog;
+
+
+ public AnalysisDialogLoggerThread(AnalysisDialog parentDialog) {
+ this.parentDialog = parentDialog;
+
+ }
+
+ @Override
+ public void logLine(String msg) {
+ System.out.println(msg);
+ /*if (msg.contains("STATUS:")) {
+ parentDialog.setProgressStatus(msg.split(":")[1]);
+ }*/
+ JTextArea logArea = parentDialog.getLogArea();
+ logArea.append(msg + "\n");
+ logArea.setCaretPosition(logArea.getText().length());
+ }
+
+ @Override
+ public void updateProgress(int progress) {
+ parentDialog.updateProgress(progress);
+ }
+}
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/utils/ButtonTabComponent.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/utils/ButtonTabComponent.java
new file mode 100644
index 0000000..fdb2e38
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/utils/ButtonTabComponent.java
@@ -0,0 +1,159 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.gui.utils;
+
+
+import java.awt.BasicStroke;
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Dimension;
+import java.awt.FlowLayout;
+import java.awt.Graphics;
+import java.awt.Graphics2D;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+
+import javax.swing.*;
+import javax.swing.plaf.basic.BasicButtonUI;
+
+/**
+ * Component to be used as tabComponent;
+ * Contains a JLabel to show the text and
+ * a JButton to close the tab it belongs to
+ */
+public class ButtonTabComponent extends JPanel {
+ private final JTabbedPane pane;
+ JLabel titleLabel;
+
+ public ButtonTabComponent(final JTabbedPane pane, ImageIcon ic, String title) {
+ //unset default FlowLayout' gaps
+ super(new FlowLayout(FlowLayout.LEFT, 0, 0));
+ if (pane == null) {
+ throw new NullPointerException("TabbedPane is null");
+ }
+ this.pane = pane;
+ setOpaque(false);
+
+ //make JLabel read titles from JTabbedPane
+ JLabel icon = new JLabel(ic);
+
+ titleLabel = new JLabel(title);
+ add(icon);
+ icon.setBorder(BorderFactory.createEmptyBorder(0, 0, 0, 5));
+
+ add(titleLabel);
+ //add more space between the label and the button
+ titleLabel.setBorder(BorderFactory.createEmptyBorder(0, 0, 0, 5));
+ //tab button
+ JButton button = new TabButton();
+ add(button);
+ //add more space to the top of the component
+ setBorder(BorderFactory.createEmptyBorder(2, 0, 0, 0));
+ }
+
+ public String getTitle() {
+ return titleLabel.getText();
+ }
+
+ public void setTitle(String title) {
+ titleLabel.setText(title);
+ }
+
+ private class TabButton extends JButton implements ActionListener {
+ public TabButton() {
+ int size = 17;
+ setPreferredSize(new Dimension(size, size));
+ setToolTipText("close this tab");
+ //Make the button looks the same for all Laf's
+ setUI(new BasicButtonUI());
+ //Make it transparent
+ setContentAreaFilled(false);
+ //No need to be focusable
+ setFocusable(false);
+ //setBorder(BorderFactory.createEtchedBorder());
+ setBorder(null);
+ setBorderPainted(false);
+ //Making nice rollover effect
+ //we use the same listener for all buttons
+ addMouseListener(buttonMouseListener);
+ setRolloverEnabled(true);
+ //Close the proper tab by clicking the button
+ addActionListener(this);
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ int res = JOptionPane.showConfirmDialog(pane,
+ "Close the report window?", "QualiMap", JOptionPane.OK_CANCEL_OPTION);
+ if (res != 0) {
+ return;
+ }
+ int i = pane.indexOfTabComponent(ButtonTabComponent.this);
+ if (i != -1) {
+ pane.remove(i);
+ }
+ }
+
+ //we don't want to update UI for this button
+ public void updateUI() {
+ }
+
+ //paint the cross
+ protected void paintComponent(Graphics g) {
+ super.paintComponent(g);
+ Graphics2D g2 = (Graphics2D) g.create();
+ //shift the image for pressed buttons
+ if (getModel().isPressed()) {
+ g2.translate(1, 1);
+ }
+ g2.setStroke(new BasicStroke(2));
+ g2.setColor(Color.GRAY);
+ if (getModel().isRollover()) {
+ g2.setColor(Color.BLACK);
+ }
+ int delta = 6;
+ g2.drawLine(delta, delta, getWidth() - delta - 1, getHeight() - delta - 1);
+ g2.drawLine(getWidth() - delta - 1, delta, delta, getHeight() - delta - 1);
+ g2.dispose();
+ }
+ }
+
+ private final static MouseListener buttonMouseListener = new MouseAdapter() {
+ public void mouseEntered(MouseEvent e) {
+ Component component = e.getComponent();
+ if (component instanceof AbstractButton) {
+ AbstractButton button = (AbstractButton) component;
+ button.setBorderPainted(true);
+ }
+ }
+
+ public void mouseExited(MouseEvent e) {
+ Component component = e.getComponent();
+ if (component instanceof AbstractButton) {
+ AbstractButton button = (AbstractButton) component;
+ button.setBorderPainted(false);
+ }
+ }
+ };
+}
+
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/utils/ExportChartDataActionListener.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/utils/ExportChartDataActionListener.java
new file mode 100644
index 0000000..d219cae
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/utils/ExportChartDataActionListener.java
@@ -0,0 +1,79 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.gui.utils;
+
+import org.apache.commons.io.FilenameUtils;
+import org.bioinfo.ngs.qc.qualimap.beans.ChartRawDataWriter;
+import org.bioinfo.ngs.qc.qualimap.gui.frames.HomeFrame;
+import org.jfree.ui.ExtensionFileFilter;
+
+import javax.swing.*;
+import javax.swing.filechooser.FileFilter;
+import java.awt.*;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.io.BufferedWriter;
+import java.io.File;
+import java.io.FileWriter;
+
+/**
+ * Created by kokonech
+ * Date: 6/13/12
+ * Time: 12:58 PM
+ */
+public class ExportChartDataActionListener implements ActionListener {
+
+ ChartRawDataWriter dataWriter;
+ Component parent;
+ String title;
+
+ public ExportChartDataActionListener(Component parent, ChartRawDataWriter writer, String title) {
+ this.dataWriter = writer;
+ this.parent = parent;
+ this.title = title;
+ }
+
+
+ @Override
+ public void actionPerformed(ActionEvent actionEvent) {
+ JFileChooser fileChooser = HomeFrame.getFileChooser();
+ fileChooser.setSelectedFile(new File(title.replace(" ", "_").toLowerCase() + ".txt"));
+ fileChooser.setFileFilter( new ExtensionFileFilter("TAB delimited data", "txt") );
+
+ int result = fileChooser.showSaveDialog(parent);
+
+ if (result == JFileChooser.APPROVE_OPTION) {
+ try {
+ String path = fileChooser.getSelectedFile().getAbsolutePath();
+ if (FilenameUtils.getExtension(path).isEmpty()) {
+ path += ".txt";
+ }
+ dataWriter.exportDataToFile(path);
+ } catch (Exception e) {
+ JOptionPane.showMessageDialog(parent,
+ "Failed to save the raw data, please check the path.",
+ "Saving plot raw data", JOptionPane.ERROR_MESSAGE);
+ }
+ }
+
+
+ }
+}
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/utils/GraphicImagePanel.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/utils/GraphicImagePanel.java
new file mode 100644
index 0000000..04ae150
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/utils/GraphicImagePanel.java
@@ -0,0 +1,72 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.gui.utils;
+
+import org.bioinfo.ngs.qc.qualimap.common.Constants;
+
+import java.awt.*;
+import java.awt.image.BufferedImage;
+
+import javax.swing.JPanel;
+
+/**
+ * Class to manage the graphic image to display in the application
+ * @author Luis Miguel Cruz
+ */
+public class GraphicImagePanel extends JPanel {
+ /** serial version UID */
+ private static final long serialVersionUID = 1L;
+
+ private BufferedImage bufferedImage;
+ private Image image;
+
+
+ /**
+ * Paint the component into the original window
+ */
+ public void paintComponent(Graphics g) {
+ if(image!=null){
+ g.drawImage(image, 0, 0, null);
+ }
+ }
+
+ /**
+ * Set the image to display
+ * @param original BufferedImage with the image
+ */
+ public void setImage(BufferedImage original){
+ this.bufferedImage = original;
+ }
+
+ /**
+ * Resize an image with the dimensions wanted
+ * @param width integer with the image width
+ * @param height integer with the image height
+ */
+ public void resizeImage(int width, int height){
+ int scale = Image.SCALE_REPLICATE;
+ if(width < Constants.GRAPHIC_TO_SAVE_WIDTH || height < Constants.GRAPHIC_TO_SAVE_HEIGHT){
+ scale = Image.SCALE_SMOOTH;
+ }
+ this.image = bufferedImage.getScaledInstance(width, height, scale);
+ }
+
+}
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/utils/JLabelMouseListener.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/utils/JLabelMouseListener.java
new file mode 100644
index 0000000..cdbaa33
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/utils/JLabelMouseListener.java
@@ -0,0 +1,40 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.gui.utils;
+
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+
+public abstract class JLabelMouseListener implements MouseListener {
+ public JLabelMouseListener(){
+ super();
+ }
+
+ public void mouseClicked(MouseEvent arg0) {}
+
+ public void mouseEntered(MouseEvent arg0) {};
+
+ public void mouseExited(MouseEvent arg0) {};
+
+ public void mousePressed(MouseEvent arg0) {};
+
+ public void mouseReleased(MouseEvent arg0) {}
+}
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/utils/JTextFieldLimit.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/utils/JTextFieldLimit.java
new file mode 100644
index 0000000..99bd802
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/utils/JTextFieldLimit.java
@@ -0,0 +1,71 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.gui.utils;
+
+import javax.swing.text.AttributeSet;
+import javax.swing.text.BadLocationException;
+import javax.swing.text.PlainDocument;
+
+/**
+ * Class to allow formatted text in the JTextField
+ * @author Luis Miguel Cruz
+ */
+public class JTextFieldLimit extends PlainDocument {
+ private static final long serialVersionUID = -6394794410341873262L;
+ private int limit;
+ private boolean toUppercase = false;
+ private boolean onlyNumbers = false;
+
+ public JTextFieldLimit(int limit, boolean onlyNumbers) {
+ super();
+ this.limit = limit;
+ this.onlyNumbers = onlyNumbers;
+ }
+
+ public JTextFieldLimit(int limit, boolean upper, boolean onlyNumbers) {
+ super();
+ this.limit = limit;
+ this.toUppercase = upper;
+ this.onlyNumbers = onlyNumbers;
+ }
+
+ public void insertString(int offset, String str, AttributeSet attr)
+ throws BadLocationException {
+ if (str == null)
+ return;
+
+ if(onlyNumbers){
+ try{
+ Integer.parseInt(str);
+ } catch(NumberFormatException nfe){
+ return;
+ }
+ }
+
+ if ((getLength() + str.length()) <= limit) {
+ if (toUppercase){
+ str = str.toUpperCase();
+ }
+ super.insertString(offset, str, attr);
+ }
+ }
+}
+
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/utils/LODFileChooser.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/utils/LODFileChooser.java
new file mode 100644
index 0000000..1a3c3bf
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/utils/LODFileChooser.java
@@ -0,0 +1,83 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.gui.utils;
+
+import javax.swing.*;
+import java.awt.*;
+import java.io.File;
+
+/**
+ * Created by kokonech
+ * Date: 2/3/12
+ * Time: 4:07 PM
+ * Last open dir file helper
+ */
+
+public class LODFileChooser extends JFileChooser {
+
+ private static File lastOpenedDir = null;
+
+ public LODFileChooser()
+ {
+ super();
+
+ if (lastOpenedDir == null) {
+ lastOpenedDir = new File(System.getProperty("user.home"));
+ }
+ setCurrentDirectory(lastOpenedDir);
+
+ }
+
+ public int showOpenDialog(Component parent)
+ {
+ int res = super.showOpenDialog(parent);
+ lastOpenedDir = getCurrentDirectory();
+ return res;
+ }
+
+ public int showSaveDialog(Component parent)
+ {
+ int res = super.showSaveDialog(parent);
+ lastOpenedDir = getCurrentDirectory();
+ return res;
+ }
+
+ @Override
+ public void approveSelection(){
+ File f = getSelectedFile();
+ if(f.exists() && getDialogType() == SAVE_DIALOG){
+ int result = JOptionPane.showConfirmDialog(this,"The file exists, overwrite?","Existing file",JOptionPane.YES_NO_CANCEL_OPTION);
+ switch(result){
+ case JOptionPane.YES_OPTION:
+ super.approveSelection();
+ return;
+ case JOptionPane.NO_OPTION:
+ return;
+ case JOptionPane.CANCEL_OPTION:
+ cancelSelection();
+ return;
+ }
+ }
+ super.approveSelection();
+ }
+
+
+}
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/utils/PopupKeyListener.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/utils/PopupKeyListener.java
new file mode 100644
index 0000000..c0d34d6
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/utils/PopupKeyListener.java
@@ -0,0 +1,69 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.gui.utils;
+
+import java.awt.event.KeyEvent;
+import java.awt.event.KeyListener;
+
+import javax.swing.JDialog;
+import javax.swing.JFrame;
+import javax.swing.JOptionPane;
+import javax.swing.JProgressBar;
+
+/**
+ * Class that do the actions to do when a user press a key in
+ * a Popup dialog.
+ * @author Luis Miguel Cruz
+ */
+public class PopupKeyListener implements KeyListener{
+ private JDialog jDialog;
+
+ private JFrame homeFrame;
+
+ private JProgressBar jProgressBar;
+
+ public PopupKeyListener(JFrame homeFrame, JDialog jDialog, JProgressBar jProgressBar){
+ super();
+ this.jDialog = jDialog;
+ this.homeFrame = homeFrame;
+ this.jProgressBar = jProgressBar;
+ }
+
+ /**
+ * Function that executes when a key is pressed
+ */
+ public void keyPressed(KeyEvent e) {
+ if (e.getKeyCode() == KeyEvent.VK_ESCAPE) {
+ // Close the jDialog
+ if(jProgressBar == null || !jProgressBar.isVisible() ){
+ jDialog.setVisible(false);
+ homeFrame.remove(jDialog);
+ } else {
+ JOptionPane.showMessageDialog(null,
+ "Unable to close the JDialog while its running", "Error", 0);
+ }
+ }
+ }
+
+ public void keyReleased(KeyEvent e) {}
+
+ public void keyTyped(KeyEvent e) {}
+}
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/utils/StatsKeeper.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/utils/StatsKeeper.java
new file mode 100644
index 0000000..ac3aac6
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/utils/StatsKeeper.java
@@ -0,0 +1,116 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.gui.utils;
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
+
+/**
+ * Created by kokonech
+ * Date: 3/13/12
+ * Time: 5:43 PM
+ */
+
+/**
+ * This class allows to keep text information
+ * in form of data rows grouped in sections.
+ * It is used for Summary and Input html-report generation.
+ */
+
+public class StatsKeeper {
+
+ static public class Section {
+ String name;
+ List<String[]> rows;
+ public Section(String name) {
+ this.name = name;
+ this.rows = new ArrayList<String[]>();
+ }
+
+ public void addRow(String val1, String val2) {
+ String[] row = new String[2];
+ row[0] = val1;
+ row[1] = val2;
+ rows.add(row);
+ }
+
+ public String getName() {
+ return name;
+ }
+
+ public List<String[]> getRows() {
+ return rows;
+ }
+
+ public void addData(Map<String, String> paramsMap) {
+
+ for (Map.Entry<String,String> entry: paramsMap.entrySet()) {
+ addRow(entry.getKey(), entry.getValue());
+
+ }
+
+ }
+
+ public void addRow(String[] tableValues) {
+ rows.add(tableValues);
+ }
+ }
+
+ List<Section> sectionList;
+ String name;
+
+ public StatsKeeper() {
+ name = "";
+ sectionList = new ArrayList<Section>();
+ }
+
+ public String getName() {
+ return name;
+ }
+
+ public void setName(String name) {
+ this.name = name;
+ }
+
+ public void addSection(Section section) {
+ sectionList.add(section);
+ }
+
+ public Section getSectionByName(String name) {
+ for (Section s : sectionList ) {
+ if (s.getName().equals(name)) {
+ return s;
+ }
+ }
+
+ return null;
+ }
+
+ public List<Section> getSections() {
+ return sectionList;
+ }
+
+
+
+
+
+}
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/utils/StringUtilsSwing.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/utils/StringUtilsSwing.java
new file mode 100644
index 0000000..e4c1400
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/utils/StringUtilsSwing.java
@@ -0,0 +1,107 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.gui.utils;
+
+import java.text.DecimalFormat;
+import java.text.NumberFormat;
+import java.text.ParseException;
+
+import org.bioinfo.commons.log.Logger;
+import org.bioinfo.commons.utils.StringUtils;
+
+
+
+public class StringUtilsSwing {
+ /** Logger to print information */
+ protected Logger logger;
+
+ public String formatInteger(int decimal){
+ return StringUtils.decimalFormat(decimal,"###,###,###,###,###,###,###.##");
+ }
+
+ public String formatLong(long decimal){
+ return StringUtils.decimalFormat(decimal,"###,###,####,###,###,###,###,###,###,###,###.##");
+ }
+
+ public String formatDecimal(double decimal){
+ return StringUtils.decimalFormat(decimal,"###,###,###,###,###,###,###.##");
+ }
+
+ public String formatPercentage(double numerator, double denominator){
+ return formatPercentage((numerator/denominator)*100.0);
+ }
+
+ public String formatPercentage(double percentage){
+ return StringUtils.decimalFormat(percentage,"###.##")+"%";
+ }
+
+ public Long parseLong(String s){
+ NumberFormat format = new DecimalFormat("###,###,####,###,###,###,###,###,###,###,###.##");
+ Long result = 0L;
+
+ if(s != null){
+ try {
+ result = (Long)format.parseObject(s);
+ } catch (ParseException e) {
+ logger.error("Cannot parse the String " + s + " from the properites file to a Long value");
+ }
+ }
+
+ return result;
+ }
+
+ public Integer parseInt(String s){
+ NumberFormat format = new DecimalFormat("###,###,###,###,###,###,###.##");
+ Integer result = 0;
+
+ if(s != null){
+ try {
+ Long l = (Long)format.parseObject(s);
+ if(l != null){
+ result = l.intValue();
+ }
+ } catch (ParseException e) {
+ logger.error("Cannot parse the String " + s + " from the properites file to a Integer value");
+ }
+ }
+
+ return result;
+ }
+
+ /**
+ * Cut the file name if it is too large and add at this case "..." at the end
+ * @param fileName name of the original file
+ * @return new name created if necessary
+ */
+ public static String formatFileName(String fileName){
+ String result = fileName;
+
+ // If the name of the file is too large, we cut it
+ if(result.length()>20){
+ // If we are only cutting the extension
+ if(fileName.length() > 24){
+ result = fileName.substring(0, 20) + "...";
+ }
+ }
+
+ return result;
+ }
+}
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/utils/TabPageController.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/utils/TabPageController.java
new file mode 100644
index 0000000..eece93a
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/gui/utils/TabPageController.java
@@ -0,0 +1,91 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.gui.utils;
+
+import org.bioinfo.ngs.qc.qualimap.beans.AnalysisResultManager;
+import org.bioinfo.ngs.qc.qualimap.beans.StatsReporter;
+import org.bioinfo.ngs.qc.qualimap.common.AnalysisType;
+
+import javax.swing.*;
+
+/**
+ * Created by kokonech
+ * Date: 7/13/13
+ * Time: 2:23 PM
+ */
+public class TabPageController extends AnalysisResultManager {
+
+
+ /**
+ * Variable that contains the GraphicImagePanel for each tab where the
+ * system load the graphic image at each moment.
+ */
+ private GraphicImagePanel graphicImage;
+
+ /** Variable that contains name of the graphic image loaded into the
+ * right panel in the screen. */
+ private String loadedGraphicName;
+
+ /** Variable to manage the last link selected in the left menu, to remove the
+ * link decoration setted before. */
+ private JLabel lastLinkSelected;
+ private int selectedReproterIndex;
+
+ public TabPageController(AnalysisType analysisType) {
+ super(analysisType);
+ this.graphicImage = new GraphicImagePanel();
+ loadedGraphicName = "";
+ lastLinkSelected = null;
+ selectedReproterIndex = 0;
+ }
+
+ public void setLastLinkSelected(JLabel linkSelected) {
+ lastLinkSelected = linkSelected;
+ }
+
+ public GraphicImagePanel getGraphicImage() {
+ return graphicImage;
+ }
+
+ public void setLoadedGraphicName(String name) {
+ loadedGraphicName = name;
+ }
+
+ public String getLoadedGraphicName() {
+ return loadedGraphicName;
+ }
+
+ public JLabel getLastLinkSelected() {
+ return lastLinkSelected;
+ }
+
+ public int getSelectedReproterIndex() {
+ return selectedReproterIndex;
+ }
+
+ public void setSelectedReporterIndex(int reporterIndex) {
+ this.selectedReproterIndex = reporterIndex;
+ }
+
+ public StatsReporter getActiveReporter() {
+ return getReporters().get(selectedReproterIndex);
+ }
+}
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/main/BamQcTool.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/main/BamQcTool.java
new file mode 100644
index 0000000..39a22c2
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/main/BamQcTool.java
@@ -0,0 +1,259 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.main;
+
+import org.apache.commons.cli.Option;
+import org.apache.commons.cli.ParseException;
+import org.apache.commons.io.FilenameUtils;
+import org.bioinfo.ngs.qc.qualimap.beans.AnalysisResultManager;
+import org.bioinfo.ngs.qc.qualimap.beans.BamQCRegionReporter;
+import org.bioinfo.ngs.qc.qualimap.common.AnalysisType;
+import org.bioinfo.ngs.qc.qualimap.common.Constants;
+import org.bioinfo.ngs.qc.qualimap.common.LibraryProtocol;
+import org.bioinfo.ngs.qc.qualimap.process.BamStatsAnalysis;
+
+
+import java.io.File;
+
+public class BamQcTool extends NgsSmartTool{
+
+ private String bamFile;
+ private String gffFile;
+ private boolean selectedRegionsAvailable;
+ private int numberOfWindows;
+ private int numThreads;
+ private int bunchSize;
+ private int minHomopolymerSize;
+ private boolean paintChromosomeLimits, skipDuplicated;
+ private boolean collectOverlappingPairedEndReads;
+ private boolean computeOutsideStats;
+ private String genomeToCompare;
+ private String coverageReportFile;
+ private LibraryProtocol protocol;
+
+ public BamQcTool(){
+ super(Constants.TOOL_NAME_BAMQC,false);
+ numThreads = Runtime.getRuntime().availableProcessors();
+ protocol = LibraryProtocol.NON_STRAND_SPECIFIC;
+ genomeToCompare = "";
+ coverageReportFile = "";
+ }
+
+ @Override
+ protected void initOptions() {
+
+ Option opt = new Option(Constants.BAMQC_OPTION_BAM_FILE, true, "Input mapping file in BAM format");
+ opt.setRequired(true);
+ options.addOption( opt );
+
+ options.addOption(Constants.BAMQC_OPTION_GFF_FILE, "feature-file", true,
+ "Feature file with regions of interest in GFF/GTF or BED format");
+ options.addOption(Constants.BAMQC_OPTION_NUM_WINDOWS, true,
+ "Number of windows (default is "+ Constants.DEFAULT_NUMBER_OF_WINDOWS + ")");
+ options.addOption(Constants.BAMQC_OPTION_NUM_THREADS, true,
+ "Number of threads (default is " + Runtime.getRuntime().availableProcessors() + ")");
+ options.addOption(Constants.BAMQC_OPTION_CHUNK_SIZE, true,
+ "Number of reads analyzed in a chunk (default is " + Constants.DEFAULT_CHUNK_SIZE + ")" );
+ options.addOption(Constants.BAMQC_OPTION_MIN_HOMOPOLYMER_SIZE, true,
+ "Minimum size for a homopolymer to be considered in indel analysis (default is "
+ + Constants.DEFAULT_HOMOPOLYMER_SIZE + ") " );
+ options.addOption(Constants.BAMQC_OPTION_COVERAGE_REPORT_FILE, "output-genome-coverage", true,
+ "File to save per base non-zero coverage. Warning: large files " +
+ "are expected for large genomes");
+ options.addOption(Constants.BAMQC_OPTION_PAINT_CHROMOSOMES, "paint-chromosome-limits", false,
+ "Paint chromosome limits inside charts");
+ options.addOption(Constants.BAMQC_OPTION_SKIP_DUPLICATED, "skip-duplicated", false,
+ "Activate this option to skip duplicated alignments from analysis. " +
+ "If the duplicates are not flagged in BAM file, then they will be detected" +
+ " by Qualimap.");
+ options.addOption(Constants.BAMQC_OPTION_COLLECT_OVERLAP_PAIRS, "collect-overlap-pairs", false,
+ "Activate this option to collect statistics of overlapping paired-end reads " );
+ options.addOption(Constants.BAMQC_OPTION_OUTSIDE_STATS, "outside-stats", false,
+ "Report information for the regions outside those defined by feature-file " +
+ " (ignored when -gff option is not set)");
+ options.addOption(Constants.BAMQC_OPTION_COMPARE_WITH_GENOME_DISTRIBUTION, "genome-gc-distr",
+ true, "Species to compare with genome GC distribution. " +
+ "Possible values: HUMAN or MOUSE.");
+ options.addOption(getProtocolOption());
+ }
+
+ @Override
+ protected void checkOptions() throws ParseException {
+
+ // input
+
+ bamFile = commandLine.getOptionValue(Constants.BAMQC_OPTION_BAM_FILE);
+ if(!exists(bamFile)) throw new ParseException("input mapping file not found");
+
+ // gff
+ if(commandLine.hasOption(Constants.BAMQC_OPTION_GFF_FILE)) {
+ gffFile = commandLine.getOptionValue(Constants.BAMQC_OPTION_GFF_FILE);
+ if(!exists(gffFile)) {
+ throw new ParseException("input region gff file not found");
+ }
+ selectedRegionsAvailable = true;
+ if(commandLine.hasOption(Constants.BAMQC_OPTION_OUTSIDE_STATS)) {
+ computeOutsideStats = true;
+ }
+
+ if (commandLine.hasOption(Constants.CMDLINE_OPTION_LIBRARY_PROTOCOL)) {
+ protocol = LibraryProtocol.getProtocolByName(
+ commandLine.getOptionValue(Constants.CMDLINE_OPTION_LIBRARY_PROTOCOL).toLowerCase()
+ );
+ }
+ }
+
+
+ numberOfWindows = commandLine.hasOption(Constants.BAMQC_OPTION_NUM_WINDOWS) ?
+ Integer.parseInt(commandLine.getOptionValue(Constants.BAMQC_OPTION_NUM_WINDOWS))
+ : Constants.DEFAULT_NUMBER_OF_WINDOWS;
+
+ numThreads = commandLine.hasOption(Constants.BAMQC_OPTION_NUM_THREADS) ?
+ Integer.parseInt(commandLine.getOptionValue(Constants.BAMQC_OPTION_NUM_THREADS)) : Runtime.getRuntime().availableProcessors();
+
+ bunchSize = commandLine.hasOption(Constants.BAMQC_OPTION_CHUNK_SIZE) ?
+ Integer.parseInt(commandLine.getOptionValue(Constants.BAMQC_OPTION_CHUNK_SIZE)) : Constants.DEFAULT_CHUNK_SIZE;
+
+
+ minHomopolymerSize = commandLine.hasOption(Constants.BAMQC_OPTION_MIN_HOMOPOLYMER_SIZE) ?
+ Integer.parseInt(commandLine.getOptionValue(Constants.BAMQC_OPTION_MIN_HOMOPOLYMER_SIZE)) : Constants.DEFAULT_HOMOPOLYMER_SIZE;
+
+
+ if (commandLine.hasOption(Constants.BAMQC_OPTION_COMPARE_WITH_GENOME_DISTRIBUTION)) {
+ String val = commandLine.getOptionValue(Constants.BAMQC_OPTION_COMPARE_WITH_GENOME_DISTRIBUTION);
+ if (val.equalsIgnoreCase(BamStatsAnalysis.HUMAN_GENOME_NAME)) {
+ genomeToCompare = BamStatsAnalysis.HUMAN_GENOME_ID;
+ } else if (val.equalsIgnoreCase(BamStatsAnalysis.MOUSE_GENOME_NAME)) {
+ genomeToCompare = BamStatsAnalysis.MOUSE_GENOME_ID;
+ } else {
+ throw new ParseException("Unknown genome \"" + val+ "\", please use HUMAN or MOUSE");
+
+ }
+ }
+
+ if (commandLine.hasOption(Constants.BAMQC_OPTION_COVERAGE_REPORT_FILE)) {
+ coverageReportFile = commandLine.getOptionValue(Constants.BAMQC_OPTION_COVERAGE_REPORT_FILE);
+ }
+
+
+ paintChromosomeLimits = commandLine.hasOption(Constants.BAMQC_OPTION_PAINT_CHROMOSOMES);
+ skipDuplicated = commandLine.hasOption(Constants.BAMQC_OPTION_SKIP_DUPLICATED);
+ collectOverlappingPairedEndReads = commandLine.hasOption(Constants.BAMQC_OPTION_COLLECT_OVERLAP_PAIRS);
+
+ }
+
+ @Override
+ protected void initOutputDir() {
+ if (outdir.equals(".")) {
+ outdir = FilenameUtils.removeExtension(new File(bamFile).getAbsolutePath()) + "_stats";
+ }
+ super.initOutputDir();
+ }
+
+ @Override
+ protected void execute() throws Exception {
+
+ long memAvailable = Runtime.getRuntime().totalMemory() / 1000000;
+ long memMax = Runtime.getRuntime().maxMemory() / 1000000;
+ System.out.println("Available memory (Mb): " + memAvailable);
+ System.out.println("Max memory (Mb): " + memMax);
+
+ // check outdir
+ initOutputDir();
+
+ // init bamqc
+ BamStatsAnalysis bamQC = new BamStatsAnalysis(bamFile);
+
+ if(selectedRegionsAvailable){
+ bamQC.setSelectedRegions(gffFile);
+ bamQC.setComputeOutsideStats(computeOutsideStats);
+ }
+
+ // reporting
+ bamQC.activeReporting(outdir);
+ if (coverageReportFile.length() > 0) {
+ bamQC.setPathToCoverageReport(coverageReportFile);
+ }
+
+ logger.println("Starting bam qc....");
+
+ // number of windows
+ bamQC.setNumberOfWindows(numberOfWindows);
+ bamQC.setNumberOfThreads(numThreads);
+ bamQC.setNumberOfReadsInBunch(bunchSize);
+ bamQC.setProtocol(protocol);
+ bamQC.setMinHomopolymerSize(minHomopolymerSize);
+ if (skipDuplicated) {
+ bamQC.setSkipDuplicatedReads(true);
+ }
+
+ if (collectOverlappingPairedEndReads){
+ bamQC.activateIntersectingPairedEndReadsStats();
+ }
+
+ // run evaluation
+ bamQC.run();
+
+ logger.println("end of bam qc");
+
+ logger.println("Computing report...");
+
+ BamQCRegionReporter reporter = new BamQCRegionReporter(selectedRegionsAvailable, true);
+ reporter.setPaintChromosomeLimits(paintChromosomeLimits);
+ if (!genomeToCompare.isEmpty()) {
+ reporter.setGenomeGCContentName(genomeToCompare);
+ }
+
+ bamQC.prepareInputDescription(reporter, paintChromosomeLimits);
+
+ // save stats
+
+ reporter.writeReport(bamQC.getBamStats(),outdir);
+
+ AnalysisResultManager resultManager = new AnalysisResultManager(AnalysisType.BAM_QC);
+
+ reporter.loadReportData(bamQC.getBamStats());
+ reporter.computeChartsBuffers(bamQC.getBamStats(), bamQC.getLocator(), bamQC.isPairedData());
+ resultManager.addReporter(reporter);
+
+ if(selectedRegionsAvailable && computeOutsideStats){
+
+ BamQCRegionReporter outsideReporter = new BamQCRegionReporter(selectedRegionsAvailable, false);
+ outsideReporter.setPaintChromosomeLimits(paintChromosomeLimits);
+ if (!genomeToCompare.isEmpty()) {
+ outsideReporter.setGenomeGCContentName(genomeToCompare);
+ }
+ bamQC.prepareInputDescription(outsideReporter, paintChromosomeLimits);
+ outsideReporter.writeReport(bamQC.getOutsideBamStats(),outdir);
+
+ outsideReporter.loadReportData(bamQC.getOutsideBamStats());
+ outsideReporter.computeChartsBuffers(bamQC.getOutsideBamStats(), bamQC.getLocator(), bamQC.isPairedData());
+
+ resultManager.addReporter(outsideReporter);
+ }
+
+
+ exportResult(resultManager);
+
+ logger.println("Finished");
+
+ }
+}
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/main/ComputeCountsTool.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/main/ComputeCountsTool.java
new file mode 100644
index 0000000..9f3d535
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/main/ComputeCountsTool.java
@@ -0,0 +1,219 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.main;
+
+import org.apache.commons.cli.Option;
+import org.apache.commons.cli.ParseException;
+import org.bioinfo.ngs.qc.qualimap.common.Constants;
+import org.bioinfo.ngs.qc.qualimap.common.LibraryProtocol;
+import org.bioinfo.ngs.qc.qualimap.process.ComputeCountsTask;
+
+import java.io.File;
+import java.io.FileWriter;
+import java.io.OutputStreamWriter;
+import java.io.PrintWriter;
+import java.util.Map;
+
+/**
+ * Created by kokonech
+ * Date: 1/27/12
+ * Time: 12:20 PM
+ */
+public class ComputeCountsTool extends NgsSmartTool {
+
+ public static String OPTION_ANNOTATION = "gtf";
+ public static String OPTION_BAM = "bam";
+ public static String OPTION_FEATURE_ID = "id";
+ public static String OPTION_FEATURE_TYPE = "type";
+ public static String OPTION_OUT_FILE = "out";
+ public static String OPTION_ALGORITHM = "a";
+ public static String OPTION_PAIRED = "pe";
+ public static String OPTION_ALREADY_SORTED = "s";
+
+ String bamFile, gffFile, outFilePath, featureType, attrName, alg;
+ LibraryProtocol protocol;
+ boolean pairedAnalysis, sortingRequired;
+
+ public ComputeCountsTool() {
+ super(Constants.TOOL_NAME_COMPUTE_COUNTS,false,false, false);
+ this.pairedAnalysis = false;
+ this.sortingRequired = false;
+ this.protocol = LibraryProtocol.NON_STRAND_SPECIFIC;
+ }
+
+ @Override
+ protected void initOptions() {
+
+ options.addOption( requiredOption(OPTION_BAM, true, "Mapping file in BAM format") );
+ options.addOption(requiredOption(OPTION_ANNOTATION, true, "Region file in GTF, GFF or BED format. " +
+ "If GTF format is provided, counting is based on attributes, otherwise based on feature name") );
+ options.addOption( getProtocolOption() );
+ options.addOption(new Option(OPTION_FEATURE_TYPE, true, "GTF-specific. Value of the third column of the GTF considered" +
+ " for counting. Other types will be ignored. Default: exon"));
+ options.addOption(new Option(OPTION_FEATURE_ID, true, "GTF-specific. Attribute of the GTF to be used as feature ID. " +
+ "Regions with the same ID will be aggregated as part of the same feature. Default: gene_id."));
+ options.addOption(new Option(OPTION_ALGORITHM, "algorithm", true,
+ "Counting algorithm: " + ComputeCountsTask.getAlgorithmTypes()));
+ options.addOption(new Option(OPTION_OUT_FILE, true, "Output file of coverage report.") );
+ options.addOption(new Option(OPTION_PAIRED, "paired", false, "Setting this flag for paired-end experiments will result " +
+ "in counting fragments instead of reads") );
+ options.addOption(new Option(OPTION_ALREADY_SORTED, "sorted", true,
+ "This flag indicates that the input file is already sorted by name. " +
+ "If not set, additional sorting by name will be performed. " +
+ "Only required for paired-end analysis. " ) );
+
+ }
+
+ @Override
+ protected void checkOptions() throws ParseException {
+
+ bamFile = commandLine.getOptionValue(OPTION_BAM);
+ if (!exists(bamFile))
+ throw new ParseException("input mapping file not found");
+
+ gffFile = commandLine.getOptionValue(OPTION_ANNOTATION);
+ if(!exists(gffFile))
+ throw new ParseException("input region gtf file not found");
+
+ if(commandLine.hasOption(Constants.CMDLINE_OPTION_LIBRARY_PROTOCOL)) {
+ String protocolName = commandLine.getOptionValue(Constants.CMDLINE_OPTION_LIBRARY_PROTOCOL);
+ if ( !ComputeCountsTask.supportedLibraryProtocol(protocolName) ) {
+ throw new ParseException("wrong protocol type! supported types: " +
+ LibraryProtocol.getProtocolNamesString());
+ } else {
+ protocol = LibraryProtocol.getProtocolByName(protocolName);
+ }
+ }
+
+ if (commandLine.hasOption(OPTION_OUT_FILE)) {
+ outFilePath = commandLine.getOptionValue(OPTION_OUT_FILE);
+ } else {
+ outFilePath = "";
+ }
+
+ if (commandLine.hasOption(OPTION_FEATURE_TYPE)) {
+ featureType = commandLine.getOptionValue(OPTION_FEATURE_TYPE);
+ } else {
+ featureType = ComputeCountsTask.EXON_TYPE_ATTR;
+ }
+
+ if (commandLine.hasOption(OPTION_FEATURE_ID)) {
+ attrName = commandLine.getOptionValue(OPTION_FEATURE_ID);
+ } else {
+ attrName = ComputeCountsTask.GENE_ID_ATTR;
+ }
+
+ if (commandLine.hasOption(OPTION_ALGORITHM)) {
+ alg = commandLine.getOptionValue(OPTION_ALGORITHM);
+ if (! ( alg.equalsIgnoreCase(ComputeCountsTask.COUNTING_ALGORITHM_ONLY_UNIQUELY_MAPPED) ||
+ alg.equalsIgnoreCase(ComputeCountsTask.COUNTING_ALGORITHM_PROPORTIONAL)) ) {
+ throw new ParseException("Unknown algorithm! Possible values are: "
+ + ComputeCountsTask.getAlgorithmTypes());
+ }
+ } else {
+ alg = ComputeCountsTask.COUNTING_ALGORITHM_ONLY_UNIQUELY_MAPPED;
+ }
+
+ if (commandLine.hasOption(OPTION_PAIRED)) {
+ pairedAnalysis = true;
+ if (!commandLine.hasOption(OPTION_ALREADY_SORTED)) {
+ sortingRequired = true;
+ }
+ }
+
+
+
+ }
+
+ @Override
+ protected void execute() throws Exception {
+
+ ComputeCountsTask computeCountsTask = new ComputeCountsTask(bamFile, gffFile);
+ computeCountsTask.setProtocol(protocol);
+ computeCountsTask.setCountingAlgorithm(alg);
+ computeCountsTask.setAttrName(attrName);
+ computeCountsTask.addSupportedFeatureType(featureType);
+ if (pairedAnalysis) {
+ computeCountsTask.setPairedEndAnalysis();
+ if (sortingRequired) {
+ computeCountsTask.setSortingRequired();
+ }
+ }
+
+
+ if (!outFilePath.isEmpty()) {
+
+ File outFile = new File(outFilePath);
+ if (outFile.isDirectory()) {
+ System.err.println("\nERROR! The given output path "+ outFilePath + " is just a folder. " +
+ "\nPlease, provide the file name.");
+ return;
+ } else {
+ File parentDir = outFile.getParentFile();
+ if (parentDir != null) {
+ if (!parentDir.exists()) {
+ System.err.println("\nERROR! The given output path " + outFilePath + " is not correct." +
+ "\nPlease, check the names of folders in the path.");
+ return;
+ }
+ }
+ }
+ }
+
+ PrintWriter outWriter = outFilePath.isEmpty() ?
+ new PrintWriter(new OutputStreamWriter(System.out)) :
+ new PrintWriter(new FileWriter(outFilePath));
+
+
+ try {
+ computeCountsTask.run();
+
+ Map<String,Double> counts = computeCountsTask.getReadCounts();
+ for (Map.Entry<String,Double> entry: counts.entrySet()) {
+ long roundedValue = entry.getValue().longValue();
+ String str = entry.getKey() + "\t" + roundedValue;
+ outWriter.println(str);
+ }
+
+
+ outWriter.flush();
+
+ } catch (Exception e) {
+ System.err.println("Error while calculating counts! " + e.getMessage());
+ e.printStackTrace();
+ return;
+ }
+
+ StringBuilder message = new StringBuilder();
+ message.append("Calculation successful!\n");
+ message.append( computeCountsTask.getOutputStatsMessage() );
+
+
+ if (!outFilePath.isEmpty()) {
+ message.append("Result is saved to file ").append(outFilePath);
+ }
+
+ System.err.println(message);
+
+ }
+
+
+}
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/main/CountsQcTool.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/main/CountsQcTool.java
new file mode 100644
index 0000000..553e63a
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/main/CountsQcTool.java
@@ -0,0 +1,191 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.main;
+
+import org.bioinfo.ngs.qc.qualimap.beans.AnalysisResultManager;
+import org.bioinfo.ngs.qc.qualimap.common.AnalysisType;
+import org.bioinfo.ngs.qc.qualimap.common.Constants;
+
+import java.io.File;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import org.apache.commons.cli.ParseException;
+import org.bioinfo.ngs.qc.qualimap.common.LoggerThread;
+import org.bioinfo.ngs.qc.qualimap.process.CountsSampleInfo;
+import org.bioinfo.ngs.qc.qualimap.process.CountsQcAnalysis;
+
+/**
+ * Created by kokonech
+ * Date: 5/19/14
+ * Time: 5:03 PM
+ */
+
+public class CountsQcTool extends NgsSmartTool{
+
+
+ private String inputFile;
+ private String infoFile;
+
+ private int k;
+
+ private static String INFO_FILE_HUMAN_68;
+ private static String INFO_FILE_MOUSE_68;
+ final private static int DEFAULT_NUMBER_OF_COUNTS = 5;
+ private static final String SPECIES_FOLDER = "species";
+ private boolean compareConditions;
+
+ public CountsQcTool(){
+ super(Constants.TOOL_NAME_COUNTS_QC, true);
+
+ INFO_FILE_HUMAN_68 = homePath + File.separator + SPECIES_FOLDER +
+ File.separator + Constants.FILE_SPECIES_INFO_HUMAN_ENS68;
+ INFO_FILE_MOUSE_68 = homePath + File.separator + SPECIES_FOLDER +
+ File.separator + Constants.FILE_SPECIES_INFO_MOUSE_ENS68;
+
+
+ compareConditions = false;
+ infoFile = "";
+ k = DEFAULT_NUMBER_OF_COUNTS;
+ }
+
+ @Override
+ protected void initOptions() {
+ options.addOption(requiredOption("d", "data", true, "File describing the input data. " +
+ "Format of the file is a 4-column tab-delimited table.\nColumn 1: sample name\nColumn 2: condition of the sample" +
+ "\nColumn 3: path to the counts data for the sample\nColumn 4: index of the column with counts"));
+ options.addOption("i", "info", true, "Path to info file containing genes GC-content, length and type.");
+ options.addOption("s", "species", true, "Use built-in info file for the given species: HUMAN or MOUSE.");
+ options.addOption("k", "threshold", true, "Threshold for the number of counts");
+ options.addOption("c", "compare", false, "Perform comparison of conditions. Currently 2 maximum is possible.");
+
+ }
+
+ @Override
+ protected void checkOptions() throws ParseException {
+
+ // input
+ if(!commandLine.hasOption("data")){
+ throw new ParseException("input data description file is required");
+ }else{
+ inputFile = commandLine.getOptionValue("data");
+ if(!exists(inputFile)) {
+ throw new ParseException("input description file (--data) " + inputFile + " is not found");
+ }
+
+ }
+
+
+ // Info file
+ if(commandLine.hasOption("info")) {
+ infoFile = commandLine.getOptionValue("info");
+ if(!exists(infoFile)) {
+ throw new ParseException("file of information (--info) " + infoFile + " not found");
+ }
+ } else if(commandLine.hasOption("species")) {
+ String species = commandLine.getOptionValue("species");
+
+ if(species.equalsIgnoreCase("human")){
+ infoFile = INFO_FILE_HUMAN_68;
+ }else if(species.equalsIgnoreCase("mouse")){
+ infoFile = INFO_FILE_MOUSE_68;
+ }else{
+ throw new ParseException("species " + species + " not found. Please select [human | mouse]");
+ }
+ }
+
+ if (commandLine.hasOption("c")) {
+ compareConditions = true;
+ }
+
+
+ // threshold for the number of counts
+ if(commandLine.hasOption("k")) {
+ k = Integer.parseInt(commandLine.getOptionValue("k"));
+ }
+ }
+
+
+ @Override
+ protected void execute() throws Exception {
+
+ if ( outdir.equals(".") ) {
+ String parentDir = new File(inputFile).getParent();
+ if (parentDir == null) {
+ parentDir = ".";
+ }
+ outdir = parentDir + File.separator + "countsQC_results";
+ }
+ // init output dir
+ initOutputDir();
+
+ AnalysisResultManager resultManager = new AnalysisResultManager(AnalysisType.COUNTS_QC);
+
+ ArrayList<String> conditionNames = new ArrayList<String>();
+ List<CountsSampleInfo> samples = CountsQcAnalysis.parseInputFile(inputFile, conditionNames);
+ if (samples.size() == 0) {
+ System.err.println("The input file " + inputFile + " does not contain any samples. " +
+ "Please check file format.");
+ System.exit(-1);
+ }
+
+ CountsQcAnalysis countsAnalysis =
+ new CountsQcAnalysis(resultManager, homePath, samples);
+
+
+ countsAnalysis.setInputFilePath(inputFile);
+
+ Map<Integer,String> cMap = new HashMap<Integer, String>();
+ for (int i = 0; i < conditionNames.size(); ++i) {
+ cMap.put(i + 1, conditionNames.get(i));
+ }
+ countsAnalysis.setConditionNames(cMap);
+
+ countsAnalysis.setThreshold( k );
+
+ if (compareConditions) {
+ countsAnalysis.activateComparison();
+ }
+
+ if (!infoFile.isEmpty()) {
+ countsAnalysis.setInfoFilePath(infoFile);
+ }
+
+ LoggerThread loggerThread = new LoggerThread() {
+ public void logLine(String msg) {
+ System.out.println(msg);
+ }
+ };
+ countsAnalysis.setOutputParsingThread(loggerThread);
+
+
+ countsAnalysis.run();
+
+ logger.println("\nPreparing result report");
+ exportResult(resultManager);
+
+ logger.println("Finished");
+ }
+
+
+}
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/main/EpiTool.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/main/EpiTool.java
new file mode 100644
index 0000000..cdf2d47
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/main/EpiTool.java
@@ -0,0 +1,191 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.main;
+
+import org.apache.commons.cli.ParseException;
+import org.bioinfo.ngs.qc.qualimap.beans.AnalysisResultManager;
+import org.bioinfo.ngs.qc.qualimap.common.AnalysisType;
+import org.bioinfo.ngs.qc.qualimap.common.Constants;
+import org.bioinfo.ngs.qc.qualimap.process.EpiAnalysis;
+import org.bioinfo.ngs.qc.qualimap.common.LoggerThread;
+
+import java.io.File;
+
+/**
+ * Created by kokonech
+ * Date: 1/27/12
+ * Time: 12:14 PM
+ */
+public class EpiTool extends NgsSmartTool {
+
+ static final String OPTION_NAME_SAMPLE = "sample";
+ static final String OPTION_NAME_CONTROL = "control";
+ static final String OPTION_NAME_REGIONS = "regions";
+
+ EpiAnalysis.Config cfg;
+
+ static String getVizTypes() {
+ return Constants.VIZ_TYPE_HEATMAP + " or " + Constants.VIZ_TYPE_LINE;
+ }
+
+ public EpiTool() {
+ super(Constants.TOOL_NAME_CLUSTERING, true);
+ cfg = new EpiAnalysis.Config();
+
+ }
+
+ @Override
+ protected void initOptions() {
+
+ options.addOption(requiredOption("sample", true, "Comma-separated list of sample BAM files"));
+ options.addOption(requiredOption("control", true, "Comma-separated list of control BAM files"));
+ options.addOption(requiredOption("regions", true, "Path to regions file"));
+ options.addOption("name", true , "Comma-separated names of the replicates");
+ options.addOption("l", true, "Upstream offset (default is 2000)");
+ options.addOption("r", true, "Downstream offset (default is 500)");
+ options.addOption("b", "bin-size", true, "Size of the bin (default is 100)");
+ options.addOption("expr", true, "Name of the experiment");
+ options.addOption("c", "clusters", true, "Comma-separated list of cluster sizes");
+ options.addOption("f", "fragment-length", true, "Smoothing length of a fragment");
+ options.addOption("viz", true, "Visualization type: " + getVizTypes());
+
+ }
+
+ @Override
+ protected void checkOptions() throws ParseException {
+
+ if (!commandLine.hasOption(OPTION_NAME_OUTDIR)) {
+ throw new ParseException("Output dir is not set.");
+ }
+
+ cfg.pathToRegions = commandLine.getOptionValue(OPTION_NAME_REGIONS);
+ if (! (new File(cfg.pathToRegions)).exists()) {
+ throw new ParseException("Regions file doesn't exists");
+ }
+
+ String[] samples = commandLine.getOptionValue(OPTION_NAME_SAMPLE).split(",");
+
+ for (String sample : samples) {
+ if (! (new File(sample)).exists()) {
+ throw new ParseException("Sample file " + sample + " doesn't exists");
+ }
+ }
+
+ String[] controls = commandLine.getOptionValue(OPTION_NAME_CONTROL).split(",");
+
+ for (String control : controls) {
+ if (! (new File(control)).exists()) {
+ throw new ParseException("Control file " + control + " doesn't exists");
+ }
+ }
+
+ if (controls.length != samples.length) {
+ throw new ParseException("Number of samples doesn't match number of controls");
+ }
+
+ int numReplicates = samples.length;
+
+
+ String names[];
+
+ if (commandLine.hasOption("name")) {
+ names = commandLine.getOptionValue("name").split(",");
+ if (names.length != numReplicates) {
+ throw new ParseException("Number of names doesn't match number of replicates");
+ }
+ } else {
+ names = new String[numReplicates];
+ for (int i = 0; i < numReplicates; ++i ) {
+ names[i] = "Sample " + (i + 1);
+ }
+ }
+
+ for (int i = 0; i < numReplicates; ++i) {
+ EpiAnalysis.ReplicateItem item = new EpiAnalysis.ReplicateItem();
+ item.medipPath = samples[i];
+ item.inputPath = controls[i];
+ item.name = names[i];
+ cfg.replicates.add(item);
+ }
+
+ if (commandLine.hasOption("expr")) {
+ cfg.experimentName = commandLine.getOptionValue("expr");
+ }
+
+ if (commandLine.hasOption("viz")) {
+ cfg.vizType = commandLine.getOptionValue("viz");
+ }
+
+ if (commandLine.hasOption("l")) {
+ cfg.leftOffset = Integer.parseInt(commandLine.getOptionValue("l"));
+ }
+
+ if (commandLine.hasOption("r")) {
+ cfg.rightOffset = Integer.parseInt(commandLine.getOptionValue("r"));
+ }
+
+ if (commandLine.hasOption("b")) {
+ cfg.binSize = Integer.parseInt(commandLine.getOptionValue("b"));
+ }
+
+ if (commandLine.hasOption("fl")) {
+ cfg.fragmentLength = Integer.parseInt(commandLine.getOptionValue("fl"));
+ }
+
+ if (commandLine.hasOption("c")) {
+ cfg.clusters = commandLine.getOptionValue("c").trim();
+ if (cfg.clusters.split(",").length == 0) {
+ throw new ParseException("Clusters are incorrectly formatted.");
+ }
+ }
+
+ }
+
+ @Override
+ protected void execute() throws Exception {
+
+ initOutputDir();
+
+ AnalysisResultManager resultManager = new AnalysisResultManager(AnalysisType.CLUSTERING);
+
+ EpiAnalysis epiAnalysis = new EpiAnalysis(resultManager,homePath,cfg);
+
+ LoggerThread loggerThread = new LoggerThread() {
+ public void logLine(String msg) {
+ System.out.println(msg);
+ }
+ };
+ epiAnalysis.setOutputParsingThread(loggerThread);
+
+ try {
+ epiAnalysis.run();
+ } catch (Exception e) {
+ System.err.println("Failed to run analysis\n" + e.getMessage());
+ e.printStackTrace();
+ System.exit(-1);
+ }
+
+ exportResult(resultManager);
+
+ System.out.println("Finished");
+
+ }
+}
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/main/GCContentTool.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/main/GCContentTool.java
new file mode 100644
index 0000000..5407934
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/main/GCContentTool.java
@@ -0,0 +1,114 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.main;
+
+import net.sf.samtools.SAMFileReader;
+import net.sf.samtools.SAMRecord;
+import net.sf.samtools.SAMRecordIterator;
+import org.apache.commons.cli.ParseException;
+import org.bioinfo.ngs.qc.qualimap.common.Constants;
+
+import java.io.File;
+
+/**
+ * Created by kokonech
+ * Date: 3/1/12
+ * Time: 2:35 PM
+ */
+public class GCContentTool extends NgsSmartTool {
+
+ GCContentTool() {
+ super(Constants.TOOL_NAME_GC_CONTENT, false);
+ }
+
+ @Override
+ protected void initOptions() {
+ options.addOption( requiredOption("i", true, "mapping file (bam format)"));
+ }
+
+ @Override
+ protected void checkOptions() throws ParseException {
+
+ }
+
+ @Override
+ protected void execute() throws Exception {
+
+
+ String pathToBamFile = commandLine.getOptionValue("i");
+
+ SAMFileReader reader = new SAMFileReader(new File(pathToBamFile));
+
+ SAMRecordIterator iter = reader.iterator();
+
+ long numBases = 0;
+ long numGC = 0;
+
+
+ while(iter.hasNext()){
+
+ SAMRecord read = null;
+
+ try {
+ read = iter.next();
+ } catch (RuntimeException e) {
+ logger.warn( e.getMessage() );
+ }
+
+ if (read == null) {
+ continue;
+ }
+
+
+ byte[] readBases = read.getReadBases();
+
+ for (byte base : readBases) {
+ switch (base) {
+ case 'A':
+ numBases++;
+ break;
+ case 'C':
+ numBases++;
+ numGC++;
+ break;
+ case 'G':
+ numBases++;
+ numGC++;
+ break;
+ case 'T':
+ numBases++;
+ break;
+ case 'N':
+ numBases++;
+ break;
+ }
+ }
+
+ }
+
+ double gcContent = (double) numGC / (double) numBases;
+
+ System.out.println("GC content is " + gcContent);
+
+
+
+ }
+}
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/main/IndelCountTool.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/main/IndelCountTool.java
new file mode 100644
index 0000000..92d32eb
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/main/IndelCountTool.java
@@ -0,0 +1,302 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.main;
+
+import net.sf.picard.PicardException;
+import net.sf.picard.reference.IndexedFastaSequenceFile;
+import net.sf.samtools.*;
+import org.apache.commons.cli.ParseException;
+import org.bioinfo.ngs.qc.qualimap.common.Constants;
+
+import java.io.File;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+
+/**
+ * Created by kokonech
+ * Date: 6/26/12
+ * Time: 3:52 PM
+ */
+public class IndelCountTool extends NgsSmartTool{
+
+
+ int numDeletions, numInsertions;
+ byte prevBase;
+ boolean reportState;
+ int homopolymerSize;
+ boolean prevBaseInsideIndelRegion, homopolymerStartsInsideIndelRegion;
+ String curReadName, curCigar;
+ StringBuffer curSequence;
+ char[] extendedCigarVector;
+ int[] homopolymerIndels;
+ private boolean saveHomopolymer;
+ final static int MIN_HOMOPOLYMER_SIZE = 5;
+
+ ArrayList<Region> intersectionRegions;
+
+
+ class Region {
+ int start;
+ int length;
+ }
+
+
+ IndelCountTool() {
+ super(Constants.TOOL_NAME_INDEL_COUNT, false);
+ homopolymerIndels = new int[5];
+ }
+
+ @Override
+ protected void initOptions() {
+ options.addOption(requiredOption("i", true, "Mapping file in BAM format."));
+ options.addOption(requiredOption("r", true, "Reference sequence in FASTA format."));
+ }
+
+ @Override
+ protected void checkOptions() throws ParseException {
+
+ }
+
+ @Override
+ protected void execute() throws Exception {
+
+ // Init BAM file
+ String pathToBamFile = commandLine.getOptionValue("i");
+ SAMFileReader reader = new SAMFileReader(new File(pathToBamFile));
+
+ // Init reference
+ String pathToRef = commandLine.getOptionValue("r");
+ IndexedFastaSequenceFile refIndex = new IndexedFastaSequenceFile(new File(pathToRef));
+
+ int numberOfProblematicReads = 0;
+ int numReads = 0;
+ SAMRecordIterator iter = reader.iterator();
+
+ while (iter.hasNext()) {
+ SAMRecord record = null;
+
+ try {
+ record = iter.next();
+ } catch (RuntimeException e) {
+ numberOfProblematicReads++;
+ }
+
+ if (record == null) {
+ continue;
+ }
+ curReadName = record.getReadName();
+ curSequence = new StringBuffer(record.getReadString());
+ curCigar = record.getCigarString();
+
+ processRecord(record, refIndex);
+
+ if (++numReads % 100000 == 0) {
+ System.err.println("Analyzed " + numReads + " records...");
+ }
+ }
+
+ System.err.println("Analyzed " + numReads + " records");
+ System.err.println("Number of problematic records: " + numberOfProblematicReads);
+
+ System.out.println("polyA indels: " + homopolymerIndels[0]);
+ System.out.println("polyC indels: " + homopolymerIndels[1]);
+ System.out.println("polyG indels: " + homopolymerIndels[2]);
+ System.out.println("polyT indels: " + homopolymerIndels[3]);
+ System.out.println("polyN indels: " + homopolymerIndels[4]);
+ int numHomopolymerIndels = 0;
+ for (int val : homopolymerIndels) {
+ numHomopolymerIndels += val;
+ }
+ int numIndels = numDeletions + numInsertions;
+ System.out.println("All indels: " + numIndels);
+ System.out.println("% homopolymer indels: " + 100.0*( numHomopolymerIndels / (double) numIndels ) );
+
+
+ }
+
+ void processRecord(SAMRecord record, IndexedFastaSequenceFile refIndex) {
+ // precompute total size of alignment
+ int totalSize = 0;
+ List<CigarElement> elementList = record.getCigar().getCigarElements();
+
+ byte[] refBytes = null;
+
+ if (curReadName.equals("IL30_5428:3:21:3146:1335#4")) {
+ System.out.println("DEBUG!");
+ }
+
+ for(CigarElement element : elementList){
+ if (element.getOperator() == CigarOperator.I) {
+ numInsertions++;
+ } else if (element.getOperator() == CigarOperator.D) {
+ numDeletions++;
+ //char[] padding = new char[element.getLength()];
+ //Arrays.fill(padding, '-' );
+ //curSequence.insert( totalSize, padding );
+ try {
+ refBytes = refIndex.getSubsequenceAt(record.getReferenceName(),
+ record.getAlignmentStart(), record.getAlignmentEnd()).getBases();
+ } catch (PicardException e) {
+ System.err.println("Bad request to reference index: (" + record.getReferenceName() +
+ ", " + record.getAlignmentStart() +
+ ", " + record.getAlignmentEnd() + ")" );
+ return;
+ }
+ }
+
+ totalSize += element.getLength();
+
+ }
+
+ // compute extended cigar
+ extendedCigarVector = new char[totalSize];
+ int mpos = 0;
+ int npos;
+ for(CigarElement element : elementList){
+ npos = mpos + element.getLength();
+ Arrays.fill(extendedCigarVector, mpos, npos, element.getOperator().name().charAt(0));
+ mpos = npos;
+ }
+
+ // init extended cigar portion
+ // char[] extendedCigarVector = extended; // Arrays.copyOfRange(extended,0,mpos);
+
+ int readPos = 0;
+ int alignmentPos = 0;
+ byte[] readBases = record.getReadBases();
+
+ resetCounters();
+
+ for ( int i = 0; i < extendedCigarVector.length; ++i ) {
+ char cigarChar = extendedCigarVector[i];
+ // M
+ if (cigarChar == 'M') {
+ byte base = readBases[readPos];
+ readPos++;
+ alignmentPos++;
+ collectBase(base, false);
+ }
+ // I
+ else if (cigarChar == 'I') {
+ byte base = readBases[readPos];
+ collectBase(base, true);
+ readPos++;
+ }
+ // D
+ else if (cigarChar == 'D') {
+ byte base = refBytes[alignmentPos];
+ //curSequence.insert(i, (char) base);
+ collectBase(base, true);
+ alignmentPos++;
+
+ }
+ // N
+ else if (cigarChar == 'N') {
+ alignmentPos++;
+ }
+ // S
+ else if (cigarChar == 'S') {
+ readPos++;
+ }
+ // H
+ else if (cigarChar == 'H') {
+
+ }
+ // P
+ else if (cigarChar == 'P') {
+ alignmentPos++;
+ }
+ }
+
+ debugOutput();
+ }
+
+ void resetCounters() {
+ prevBase = 'X';
+ homopolymerSize = 0;
+ saveHomopolymer = false;
+ }
+
+ void collectBase(byte base, boolean insideIndelRegion) {
+ if (base == prevBase) {
+ homopolymerSize ++;
+ } else {
+ if ( prevBaseInsideIndelRegion || homopolymerStartsInsideIndelRegion ) {
+ saveHomopolymerData();
+ }
+ homopolymerSize = 1;
+ homopolymerStartsInsideIndelRegion = insideIndelRegion;
+ }
+
+ /*if (!insideIndelRegion && homopolymerSize == 1) {
+ saveHomopolymer = false;
+ }*/
+
+ prevBase = base;
+ prevBaseInsideIndelRegion = insideIndelRegion;
+ }
+
+
+ static String charArrayToString(char[] array) {
+ String res = "";
+ for (char c : array) {
+ res += c;
+ }
+ return res;
+
+ }
+
+ private void saveHomopolymerData() {
+
+ if (homopolymerSize >= MIN_HOMOPOLYMER_SIZE) {
+ if (prevBase == 'A') {
+ homopolymerIndels[0]++;
+
+ } else if (prevBase == 'C') {
+ //reportState = true;
+ homopolymerIndels[1]++;
+ } else if (prevBase == 'G') {
+ homopolymerIndels[2]++;
+ } else if (prevBase == 'T') {
+ homopolymerIndels[3]++;
+ } else if (prevBase == 'N') {
+ homopolymerIndels[4]++;
+ }
+ saveHomopolymer = false;
+ }
+
+ }
+
+
+ private void debugOutput() {
+ if (reportState) {
+ System.out.println("Homopolymer indel in " + curReadName + ", " + " sequence is \n"
+ + curSequence + "\n" +
+ charArrayToString(extendedCigarVector) + "\n"
+ + curCigar + "\n");
+ reportState = false;
+ }
+ }
+
+
+
+}
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/main/MultisampleBamQcTool.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/main/MultisampleBamQcTool.java
new file mode 100644
index 0000000..0798aaf
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/main/MultisampleBamQcTool.java
@@ -0,0 +1,164 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.main;
+
+import org.apache.commons.cli.ParseException;
+import org.bioinfo.ngs.qc.qualimap.beans.AnalysisResultManager;
+import org.bioinfo.ngs.qc.qualimap.common.AnalysisType;
+import org.bioinfo.ngs.qc.qualimap.common.Constants;
+import org.bioinfo.ngs.qc.qualimap.common.LoggerThread;
+import org.bioinfo.ngs.qc.qualimap.process.BamStatsAnalysisConfig;
+import org.bioinfo.ngs.qc.qualimap.process.MultisampleBamQcAnalysis;
+import org.bioinfo.ngs.qc.qualimap.process.SampleInfo;
+
+import java.io.File;
+import java.util.List;
+
+/**
+ * Created by kokonech
+ * Date: 6/5/14
+ * Time: 12:48 PM
+ */
+public class MultisampleBamQcTool extends NgsSmartTool{
+
+
+ String inputFile;
+ boolean runBamQCFirst;
+ BamStatsAnalysisConfig bamQcCfg;
+
+ public MultisampleBamQcTool() {
+ super(Constants.TOOL_NAME_MULTISAMPLE_BAM_QC, false);
+ }
+
+ @Override
+ protected void initOptions() {
+ options.addOption(requiredOption("d", "data", true,
+ "File describing the input data. Format of the file is a 2-column tab-delimited table." +
+ "\nColumn 1: sample name \nColumn 2: either path to the BAM QC result or path to BAM file (-r mode)"));
+
+ options.addOption("r", "run-bamqc", false, "Raw BAM files are provided as input. If this option is activated" +
+ " BAM QC process first will be run for each sample, then multi-sample " +
+ "analysis will be performed.");
+
+ // BAM QC options
+
+ options.addOption(Constants.BAMQC_OPTION_GFF_FILE, "feature-file", true,
+ "Only for -r mode. Feature file with regions of interest in GFF/GTF or BED format");
+ options.addOption(Constants.BAMQC_OPTION_NUM_WINDOWS, true,
+ "Only for -r mode. Number of windows (default is "+ Constants.DEFAULT_NUMBER_OF_WINDOWS + ")");
+ options.addOption(Constants.BAMQC_OPTION_CHUNK_SIZE, true,
+ "Only for -r mode. Number of reads analyzed in a chunk (default is " + Constants.DEFAULT_CHUNK_SIZE + ")" );
+ options.addOption(Constants.BAMQC_OPTION_MIN_HOMOPOLYMER_SIZE, true,
+ "Only for -r mode. Minimum size for a homopolymer to be considered in indel analysis (default is "
+ + Constants.DEFAULT_HOMOPOLYMER_SIZE + ") " );
+ options.addOption(Constants.BAMQC_OPTION_PAINT_CHROMOSOMES, "paint-chromosome-limits", false,
+ "Only for -r mode. Paint chromosome limits inside charts");
+
+
+
+ }
+
+ @Override
+ protected void checkOptions() throws ParseException {
+ inputFile = commandLine.getOptionValue("d");
+ if(!exists(inputFile)) {
+ throw new ParseException("input data description file (--data) " + inputFile + " is not found");
+ }
+
+ runBamQCFirst = commandLine.hasOption("r");
+ if (runBamQCFirst) {
+ bamQcCfg = new BamStatsAnalysisConfig();
+
+ if(commandLine.hasOption(Constants.BAMQC_OPTION_GFF_FILE)) {
+ bamQcCfg.gffFile = commandLine.getOptionValue(Constants.BAMQC_OPTION_GFF_FILE);
+ if(!exists(bamQcCfg.gffFile)) {
+ throw new ParseException("input region gff file not found");
+ }
+ }
+
+
+ bamQcCfg.numberOfWindows = commandLine.hasOption(Constants.BAMQC_OPTION_NUM_WINDOWS) ?
+ Integer.parseInt(commandLine.getOptionValue(Constants.BAMQC_OPTION_NUM_WINDOWS))
+ : Constants.DEFAULT_NUMBER_OF_WINDOWS;
+
+ bamQcCfg.bunchSize = commandLine.hasOption(Constants.BAMQC_OPTION_CHUNK_SIZE) ?
+ Integer.parseInt(commandLine.getOptionValue(Constants.BAMQC_OPTION_CHUNK_SIZE)) :
+ Constants.DEFAULT_CHUNK_SIZE;
+
+
+ bamQcCfg.minHomopolymerSize = commandLine.hasOption(Constants.BAMQC_OPTION_MIN_HOMOPOLYMER_SIZE) ?
+ Integer.parseInt(commandLine.getOptionValue(Constants.BAMQC_OPTION_MIN_HOMOPOLYMER_SIZE)) :
+ Constants.DEFAULT_HOMOPOLYMER_SIZE;
+
+ bamQcCfg.drawChromosomeLimits = commandLine.hasOption(Constants.BAMQC_OPTION_PAINT_CHROMOSOMES);
+
+ }
+ }
+
+ @Override
+ protected void initOutputDir() {
+ if (outdir.equals(".")) {
+ String parentDir = new File(inputFile).getParent();
+ if (parentDir == null) {
+ parentDir = ".";
+ }
+ outdir = parentDir + File.separator + "multi_bamqc";
+ }
+ super.initOutputDir();
+ }
+
+
+ @Override
+ protected void execute() throws Exception {
+
+ initOutputDir();
+
+ AnalysisResultManager resultManager = new AnalysisResultManager(AnalysisType.MULTISAMPLE_BAM_QC);
+
+ List<SampleInfo> bamQcResults = MultisampleBamQcAnalysis.parseInputFile(inputFile);
+ if (bamQcResults.size() == 0) {
+ System.err.println("The input file " + inputFile + " does not contain any samples. " +
+ "Please check file format.");
+ System.exit(-1);
+ }
+
+ MultisampleBamQcAnalysis multiBamQCAnalysis =
+ new MultisampleBamQcAnalysis(resultManager, homePath, bamQcResults);
+ if (runBamQCFirst) {
+ multiBamQCAnalysis.setRunBamQcFirst(bamQcCfg);
+ }
+
+ LoggerThread loggerThread = new LoggerThread() {
+ public void logLine(String msg) {
+ System.out.println(msg);
+ }
+ };
+
+ multiBamQCAnalysis.setOutputParsingThread(loggerThread);
+
+ multiBamQCAnalysis.run();
+
+ logger.println("\nPreparing result report");
+ exportResult(resultManager);
+
+ logger.println("Finished");
+ }
+}
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/main/NgsSmartMain.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/main/NgsSmartMain.java
new file mode 100644
index 0000000..b50e991
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/main/NgsSmartMain.java
@@ -0,0 +1,195 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.main;
+
+import java.io.IOException;
+import java.io.InputStream;
+import java.util.Properties;
+
+import org.apache.commons.cli.ParseException;
+import org.bioinfo.commons.io.utils.IOUtils;
+import org.bioinfo.commons.log.Logger;
+import org.bioinfo.ngs.qc.qualimap.common.AppSettings;
+import org.bioinfo.ngs.qc.qualimap.common.Constants;
+import org.bioinfo.ngs.qc.qualimap.gui.frames.HomeFrame;
+
+public class NgsSmartMain {
+
+
+ public static String APP_VERSION = "debug";
+ public static String APP_BUILT_DATE = "unknown";
+ public static final String OUT_OF_MEMORY_REPORT = "\nWARNING: out of memory!\n" +
+ "Qualimap allows to set RAM size using special argument: --java-mem-size\n" +
+ "Check more details using --help command or read the manual.";
+
+
+ public static void main(String[] args) throws OutOfMemoryError,Exception {
+ Logger logger = new Logger();
+ NgsSmartTool tool = null;
+
+ loadAppPropertiesFile();
+ loadAppSettings();
+
+ if(args.length == 0 || args[0].equals("--home")){
+ try {
+ launchGUI(args);
+ } catch (Exception e) {
+ System.err.println("Failed to launch GUI.");
+ e.printStackTrace();
+ }
+ } else {
+
+ String toolName = args[0];
+
+ // TODO: use factories map to create tools
+
+ if(toolName.equalsIgnoreCase(Constants.TOOL_NAME_BAMQC)){
+ tool = new BamQcTool();
+ }
+
+ if(toolName.equalsIgnoreCase(Constants.TOOL_NAME_RNASEQ_QC)){
+ tool = new RnaSeqQcTool();
+ }
+
+ if(toolName.equalsIgnoreCase(Constants.TOOL_NAME_COUNTS_QC)){
+ tool = new CountsQcTool();
+ }
+
+ if (toolName.equals(Constants.TOOL_NAME_COMPUTE_COUNTS)) {
+ tool = new ComputeCountsTool();
+ }
+
+ if (toolName.equals(Constants.TOOL_NAME_CLUSTERING)) {
+ tool = new EpiTool();
+ }
+
+ if (toolName.equals(Constants.TOOL_NAME_GC_CONTENT)) {
+ tool = new GCContentTool();
+ }
+
+ if (toolName.equals(Constants.TOOL_NAME_INDEL_COUNT)) {
+ tool = new IndelCountTool();
+ }
+
+ if (toolName.equals(Constants.TOOL_NAME_MULTISAMPLE_BAM_QC)) {
+ tool = new MultisampleBamQcTool();
+ }
+
+ if (toolName.equalsIgnoreCase("run-tests")) {
+ System.out.println("Supposed to run tests... Needs testing");
+ //runTests();
+ } else if(toolName.equalsIgnoreCase("-h") || toolName.equalsIgnoreCase("-help")
+ || toolName.equalsIgnoreCase("--h") || toolName.equalsIgnoreCase("--help")){
+ logger.println("");
+ logger.println(getHelp());
+ } else {
+ logger.println("");
+ logger.println("Selected tool: " + toolName);
+ if(tool==null){
+ logger.println("No proper tool name is provided.\n");
+ logger.println(getHelp());
+ } else {
+ try {
+ tool.run(args);
+ } catch(ParseException pe){
+ logger.println("");
+ logger.println("ERROR: " + pe.getMessage());
+ logger.println("");
+ tool.printHelp();
+ } catch (OutOfMemoryError memErr) {
+ System.err.println(OUT_OF_MEMORY_REPORT);
+ }catch(Exception e){
+ e.printStackTrace();
+ }
+ }
+ }
+ }
+ }
+
+ private static void loadAppSettings() {
+ AppSettings appSettings = new AppSettings();
+ AppSettings.setGlobalSettings(appSettings);
+ }
+
+ private static void loadAppPropertiesFile() {
+ InputStream inStream = ClassLoader.getSystemClassLoader().getResourceAsStream("app.properties");
+ if (inStream == null) {
+ return;
+ }
+
+ Properties appProperties = new Properties();
+ try {
+ appProperties.load(inStream);
+ } catch (IOException e) {
+ System.err.println("Failed to load app propreties");
+ return;
+ }
+
+ String version = appProperties.get("app.version").toString();
+ String timestamp = appProperties.get("app.buildTime").toString();
+
+ if (version != null) {
+ System.out.println("QualiMap v." + appProperties.get("app.version").toString());
+ APP_VERSION = "v." + version;
+ }
+
+ if (timestamp != null) {
+ System.out.println("Built on " + appProperties.get("app.buildTime").toString());
+ APP_BUILT_DATE = timestamp;
+ }
+ }
+
+ public static void launchGUI(String[] args) throws ParseException{
+
+
+ String qualimapHomeDir = System.getenv("QUALIMAP_HOME");
+ if ( args.length > 1 && args[0].equals("--home")) {
+ qualimapHomeDir = args[1];
+ }
+
+ // launching GUI
+ System.setProperty("java.awt.headless", "false");
+ HomeFrame inst = new HomeFrame(qualimapHomeDir);
+
+ inst.setLocationRelativeTo(null);
+ inst.setVisible(true);
+
+ }
+
+ public static String getHelp() {
+ InputStream resource = ClassLoader.getSystemResourceAsStream("org/bioinfo/ngs/qc/qualimap/help/main-help.txt");
+ String helpMessage = "";
+ try {
+ helpMessage = IOUtils.toString(resource)+"\n";
+ } catch (IOException e) {
+ System.err.println("Failed to load help report.");
+ }
+
+ return helpMessage;
+ }
+
+ public static void error(Logger logger, String message) throws IOException{
+ logger.println("");
+ logger.println(message);
+ logger.println("");
+ logger.println(getHelp());
+ }
+}
\ No newline at end of file
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/main/NgsSmartTool.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/main/NgsSmartTool.java
new file mode 100644
index 0000000..f053251
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/main/NgsSmartTool.java
@@ -0,0 +1,294 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.main;
+
+import java.io.*;
+
+import org.apache.commons.cli.*;
+import org.apache.commons.io.FileUtils;
+import org.bioinfo.commons.log.Logger;
+import org.bioinfo.ngs.qc.qualimap.beans.AnalysisResultManager;
+import org.bioinfo.ngs.qc.qualimap.common.AppSettings;
+import org.bioinfo.ngs.qc.qualimap.common.Constants;
+import org.bioinfo.ngs.qc.qualimap.common.LibraryProtocol;
+import org.bioinfo.ngs.qc.qualimap.gui.threads.ExportHtmlThread;
+import org.bioinfo.ngs.qc.qualimap.gui.threads.ExportPdfThread;
+
+public abstract class NgsSmartTool {
+
+ // log
+ protected Logger logger;
+
+ // environment
+ protected String homePath;
+
+ // arguments
+ protected Options options;
+ protected CommandLine commandLine;
+ protected CommandLineParser parser;
+
+ // common params
+ protected String outdir;
+ protected String reportFileName;
+ protected String toolName;
+ protected String outputType;
+ protected boolean outDirIsRequired,outFormatIsRequired, rIsRequired, createdOutDir;
+
+ static String OPTION_NAME_OUTDIR = "outdir";
+ static String OPTION_NAME_OUTFILE = "outfile";
+ static String OPTION_NAME_OUTPUT_TYPE = "outformat";
+ static String OPTION_NAME_PATH_TO_RSCRIPT = "R";
+
+ public NgsSmartTool(String toolName, boolean rIsRequired){
+
+ this.toolName = toolName;
+ this.outDirIsRequired = true;
+ this.outFormatIsRequired = true;
+ this.createdOutDir = false;
+ this.rIsRequired = rIsRequired;
+ init();
+ }
+
+ public NgsSmartTool(String toolName, boolean outDirIsRequired, boolean outFormatIsRequired, boolean rIsRequired){
+
+ this.toolName = toolName;
+ this.outDirIsRequired = outDirIsRequired;
+ this.outFormatIsRequired = outFormatIsRequired;
+ this.rIsRequired = rIsRequired;
+ init();
+ }
+
+
+
+ public void init() {
+
+ // log
+ logger = new Logger();
+
+ // environment
+ homePath = System.getenv("QUALIMAP_HOME");
+ if (homePath == null) {
+ homePath = new File("").getAbsolutePath() + File.separator;
+ }
+ if(homePath.endsWith(File.separator)){
+ homePath = homePath.substring(0,homePath.length()-1);
+ }
+
+ // arguments
+ options = new Options();
+ parser = new PosixParser();
+ outdir = ".";
+ reportFileName = "";
+ outputType = Constants.REPORT_TYPE_HTML;
+
+ initCommonOptions();
+
+ initOptions();
+
+ }
+
+ private void initCommonOptions(){
+
+ if (outDirIsRequired) {
+ options.addOption( OPTION_NAME_OUTDIR, true, "Output folder for HTML report and raw data." );
+ options.addOption( OPTION_NAME_OUTFILE, true, "Output file for PDF report (default value is report.pdf).");
+ }
+ if (outFormatIsRequired) {
+ options.addOption( OPTION_NAME_OUTPUT_TYPE, true,
+ "Format of the ouput report (PDF or HTML, default is HTML).");
+ }
+
+ if (rIsRequired) {
+ options.addOption( OPTION_NAME_PATH_TO_RSCRIPT, "rscriptpath", true,
+ "Path to Rscript executable (by default it is assumed " +
+ "to be available from system $PATH)" );
+ }
+ }
+
+ // init options
+ protected abstract void initOptions();
+
+ // parse options
+ protected void parse(String[] args) throws ParseException{
+ // get command line
+ commandLine = parser.parse(options, args);
+
+ // fill common options
+ if(commandLine.hasOption(OPTION_NAME_OUTDIR)){
+ outdir = commandLine.getOptionValue(OPTION_NAME_OUTDIR);
+ }
+
+ if (commandLine.hasOption(OPTION_NAME_OUTFILE)) {
+ reportFileName = commandLine.getOptionValue(OPTION_NAME_OUTFILE);
+ outputType = Constants.REPORT_TYPE_PDF;
+ if (!reportFileName.endsWith(".pdf")) {
+ reportFileName += ".pdf";
+ }
+ }
+
+
+ if (commandLine.hasOption(OPTION_NAME_OUTPUT_TYPE)) {
+ outputType = commandLine.getOptionValue(OPTION_NAME_OUTPUT_TYPE).toUpperCase();
+ if (!outputType.equals(Constants.REPORT_TYPE_HTML) && !outputType.equals(Constants.REPORT_TYPE_PDF)) {
+ throw new ParseException("Unknown output report format " + outputType);
+ }
+
+ }
+
+ if (commandLine.hasOption(OPTION_NAME_PATH_TO_RSCRIPT)) {
+ String pathToRScript = commandLine.getOptionValue(OPTION_NAME_PATH_TO_RSCRIPT);
+ if (! (new File(pathToRScript).canExecute()) ) {
+ throw new ParseException("Wrong path to RScript command: " + pathToRScript);
+ }
+ AppSettings.getGlobalSettings().setPathToRScript(pathToRScript);
+ }
+
+
+
+
+
+ }
+
+ // check options
+ protected abstract void checkOptions() throws ParseException;
+
+ // execute tool
+ protected abstract void execute() throws Exception;
+
+
+ // public run (parse and execute)
+ public void run(String[] args) throws Exception{
+ // parse
+ parse(args);
+
+ // check options
+ checkOptions();
+
+ // execute
+ try {
+ execute();
+ } catch (Exception e) {
+
+
+ System.err.println("Failed to run " + toolName);
+
+ StringWriter errorsWriter = new StringWriter();
+ e.printStackTrace(new PrintWriter(errorsWriter));
+ String errorReport = errorsWriter.toString();
+
+ if (errorReport.contains("java.lang.OutOfMemoryError") ) {
+ System.err.println(NgsSmartMain.OUT_OF_MEMORY_REPORT);
+ } else {
+ System.err.println(errorReport);
+ }
+ cleanupOutputDir();
+ System.exit(-1);
+ }
+ }
+
+ protected void printHelp(){
+ HelpFormatter h = new HelpFormatter();
+ h.setWidth(80);
+ h.printHelp("qualimap " + toolName, options, true);
+ logger.println("");
+ logger.println("");
+ logger.println("");
+ }
+
+ protected void initOutputDir(){
+
+ if(!outdir.isEmpty()){
+ if(new File(outdir).exists()){
+ logger.warn("Output folder already exists, the results will be saved there\n");
+ } else {
+ boolean ok = new File(outdir).mkdirs();
+ if (ok) {
+ createdOutDir = true;
+ } else {
+ logger.error("Failed to create output directory.");
+ }
+ }
+ }
+ }
+
+ protected void cleanupOutputDir() {
+
+ if (createdOutDir) {
+
+ File outDirFile = new File(outdir);
+ if (outDirFile.exists()) {
+ logger.warn("Cleanup output dir");
+ try {
+ FileUtils.deleteDirectory(outDirFile);
+ } catch (IOException e) {
+ logger.error("Failed to delete output dir");
+ }
+ }
+
+ }
+
+ }
+
+ protected static Option requiredOption(String shortName, String longName, boolean hasArgument, String shortDescription ) {
+ Option option = new Option(shortName, longName, hasArgument, shortDescription);
+ option.setRequired(true);
+ return option;
+ }
+
+
+ protected static Option requiredOption(String shortName, boolean hasArgument, String shortDescription ) {
+ Option option = new Option(shortName, null, hasArgument, shortDescription);
+ option.setRequired(true);
+ return option;
+ }
+
+
+ protected static Option getProtocolOption() {
+ return new Option(Constants.CMDLINE_OPTION_LIBRARY_PROTOCOL, "sequencing-protocol", true,
+ "Sequencing library protocol: " + LibraryProtocol.getProtocolNamesString() + " (default)" );
+ }
+
+
+ protected boolean exists(String fileName){
+ return new File(fileName).exists();
+ }
+
+ protected void exportResult(AnalysisResultManager resultManager) {
+
+ // check output options
+ if (outputType.equals(Constants.REPORT_TYPE_PDF)) {
+
+ if (reportFileName.isEmpty()) {
+ reportFileName = "report.pdf";
+ }
+
+ reportFileName = outdir + File.separator + reportFileName;
+
+ }
+
+ Thread exportReportThread = outputType.equals( Constants.REPORT_TYPE_PDF ) ?
+ new ExportPdfThread(resultManager, reportFileName ) :
+ new ExportHtmlThread(resultManager, outdir);
+
+ exportReportThread.run();
+ }
+
+}
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/main/RnaSeqQcTool.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/main/RnaSeqQcTool.java
new file mode 100644
index 0000000..ed12d6d
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/main/RnaSeqQcTool.java
@@ -0,0 +1,194 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.main;
+
+import org.apache.commons.cli.Option;
+import org.apache.commons.cli.ParseException;
+import org.apache.commons.io.FilenameUtils;
+import org.bioinfo.ngs.qc.qualimap.beans.AnalysisResultManager;
+import org.bioinfo.ngs.qc.qualimap.common.AnalysisType;
+import org.bioinfo.ngs.qc.qualimap.common.Constants;
+import org.bioinfo.ngs.qc.qualimap.common.LibraryProtocol;
+import org.bioinfo.ngs.qc.qualimap.process.ComputeCountsTask;
+import org.bioinfo.ngs.qc.qualimap.process.RNASeqQCAnalysis;
+import java.io.File;
+
+/**
+ * Created by kokonech
+ * Date: 7/14/13
+ * Time: 4:15 PM
+ */
+
+public class RnaSeqQcTool extends NgsSmartTool {
+
+ public static String OPTION_ANNOTATION = "gtf";
+ public static String OPTION_BAM = "bam";
+ public static String OPTION_COUNTS_FILE = "oc";
+ public static String OPTION_ALGORITHM = "a";
+ public static String OPTION_PAIRED = "pe";
+ public static String OPTION_ALREADY_SORTED = "s";
+
+ String bamFile, gffFile, countsFilePath, protocol,alg;
+ boolean pairedAnalysis, sortingRequired;
+
+ public RnaSeqQcTool() {
+ super(Constants.TOOL_NAME_RNASEQ_QC, false);
+ pairedAnalysis = false;
+ sortingRequired = false;
+ }
+
+ @Override
+ protected void initOptions() {
+ options.addOption( requiredOption(OPTION_BAM, true, "Input mapping file in BAM format.") );
+ options.addOption(requiredOption(OPTION_ANNOTATION, true, "Annotations file in Ensembl GTF format.") );
+ options.addOption(new Option(OPTION_COUNTS_FILE, true, "Output file for computed counts. " +
+ "If only name of the file is provided, then the file will be saved in the output folder.") );
+ options.addOption( getProtocolOption() );
+ options.addOption(new Option(OPTION_ALGORITHM, "algorithm", true, "Counting algorithm: " +
+ ComputeCountsTask.getAlgorithmTypes() + ".") );
+
+ options.addOption(new Option(OPTION_PAIRED, "paired", false, "Setting this flag for paired-end experiments will result " +
+ "in counting fragments instead of reads") );
+ options.addOption(new Option(OPTION_ALREADY_SORTED, "sorted", false,
+ "This flag indicates that the input file is already sorted by name. " +
+ "If not set, additional sorting by name will be performed. " +
+ "Only required for paired-end analysis. " ) );
+
+
+ }
+
+ @Override
+ protected void checkOptions() throws ParseException {
+
+ bamFile = commandLine.getOptionValue(OPTION_BAM);
+ if (!exists(bamFile))
+ throw new ParseException("input mapping file not found");
+
+ gffFile = commandLine.getOptionValue(OPTION_ANNOTATION);
+ if(!exists(gffFile))
+ throw new ParseException("input region gtf file not found");
+
+ if(commandLine.hasOption(Constants.CMDLINE_OPTION_LIBRARY_PROTOCOL)) {
+ protocol = commandLine.getOptionValue(Constants.CMDLINE_OPTION_LIBRARY_PROTOCOL);
+ if ( !(protocol.equals( LibraryProtocol.PROTOCOL_FORWARD_STRAND ) ||
+ protocol.equals( LibraryProtocol.PROTOCOL_REVERSE_STRAND ) ||
+ protocol.equals( LibraryProtocol.PROTOCOL_NON_STRAND_SPECIFIC)) ) {
+ throw new ParseException("wrong protocol type! supported types: " +
+ LibraryProtocol.getProtocolNamesString());
+ }
+ } else {
+ protocol = LibraryProtocol.PROTOCOL_NON_STRAND_SPECIFIC;
+ }
+
+ if (commandLine.hasOption(OPTION_PAIRED)) {
+ pairedAnalysis = true;
+ if (!commandLine.hasOption(OPTION_ALREADY_SORTED)) {
+ sortingRequired = true;
+ }
+ }
+
+
+
+ if (commandLine.hasOption(OPTION_COUNTS_FILE)) {
+ countsFilePath = commandLine.getOptionValue(OPTION_COUNTS_FILE);
+ } else {
+ countsFilePath = "";
+ }
+
+
+ if (commandLine.hasOption(OPTION_ALGORITHM)) {
+ alg = commandLine.getOptionValue(OPTION_ALGORITHM);
+ if (! ( alg.equalsIgnoreCase(ComputeCountsTask.COUNTING_ALGORITHM_ONLY_UNIQUELY_MAPPED) ||
+ alg.equalsIgnoreCase(ComputeCountsTask.COUNTING_ALGORITHM_PROPORTIONAL)) ) {
+ throw new ParseException("Unknown algorithm! Possible values are: "
+ + ComputeCountsTask.getAlgorithmTypes());
+ }
+ } else {
+ alg = ComputeCountsTask.COUNTING_ALGORITHM_ONLY_UNIQUELY_MAPPED;
+ }
+
+
+ }
+
+ @Override
+ protected void initOutputDir() {
+ if (outdir.equals(".")) {
+ outdir = FilenameUtils.removeExtension(new File(bamFile).getAbsolutePath()) + "_rnaseq_qc";
+ }
+ super.initOutputDir();
+ }
+
+
+ @Override
+ protected void execute() throws Exception {
+
+
+
+ initOutputDir();
+
+ ComputeCountsTask computeCountsTask = new ComputeCountsTask(bamFile, gffFile);
+ computeCountsTask.setProtocol(LibraryProtocol.getProtocolByName(protocol));
+ computeCountsTask.setCountingAlgorithm(alg);
+ computeCountsTask.setCollectRnaSeqStats(true);
+
+ if (pairedAnalysis) {
+ computeCountsTask.setPairedEndAnalysis();
+ if (sortingRequired) {
+ computeCountsTask.setSortingRequired();
+ }
+ }
+
+ AnalysisResultManager resultManager = new AnalysisResultManager(AnalysisType.RNA_SEQ_QC);
+
+ RNASeqQCAnalysis rnaSeqQCAnalysis = new RNASeqQCAnalysis(resultManager, computeCountsTask);
+ rnaSeqQCAnalysis.setReportFilePath(outdir + "/rnaseq_qc_results.txt");
+
+ if (!countsFilePath.isEmpty()) {
+
+ File outFile = new File(countsFilePath);
+ if (outFile.isDirectory()) {
+ System.err.println("\nERROR! The given output path "+ countsFilePath + " is just a folder. " +
+ "\nPlease, add file name.");
+ return;
+ } else {
+ File parentDir = outFile.getParentFile();
+ if (parentDir == null) {
+ logger.warn("the directory used to write counts will be the output dir\n");
+ countsFilePath = outdir + "/" + countsFilePath;
+ } else if (!parentDir.exists()) {
+ System.err.println("\nERROR! The given output path " + countsFilePath + " is not correct." +
+ "\nPlease, check the names of folders in the path.");
+ return;
+ }
+ }
+ }
+
+ if (countsFilePath.length() > 0) {
+ rnaSeqQCAnalysis.setCountsFilePath(countsFilePath);
+ }
+
+ rnaSeqQCAnalysis.run();
+
+ exportResult(resultManager);
+
+
+ }
+}
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/process/AnalysisProcess.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/process/AnalysisProcess.java
new file mode 100644
index 0000000..80c62e8
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/process/AnalysisProcess.java
@@ -0,0 +1,53 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.process;
+
+import org.bioinfo.ngs.qc.qualimap.beans.AnalysisResultManager;
+import org.bioinfo.ngs.qc.qualimap.common.LoggerThread;
+
+/**
+ * Created by kokonech
+ * Date: 5/15/14
+ * Time: 5:49 PM
+ */
+
+public abstract class AnalysisProcess {
+
+ protected AnalysisResultManager tabProperties;
+ protected LoggerThread loggerThread;
+ protected String homePath;
+
+ public AnalysisProcess(AnalysisResultManager tabProperties, String homePath) {
+ this.tabProperties = tabProperties;
+ this.homePath = homePath;
+ this.loggerThread = null;
+ }
+
+ public abstract void run() throws Exception;
+
+ void logLine(String line) {
+ if (loggerThread != null) {
+ loggerThread.logLine(line);
+ }
+ }
+
+
+}
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/process/BamStatsAnalysis.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/process/BamStatsAnalysis.java
new file mode 100644
index 0000000..f6a1ccb
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/process/BamStatsAnalysis.java
@@ -0,0 +1,1219 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.process;
+
+import net.sf.samtools.*;
+import net.sf.samtools.util.RuntimeIOException;
+import org.bioinfo.commons.log.Logger;
+import org.bioinfo.formats.core.sequence.Fasta;
+import org.bioinfo.formats.core.sequence.io.FastaReader;
+import org.bioinfo.formats.exception.FileFormatException;
+import org.bioinfo.ngs.qc.qualimap.beans.*;
+import org.bioinfo.ngs.qc.qualimap.beans.BamDetailedGenomeWindow;
+import org.bioinfo.ngs.qc.qualimap.beans.BamGenomeWindow;
+import org.bioinfo.ngs.qc.qualimap.beans.BamStats;
+import org.bioinfo.ngs.qc.qualimap.beans.ContigRecord;
+import org.bioinfo.ngs.qc.qualimap.beans.GenomeLocator;
+import org.bioinfo.ngs.qc.qualimap.common.Constants;
+import org.bioinfo.ngs.qc.qualimap.common.LibraryProtocol;
+import org.bioinfo.ngs.qc.qualimap.common.*;
+import org.bioinfo.ngs.qc.qualimap.common.CommandLineBuilder;
+import org.bioinfo.ngs.qc.qualimap.gui.utils.StatsKeeper;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.*;
+import java.util.concurrent.*;
+
+/**
+ * Created by kokonech
+ * Date: 11/7/11
+ * Time: 4:06 PM
+ */
+public class BamStatsAnalysis {
+
+ // input alignment
+ private String bamFile;
+
+ // reference
+ private String referenceFile;
+ private boolean referenceAvailable;
+ private byte[] reference;
+ private long referenceSize;
+ private int numberOfReferenceContigs;
+
+ // currentWindow management
+ private int numberOfWindows;
+ private int effectiveNumberOfWindows;
+ private int windowSize;
+
+ // coordinates transformer
+ private GenomeLocator locator;
+
+ // globals
+ private long numberOfReads;
+ private long numberOfValidReads;
+ private long numberOfDuplicatedReads;
+ private long numberOfCorrectStrandReads;
+ private long numberOfProblematicReads;
+ private long numberOfReadsWithStartGreatThenEnd;
+
+ // statistics
+ private BamStats bamStats;
+
+ private Logger logger;
+ private LoggerThread loggerThread;
+
+ // working variables
+ private BamGenomeWindow currentWindow;
+ private ConcurrentMap<Long,BamGenomeWindow> openWindows;
+ private int threadNumber;
+ private int numReadsInBunch;
+ private int progress;
+ private int minHomopolymerSize;
+
+ // nucleotide reporting
+ private String outdir;
+
+ // gff support
+ private boolean selectedRegionsAvailable;
+ private String featureFile;
+ private int numberOfSelectedRegions;
+
+ // inside
+ private long insideReferenceSize;
+ private boolean skipDuplicatedReads;
+ private boolean collectIntersectingPairedEndReads;
+
+ // outside
+ private boolean computeOutsideStats;
+ private BamGenomeWindow currentOutsideWindow;
+ private HashMap<Long,BamGenomeWindow> openOutsideWindows;
+ private BamStats outsideBamStats;
+
+ // read size
+ long acumReadSize;
+ int maxReadSize;
+ int minReadSize;
+
+ //regions
+ private long[] selectedRegionStarts;
+ private long[] selectedRegionEnds;
+ RegionOverlapLookupTable regionOverlapLookupTable;
+ LibraryProtocol protocol;
+
+ BamStatsCollector bamStatsCollector;
+ BamStatsCollector outsideBamStatsCollector;
+
+ // chromosome
+ private ArrayList<Integer> chromosomeWindowIndexes;
+
+ private int maxSizeOfTaskQueue;
+
+ // reporting
+ private boolean activeReporting;
+ private boolean saveCoverage, nonZeroCoverageOnly;
+ private String pathToCoverageReport;
+
+ // analysis
+ private boolean isPairedData;
+ List<Future<ProcessBunchOfReadsTask.Result>> results;
+ Future<Integer> finalizeWindowResult;
+ long timeToCalcOverlappers;
+ private String pgProgram, pgCommandString;
+
+ public static final String WARNING_ID_CHROMOSOME_NOT_FOUND = "Some regions are not loaded";
+ public static final String WARNING_ID_NO_MAPPED_READS = "NO MAPPED READS";
+
+
+ public static final String HUMAN_GENOME_ID = "HUMAN (hg19)";
+ public static final String MOUSE_GENOME_ID = "MOUSE (mm9)";
+ public static final String MM9_GENOME_ID = "MOUSE (mm10)";
+ public static final String HUMAN_GENOME_NAME = "human";
+ public static final String MOUSE_GENOME_NAME = "mouse";
+
+ private static Map<String,String> genomeGcContentMap;
+
+ public static synchronized Map<String, String> getGcContentFileMap() {
+
+ if (genomeGcContentMap == null) {
+ genomeGcContentMap = new HashMap<String,String>();
+ genomeGcContentMap.put(HUMAN_GENOME_ID, "species/human.hg19.gc_histogram.txt");
+ genomeGcContentMap.put(MOUSE_GENOME_ID, "species/mouse.mm9.gc_histogram.txt");
+ genomeGcContentMap.put(MM9_GENOME_ID, "species/mouse.mm10.gc_histogram.txt");
+ }
+
+ return genomeGcContentMap;
+ }
+
+ private ExecutorService workerThreadPool;
+
+ public BamStatsAnalysis(String bamFile) {
+ this.bamFile = bamFile;
+ this.numberOfWindows = Constants.DEFAULT_NUMBER_OF_WINDOWS;
+ this.numReadsInBunch = Constants.DEFAULT_CHUNK_SIZE;
+ this.minHomopolymerSize = Constants.DEFAULT_HOMOPOLYMER_SIZE;
+ this.maxSizeOfTaskQueue = 10;
+ this.minReadSize = Integer.MAX_VALUE;
+ this.threadNumber = 4;
+ this.selectedRegionsAvailable =false;
+ this.computeOutsideStats = false;
+ this.skipDuplicatedReads = false;
+ this.collectIntersectingPairedEndReads = false;
+ this.outdir = ".";
+ this.saveCoverage = false;
+ this.nonZeroCoverageOnly = true;
+ protocol = LibraryProtocol.NON_STRAND_SPECIFIC;
+ pgProgram = "";
+ pgCommandString = "";
+ logger = new Logger();
+ chromosomeWindowIndexes = new ArrayList<Integer>();
+ }
+
+ public void run() throws Exception{
+
+ long startTime = System.currentTimeMillis();
+
+ workerThreadPool = Executors.newFixedThreadPool(threadNumber);
+
+ SAMFileReader reader = new SAMFileReader(new File(bamFile));
+
+ // org.bioinfo.ntools.process header
+ String lastActionDone = "Loading sam header...";
+ logger.println(lastActionDone);
+ SAMFileHeader header = reader.getFileHeader();
+
+
+ String textHeader = header.getTextHeader();
+ if (textHeader != null && !textHeader.isEmpty()) {
+ if (textHeader.contains("@HD")){
+ try {
+ SAMFileHeader.SortOrder sortOrder = header.getSortOrder();
+ if (sortOrder != SAMFileHeader.SortOrder.coordinate) {
+ logger.warn("According to header the BAM file is not sorted by coordinate!");
+ }
+ } catch (IllegalArgumentException ex) {
+ logger.warn("Non-standard header SortOrder value!");
+ }
+ }else {
+ logger.warn("@HD line is not presented in the BAM file header.");
+ }
+ }
+
+ // load locator
+ lastActionDone = "Loading locator...";
+ logger.println(lastActionDone);
+ loadLocator(header);
+ loadProgramRecords(header.getProgramRecords());
+
+ // load reference
+ lastActionDone = "Loading reference...";
+ logger.println(lastActionDone);
+ loadReference();
+
+ // init window set
+ windowSize = computeWindowSize(referenceSize,numberOfWindows);
+ //effectiveNumberOfWindows = computeEffectiveNumberOfWindows(referenceSize,windowSize);
+ List<Long> windowPositions = computeWindowPositions(windowSize);
+ effectiveNumberOfWindows = windowPositions.size();
+ bamStats = new BamStats("genome", locator, referenceSize,effectiveNumberOfWindows);
+ logger.println("Number of windows: " + numberOfWindows +
+ ", effective number of windows: " + effectiveNumberOfWindows);
+ logger.println("Chunk of reads size: " + numReadsInBunch);
+ logger.println("Number of threads: " + threadNumber);
+ bamStats.setSourceFile(bamFile);
+ //bamStats.setWindowReferences("w",windowSize);
+ bamStats.setWindowReferences("w", windowPositions);
+ bamStatsCollector = new BamStatsCollector();
+ if (collectIntersectingPairedEndReads) {
+ bamStatsCollector.enableIntersectingReadsCollection();
+ }
+
+ openWindows = new ConcurrentHashMap<Long,BamGenomeWindow>();
+
+ if (saveCoverage) {
+ bamStats.activateCoverageReporting(pathToCoverageReport, nonZeroCoverageOnly);
+ }
+
+ //regions
+ if(selectedRegionsAvailable){
+
+ // load selected regions
+ loadSelectedRegions();
+ outsideBamStatsCollector = new BamStatsCollector();
+
+ // outside of regions stats
+ if (computeOutsideStats) {
+ outsideBamStats = new BamStats("outside", locator, referenceSize, effectiveNumberOfWindows);
+ outsideBamStats.setSourceFile(bamFile);
+ outsideBamStats.setWindowReferences("out_w", windowPositions);
+ openOutsideWindows = new HashMap<Long,BamGenomeWindow>();
+ currentOutsideWindow = nextWindow(outsideBamStats,openOutsideWindows,reference,true);
+
+ if(activeReporting) {
+ outsideBamStats.activateWindowReporting(outdir + "/outside_window.txt");
+ }
+
+ if(saveCoverage){
+ outsideBamStats.activateCoverageReporting(outdir + "/outside_coverage.txt", nonZeroCoverageOnly);
+ }
+
+ // we have twice more data from the bunch, so the queue is limited now
+ maxSizeOfTaskQueue /= 2;
+ }
+
+ }
+
+ currentWindow = nextWindow(bamStats, openWindows, reference, true);
+
+ // run reads
+ SAMRecordIterator iter = reader.iterator();
+
+ ArrayList<SAMRecord> readsBunch = new ArrayList<SAMRecord>();
+ results = new ArrayList<Future<ProcessBunchOfReadsTask.Result>>();
+
+ timeToCalcOverlappers = 0;
+
+ while(iter.hasNext()){
+
+ SAMRecord read = null;
+
+ try {
+ read = iter.next();
+ } catch (RuntimeException e) {
+ numberOfProblematicReads++;
+ }
+
+ if (read == null) {
+ continue;
+ }
+
+ // compute absolute position
+ long position = locator.getAbsoluteCoordinates(read.getReferenceName(),read.getAlignmentStart());
+
+ //compute read size
+ int readSize = read.getReadLength();
+ acumReadSize += readSize;
+ if (readSize > maxReadSize) {
+ maxReadSize = readSize;
+ }
+ if (readSize < minReadSize) {
+ minReadSize = readSize;
+ }
+
+ ++numberOfReads;
+
+ // filter invalid reads
+ if(read.isValid() == null){
+ if (read.getDuplicateReadFlag()) {
+ numberOfDuplicatedReads++;
+ if (skipDuplicatedReads) {
+ if (numberOfDuplicatedReads == 1) {
+ logger.println("Note: detected marked duplicates will be skipped...");
+ }
+ bamStatsCollector.updateStats(read);
+ continue;
+ }
+ }
+ // accumulate only mapped reads
+ if(read.getReadUnmappedFlag()) {
+ continue;
+ }
+
+ int insertSize = 0;
+ if (read.getReadPairedFlag()) {
+ insertSize = read.getInferredInsertSize();
+ }
+
+ if (position < currentWindow.getStart()) {
+ throw new RuntimeException("The alignment file is unsorted.\n" +
+ "Please sort the BAM file by coordinate.");
+ }
+
+ long findOverlappersStart = System.currentTimeMillis();
+
+ if (selectedRegionsAvailable) {
+ //boolean readOverlapsRegions = readOverlapsRegions(position, position + read.getReadLength() - 1);
+ boolean readOverlapsRegions = readOverlapsRegions(read);
+
+ if (readOverlapsRegions) {
+ bamStatsCollector.updateStats(read);
+ read.setAttribute(Constants.READ_IN_REGION, 1);
+ if (bamStats.updateReadStartsHistogram(position) && skipDuplicatedReads ) {
+ continue;
+ }
+ if (collectIntersectingPairedEndReads) {
+ bamStatsCollector.collectPairedReadInfo(read);
+ }
+ bamStats.updateInsertSizeHistogram(insertSize);
+ } else {
+ read.setAttribute(Constants.READ_IN_REGION, 0);
+ outsideBamStatsCollector.updateStats(read);
+ if (computeOutsideStats) {
+ if (outsideBamStats.updateReadStartsHistogram(position) && skipDuplicatedReads) {
+ continue;
+ }
+ outsideBamStats.updateInsertSizeHistogram(insertSize);
+ }
+ }
+ } else {
+ read.setAttribute(Constants.READ_IN_REGION, 1);
+ bamStatsCollector.updateStats(read);
+ if (bamStats.updateReadStartsHistogram(position) && skipDuplicatedReads) {
+ continue;
+ }
+ if (collectIntersectingPairedEndReads) {
+ bamStatsCollector.collectPairedReadInfo(read);
+
+ }
+ bamStats.updateInsertSizeHistogram(insertSize);
+ }
+
+ timeToCalcOverlappers += System.currentTimeMillis() - findOverlappersStart;
+
+ // finalize current and get next window
+ if(position > currentWindow.getEnd() ){
+ //analyzeReads(readsBunch);
+ collectAnalysisResults(readsBunch);
+ //finalize
+ currentWindow = finalizeAndGetNextWindow(position, currentWindow, openWindows,
+ bamStats, reference, true);
+
+ if (selectedRegionsAvailable && computeOutsideStats) {
+ currentOutsideWindow.inverseRegions();
+ currentOutsideWindow = finalizeAndGetNextWindow(position, currentOutsideWindow,
+ openOutsideWindows, outsideBamStats, reference, true);
+ }
+
+ }
+
+ if (currentWindow == null) {
+ //Some reads are out of reference bounds?
+ break;
+ }
+
+ readsBunch.add(read);
+ if (readsBunch.size() >= numReadsInBunch) {
+ if (results.size() >= maxSizeOfTaskQueue ) {
+ //System.out.println("Max size of task queue is exceeded!");
+ collectAnalysisResults(readsBunch);
+ } else {
+ analyzeReadsBunch(readsBunch);
+ }
+ }
+
+ numberOfValidReads++;
+
+ }
+
+ }
+
+ // close stream
+ reader.close();
+
+ if (!readsBunch.isEmpty()) {
+ int numWindows = bamStats.getNumberOfWindows();
+ long lastPosition = bamStats.getWindowEnd(numWindows - 1) + 1;
+ collectAnalysisResults(readsBunch);
+ //finalize
+ finalizeAndGetNextWindow(lastPosition, currentWindow, openWindows, bamStats, reference, true);
+ if (selectedRegionsAvailable && computeOutsideStats) {
+ currentOutsideWindow.inverseRegions();
+ finalizeAndGetNextWindow(lastPosition,currentOutsideWindow, openOutsideWindows,
+ outsideBamStats, reference, true);
+ }
+ }
+
+ workerThreadPool.shutdown();
+ workerThreadPool.awaitTermination(2, TimeUnit.MINUTES);
+
+ long endTime = System.currentTimeMillis();
+
+ logger.println("Total processed windows:" + bamStats.getNumberOfProcessedWindows());
+ logger.println("Number of reads: " + numberOfReads);
+ logger.println("Number of valid reads: " + numberOfValidReads);
+ logger.println("Number of duplicated reads: " + numberOfDuplicatedReads);
+ logger.println("Number of correct strand reads:" + numberOfCorrectStrandReads);
+ logger.println("Number of reads with");
+
+ if (numberOfReadsWithStartGreatThenEnd > 0) {
+ logger.warn("WARNING:" + numberOfReadsWithStartGreatThenEnd +
+ " read alignments have start greater than end" );
+ }
+
+ if (numberOfProblematicReads > 0) {
+ logger.warn("SAMRecordParser failed to process " + numberOfProblematicReads + " reads.");
+ }
+
+ if (collectIntersectingPairedEndReads) {
+ bamStatsCollector.finalizeAlignmentInfo();
+ }
+
+ logger.println("\nInside of regions...");
+ logger.print(bamStatsCollector.report());
+
+ if (computeOutsideStats) {
+ logger.println("\nOuside of regions...");
+ logger.print(outsideBamStatsCollector.report());
+ }
+
+ logger.println("Time taken to analyze reads: " + (endTime - startTime) / 1000);
+ logger.println();
+
+ if (numberOfReads == 0) {
+ throw new RuntimeException("The BAM file is empty or corrupt");
+ }
+
+ bamStats.setNumberOfReads(numberOfReads);
+ bamStats.setNumDetectedDuplcateReads(numberOfDuplicatedReads);
+
+ long totalNumberOfMappedReads = bamStatsCollector.getNumMappedReads();
+ long totalNumberOfPairedReads = bamStatsCollector.getNumPairedReads();
+ long totalNumberOfMappedFirstOfPair = bamStatsCollector.getNumMappedFirstInPair();
+ long totalNumberOfMappedSecondOfPair = bamStatsCollector.getNumMappedSecondInPair();
+ long totalNumberOfSingletons = bamStatsCollector.getNumSingletons();
+
+ if (totalNumberOfMappedReads == 0) {
+ logger.println("\nWARNING: total number of mapped reads equals zero");
+ bamStats.addWarning(WARNING_ID_NO_MAPPED_READS, "Total number of mapped reads equals zero.\n" +
+ "For more details, check the number of Unmapped reads.");
+ return;
+ }
+
+ if (selectedRegionsAvailable) {
+
+ bamStats.setNumSelectedRegions(numberOfSelectedRegions);
+ if (computeOutsideStats) {
+ // Size was calculated two times during the analysis
+ insideReferenceSize /= 2;
+ }
+ bamStats.setInRegionReferenceSize(insideReferenceSize);
+
+ // update totals
+ totalNumberOfMappedReads += outsideBamStatsCollector.getNumMappedReads();
+ totalNumberOfPairedReads += outsideBamStatsCollector.getNumPairedReads();
+ totalNumberOfMappedFirstOfPair += outsideBamStatsCollector.getNumMappedFirstInPair();
+ totalNumberOfMappedSecondOfPair += outsideBamStatsCollector.getNumMappedSecondInPair();
+ totalNumberOfSingletons += outsideBamStatsCollector.getNumSingletons();
+
+ // inside of regions
+ bamStats.setNumberOfMappedReadsInRegions(bamStatsCollector.getNumMappedReads());
+ bamStats.setNumberOfPairedReadsInRegions(bamStatsCollector.getNumPairedReads());
+ bamStats.setNumberOfMappedFirstOfPairInRegions(bamStatsCollector.getNumMappedFirstInPair());
+ bamStats.setNumberOfMappedSecondOfPairInRegions(bamStatsCollector.getNumMappedSecondInPair());
+ bamStats.setNumberOfSingletonsInRegions(bamStatsCollector.getNumSingletons());
+ bamStats.setNumberOfCorrectStrandReads(numberOfCorrectStrandReads);
+ }
+
+ bamStats.setNumberOfMappedReads(totalNumberOfMappedReads);
+ bamStats.setNumberOfPairedReads(totalNumberOfPairedReads);
+ bamStats.setNumberOfMappedFirstOfPair(totalNumberOfMappedFirstOfPair);
+ bamStats.setNumberOfMappedSecondOfPair(totalNumberOfMappedSecondOfPair);
+ bamStats.setNumberOfSingletons( totalNumberOfSingletons );
+ if (collectIntersectingPairedEndReads) {
+ bamStats.setNumberOfIntersectingReadPairs(bamStatsCollector.getNumOverlappingReadPairs(),
+ bamStatsCollector.getNumOverlappingBases());
+ }
+
+ bamStats.setReferenceSize(referenceSize);
+ bamStats.setNumberOfReferenceContigs(locator.getContigs().size());
+ bamStats.setReadMaxSize(maxReadSize);
+ bamStats.setReadMinSize(minReadSize);
+ bamStats.setReadMeanSize( acumReadSize / (double) numberOfReads );
+
+
+ isPairedData = bamStats.getNumberOfPairedReads() > 0;
+
+ logger.println("Computing descriptors...");
+ bamStats.computeDescriptors();
+ logger.println("Computing per chromosome statistics...");
+ bamStats.computeChromosomeStats(locator, chromosomeWindowIndexes);
+ logger.println("Computing histograms...");
+ bamStats.computeHistograms();
+
+ if(selectedRegionsAvailable && computeOutsideStats){
+ outsideBamStats.setReferenceSize(referenceSize);
+ outsideBamStats.setNumberOfReferenceContigs(locator.getContigs().size());
+ outsideBamStats.setNumSelectedRegions(numberOfSelectedRegions);
+ outsideBamStats.setInRegionReferenceSize(referenceSize - insideReferenceSize);
+ outsideBamStats.setNumberOfReads(numberOfReads);
+
+ outsideBamStats.setNumberOfMappedReads(totalNumberOfMappedReads);
+ outsideBamStats.setNumberOfPairedReads(totalNumberOfPairedReads);
+ outsideBamStats.setNumberOfMappedFirstOfPair(totalNumberOfMappedFirstOfPair);
+ outsideBamStats.setNumberOfMappedSecondOfPair(totalNumberOfMappedSecondOfPair);
+ outsideBamStats.setNumberOfSingletons(totalNumberOfSingletons);
+
+ outsideBamStats.setNumberOfMappedReadsInRegions(outsideBamStatsCollector.getNumMappedReads());
+ outsideBamStats.setNumberOfPairedReadsInRegions(outsideBamStatsCollector.getNumPairedReads());
+ outsideBamStats.setNumberOfMappedFirstOfPairInRegions(outsideBamStatsCollector.getNumMappedFirstInPair());
+ outsideBamStats.setNumberOfMappedSecondOfPairInRegions(outsideBamStatsCollector.getNumMappedSecondInPair());
+ outsideBamStats.setNumberOfSingletonsInRegions(outsideBamStatsCollector.getNumSingletons());
+
+ outsideBamStats.setReadMaxSize(maxReadSize);
+ outsideBamStats.setReadMinSize(minReadSize);
+ outsideBamStats.setReadMeanSize( acumReadSize / (double) numberOfReads );
+
+ logger.println("Computing descriptors for outside regions...");
+ outsideBamStats.computeDescriptors();
+ logger.println("Computing per chromosome statistics for outside regions...");
+ outsideBamStats.computeChromosomeStats(locator, chromosomeWindowIndexes);
+ logger.println("Computing histograms for outside regions...");
+ outsideBamStats.computeHistograms();
+
+ }
+
+ long overallTime = System.currentTimeMillis();
+ logger.println("Overall analysis time: " + (overallTime - startTime) / 1000);
+
+ }
+
+ private void loadProgramRecords(List<SAMProgramRecord> programRecords) {
+ if (!programRecords.isEmpty()) {
+ SAMProgramRecord rec = programRecords.get(0);
+ pgProgram = rec.getProgramGroupId();
+ String ver = rec.getProgramVersion();
+ if (ver != null ) {
+ pgProgram += " (" + ver + ")";
+ }
+ String cmd = rec.getCommandLine();
+ if (cmd != null ) {
+ pgCommandString = cmd;
+ }
+ }
+ }
+
+ private static List<SAMRecord> getShallowCopy(List<SAMRecord> list) {
+ ArrayList<SAMRecord> result = new ArrayList<SAMRecord>(list.size());
+
+ for (SAMRecord r : list) {
+ result.add(r);
+ }
+
+ return result;
+
+ }
+
+ private void analyzeReadsBunch( ArrayList<SAMRecord> readsBunch ) throws ExecutionException, InterruptedException {
+ List<SAMRecord> bunch = getShallowCopy(readsBunch);
+ Callable<ProcessBunchOfReadsTask.Result> task = new ProcessBunchOfReadsTask(bunch,currentWindow, this);
+ Future<ProcessBunchOfReadsTask.Result> result = workerThreadPool.submit(task);
+ results.add( result );
+ readsBunch.clear();
+ }
+
+ private void collectAnalysisResults(ArrayList<SAMRecord> readsBunch) throws InterruptedException, ExecutionException {
+
+ // start last bunch
+ analyzeReadsBunch(readsBunch);
+
+ // wait till all tasks are finished
+ for (Future<ProcessBunchOfReadsTask.Result> result : results) {
+ ProcessBunchOfReadsTask.Result taskResult = result.get();
+ Collection<SingleReadData> dataset = taskResult.getReadAlignmentData();
+ for (SingleReadData rd : dataset) {
+ BamGenomeWindow w = openWindows.get(rd.getWindowStart());
+ w.addReadAlignmentData(rd);
+ }
+ bamStats.addReadStatsData( taskResult.getReadStatsCollector() );
+
+ if (selectedRegionsAvailable && computeOutsideStats) {
+ Collection<SingleReadData> outsideData = taskResult.getOutOfRegionReadsData();
+ for (SingleReadData rd : outsideData) {
+ BamGenomeWindow w = openOutsideWindows.get( rd.getWindowStart() );
+ w.addReadAlignmentData(rd);
+ }
+ outsideBamStats.addReadStatsData( taskResult.getOutRegionReadStatsCollector() );
+
+ }
+ }
+
+ results.clear();
+
+ }
+
+
+ public BamGenomeWindow getOpenWindow(long windowStart,BamStats bamStats,
+ Map<Long,BamGenomeWindow> openWindows) {
+ BamGenomeWindow window;
+ if(openWindows.containsKey(windowStart)){
+ window = openWindows.get(windowStart);
+ } else {
+ int numInitWindows = bamStats.getNumberOfInitializedWindows();
+ String windowName = bamStats.getWindowName(numInitWindows);
+ long windowEnd = bamStats.getWindowEnd(numInitWindows);
+ window = initWindow(windowName, windowStart,
+ Math.min(windowEnd, bamStats.getReferenceSize()), reference, true);
+ bamStats.incInitializedWindows();
+ openWindows.put(windowStart,window);
+ }
+
+ return window;
+ }
+
+ //TODO: try using this method for better performance
+ /*private void calculateRegionsLookUpTableForWindowNew(BamGenomeWindow w) {
+
+ int windowSize = (int) w.getWindowSize();
+
+ BitSet bitSet = new BitSet((int)w.getWindowSize());
+
+ ContigRecord windowContig = locator.getContigCoordinates(w.getStart());
+
+ int relativeWindowStart = (int) windowContig.getRelative();
+ int relativeWindowEnd = relativeWindowStart + windowSize - 1;
+ String contigName = windowContig.getName();
+
+ regionOverlapLookupTable.markIntersectingRegions(bitSet, relativeWindowStart,
+ relativeWindowEnd, contigName);
+
+ w.setSelectedRegions(bitSet);
+ w.setSelectedRegionsAvailable(true);
+ }*/
+
+
+ private void calculateRegionsLookUpTableForWindow(BamGenomeWindow w) {
+
+ long windowStart = w.getStart();
+ long windowEnd = w.getEnd();
+
+
+ BitSet bitSet = new BitSet((int)w.getWindowSize());
+
+ int numRegions = selectedRegionStarts.length;
+
+ for (int i = 0; i < numRegions; ++i) {
+ long regionStart = selectedRegionStarts[i];
+ long regionEnd = selectedRegionEnds[i];
+
+ if (regionStart == -1) {
+ continue;
+ }
+
+ if ( regionStart >= windowStart && regionStart <= windowEnd ) {
+ //System.out.println("Have match! Type1 " + w.getName());
+ long end = Math.min(windowEnd,regionEnd);
+ bitSet.set((int)(regionStart-windowStart), (int)(end-windowStart + 1),true);
+ } else if (regionEnd >= windowStart && regionEnd <= windowEnd) {
+ //System.out.println("Have match! Type2 " + w.getName());
+ bitSet.set(0, (int)(regionEnd - windowStart + 1), true);
+ } else if (regionStart <= windowStart && regionEnd >= windowEnd) {
+ //System.out.println("Have match! Type3 " + w.getName());
+ bitSet.set(0, (int)(windowEnd - windowStart + 1),true);
+ }
+
+ }
+
+ w.setSelectedRegions(bitSet);
+ w.setSelectedRegionsAvailable(true);
+
+ insideReferenceSize += bitSet.cardinality();
+
+ }
+
+
+
+ public BamGenomeWindow initWindow(String name,long windowStart,long windowEnd, byte[]reference,
+ boolean detailed){
+
+ byte[]miniReference = null;
+ if(reference != null) {
+ miniReference = Arrays.copyOfRange(reference, (int) (windowStart - 1), (int) (windowEnd - 1));
+ }
+
+ BamGenomeWindow w = detailed ? new BamDetailedGenomeWindow(name,windowStart,windowEnd,miniReference) :
+ new BamGenomeWindow(name,windowStart,windowEnd,miniReference);
+
+ if (selectedRegionsAvailable) {
+ calculateRegionsLookUpTableForWindow(w);
+ }
+
+ return w;
+ }
+
+
+ private BamGenomeWindow nextWindow(BamStats bamStats, Map<Long,BamGenomeWindow> openWindows,byte[]reference,boolean detailed){
+ // init new current
+ BamGenomeWindow currentWindow = null;
+
+ if(bamStats.getNumberOfProcessedWindows() < bamStats.getNumberOfWindows()){
+ int numProcessed = bamStats.getNumberOfProcessedWindows();
+ long windowStart = bamStats.getWindowStart(numProcessed);
+
+ if(windowStart <= bamStats.getReferenceSize()){
+ long windowEnd = bamStats.getCurrentWindowEnd();
+ if(openWindows.containsKey(windowStart)){
+ currentWindow = openWindows.get(windowStart);
+ //openWindows.remove(windowStart);
+ } else {
+ currentWindow = initWindow(bamStats.getCurrentWindowName(),windowStart,Math.min(windowEnd,bamStats.getReferenceSize()),reference,detailed);
+ bamStats.incInitializedWindows();
+ openWindows.put(windowStart, currentWindow);
+ }
+ }
+ }
+
+ return currentWindow;
+ }
+
+ private BamGenomeWindow finalizeAndGetNextWindow(long position, BamGenomeWindow lastWindow,
+ Map<Long,BamGenomeWindow> openWindows,BamStats bamStats,
+ byte[]reference, boolean detailed)
+ throws CloneNotSupportedException, ExecutionException, InterruptedException {
+ // position is still far away
+ while(position > lastWindow.getEnd() ) {
+ updateProgress();
+ //finalizeWindowInSameThread(lastWindow, bamStats, openWindows);
+ finalizeWindow(lastWindow, bamStats, openWindows);
+ lastWindow = nextWindow(bamStats,openWindows,reference,detailed);
+ if (lastWindow == null) {
+ break;
+ }
+
+ }
+
+ return lastWindow;
+ }
+
+
+ private void updateProgress() {
+ if (!computeOutsideStats) {
+ progress = (bamStats.getNumberOfProcessedWindows() * 100) / effectiveNumberOfWindows;
+ } else {
+ progress = ((bamStats.getNumberOfProcessedWindows() +
+ outsideBamStats.getNumberOfProcessedWindows()) * 50) / (effectiveNumberOfWindows);
+ }
+ if (loggerThread != null) {
+ loggerThread.updateProgress(progress);
+ }
+
+ }
+ private void finalizeWindow(BamGenomeWindow window, BamStats bamStats,
+ Map<Long,BamGenomeWindow> openWindows) throws ExecutionException, InterruptedException {
+ if (finalizeWindowResult != null) {
+ // We only run finalization of one window in parallel to prevent to many open windows
+ finalizeWindowResult.get();
+
+ }
+
+
+ long windowStart = bamStats.getCurrentWindowStart();
+ openWindows.remove(windowStart);
+ bamStats.incProcessedWindows();
+
+ // report progress
+ int numProcessedWindows = bamStats.getNumberOfProcessedWindows();
+ if (numProcessedWindows % 50 == 0 && bamStats == this.bamStats) {
+ logger.println("Processed " + numProcessedWindows + " out of " + effectiveNumberOfWindows + " windows...");
+ }
+
+ //System.out.println("Time taken to count overlappers: " + timeToCalcOverlappers);
+ timeToCalcOverlappers = 0;
+ finalizeWindowResult = workerThreadPool.submit( new FinalizeWindowTask(bamStats,window));
+
+ }
+
+ // For debug purposes
+ /*private static Integer finalizeWindowInSameThread(BamGenomeWindow window,BamStats bamStats,
+ Map<Long,BamGenomeWindow> openWindows) {
+ long windowStart = bamStats.getCurrentWindowStart();
+ openWindows.remove(windowStart);
+ bamStats.incProcessedWindows();
+ FinalizeWindowTask task = new FinalizeWindowTask(bamStats,window);
+ return task.call();
+ }*/
+
+
+ private void loadLocator(SAMFileHeader header){
+ locator = new GenomeLocator();
+ for(int i=0; i<header.getSequenceDictionary().getSequences().size(); i++){
+ locator.addContig(header.getSequence(i).getSequenceName(), header.getSequence(i).getSequenceLength());
+ }
+ }
+
+
+ private void loadReference() throws Exception{
+ if(referenceAvailable){
+ // prepare reader
+ FastaReader reader = new FastaReader(referenceFile);
+
+ // init buffer
+ StringBuilder referenceBuffer = new StringBuilder();
+
+ numberOfReferenceContigs = 0;
+ Fasta contig;
+ while((contig=reader.read())!=null){
+ referenceBuffer.append(contig.getSeq().toUpperCase());
+ numberOfReferenceContigs++;
+ }
+
+ reader.close();
+ reference = referenceBuffer.toString().getBytes();
+ referenceSize = reference.length;
+ if(reference.length!=locator.getTotalSize()){
+ throw new Exception("invalid reference file, number of nucleotides differs");
+ }
+ } else {
+ referenceSize = locator.getTotalSize();
+ numberOfReferenceContigs = locator.getContigs().size();
+ }
+ }
+
+ private void loadSelectedRegions() throws SecurityException, IOException, NoSuchMethodException, FileFormatException {
+
+
+ FeatureFileFormat featureFileFormat = DocumentUtils.guessFeaturesFileFormat(featureFile);
+
+ if (featureFileFormat == FeatureFileFormat.UNKNOWN) {
+ throw new RuntimeIOException("Unknown feature file format. Please provide file in GFF/GTF or BED format.");
+ }
+
+ if (featureFileFormat == FeatureFileFormat.GTF) {
+ // while not interested in GTF-specific information we save some memory by using GFF reader
+ featureFileFormat = FeatureFileFormat.GFF;
+ }
+
+ // init gff reader
+ numberOfSelectedRegions = 0;
+ GenomicFeatureStreamReader featureFileReader = new GenomicFeatureStreamReader(featureFile, featureFileFormat);
+ System.out.println("Initializing regions from " + featureFile + ".....");
+ while(featureFileReader.skipNextRecord()){
+ numberOfSelectedRegions++;
+ }
+ if (numberOfSelectedRegions == 0) {
+ throw new RuntimeException("Failed to load selected regions.");
+ }
+ System.out.println("Found " + numberOfSelectedRegions + " regions");
+
+ selectedRegionStarts = new long[numberOfSelectedRegions];
+ selectedRegionEnds = new long[numberOfSelectedRegions];
+ regionOverlapLookupTable = new RegionOverlapLookupTable();
+ //selectedRegionRelativePositions = new long[numberOfSelectedRegions];
+
+ featureFileReader.reset();
+ System.out.println("Filling region references... ");
+ int index = 0;
+ long pos;
+ insideReferenceSize = 0;
+ GenomicFeature region;
+ int regionsWithMissingChromosomesCount = 0;
+
+ while((region = featureFileReader.readNextRecord()) != null){
+ /*if (!region.getFeature().equalsIgnoreCase("exon")) {
+ continue;
+ }*/
+ pos = locator.getAbsoluteCoordinates(region.getSequenceName(),region.getStart());
+ if (pos == -1) {
+ selectedRegionStarts[index] = -1;
+ selectedRegionEnds[index] = -1;
+ regionsWithMissingChromosomesCount++;
+ continue;
+ }
+ int regionLength = region.getEnd() - region.getStart() + 1;
+ // TEMPTODO: delete next line
+ //insideReferenceSize += regionLength;
+ selectedRegionStarts[index] = pos;
+ selectedRegionEnds[index] = pos + regionLength - 1;
+ regionOverlapLookupTable.putRegion(region.getStart(), region.getEnd(),
+ region.getSequenceName(), region.isPositiveStrand() );
+
+ index++;
+ }
+
+ if (regionsWithMissingChromosomesCount > 0) {
+ if (regionsWithMissingChromosomesCount == numberOfSelectedRegions) {
+ throw new RuntimeException("The feature file with regions can not be associated with the BAM file.\n" +
+ "Please check, if the chromosome names match in the annotation file and the alignment file.");
+ } else {
+ String msg = regionsWithMissingChromosomesCount + " regions were skipped because chromosome" +
+ " name was not found in the BAM file.";
+ bamStats.addWarning(WARNING_ID_CHROMOSOME_NOT_FOUND, msg);
+ }
+
+ }
+
+ featureFileReader.close();
+
+ }
+
+ private int computeWindowSize(long referenceSize, int numberOfWindows){
+ int windowSize = (int)Math.floor((double)referenceSize/(double)numberOfWindows);
+ if(((double)referenceSize/(double)numberOfWindows)>windowSize){
+ windowSize++;
+ }
+
+ return windowSize;
+ }
+
+
+ /*private int computeEffectiveNumberOfWindows(long referenceSize, int windowSize){
+ int numberOfWindows = (int)Math.floor((double)referenceSize/(double)windowSize);
+ if(((double)referenceSize/(double)windowSize)>numberOfWindows){
+ numberOfWindows++;
+ }
+
+ return numberOfWindows;
+ }*/
+
+ private ArrayList<Long> computeWindowPositions(int windowSize){
+ List<ContigRecord> contigs = locator.getContigs();
+ ArrayList<Long> windowStarts = new ArrayList<Long>();
+
+ long startPos = 1;
+ int i = 0;
+ int numContigs = contigs.size();
+ chromosomeWindowIndexes.add(0);
+ while (startPos < referenceSize) {
+ windowStarts.add(startPos);
+ startPos += windowSize;
+
+ while (i < numContigs) {
+ long nextContigStart = contigs.get(i).getEnd() + 1;
+ if (startPos >= nextContigStart ) {
+ if (startPos > nextContigStart && nextContigStart < referenceSize) {
+ //System.out.println("Chromosome window break: " + (windowStarts.size() + 1));
+ chromosomeWindowIndexes.add(windowStarts.size());
+ windowStarts.add(nextContigStart);
+ //System.out.println("window start: " + nextContigStart);
+ }
+ i++;
+ } else {
+ break;
+ }
+ }
+ }
+
+ return windowStarts;
+ }
+
+ private boolean readOverlapsRegions(SAMRecord read) {
+
+
+
+ if (protocol == LibraryProtocol.NON_STRAND_SPECIFIC) {
+ return regionOverlapLookupTable.overlaps(read.getAlignmentStart(),
+ read.getAlignmentEnd(), read.getReferenceName());
+ } else {
+
+ boolean readHasForwardStrand = !read.getReadNegativeStrandFlag();
+ boolean forwardTranscriptStrandIsExpected;
+ if (protocol == LibraryProtocol.STRAND_SPECIFIC_FORWARD) {
+ forwardTranscriptStrandIsExpected =
+ ( ( read.getFirstOfPairFlag() || !read.getReadPairedFlag() ) && readHasForwardStrand) ||
+ (read.getSecondOfPairFlag() && !readHasForwardStrand);
+ } else {
+ forwardTranscriptStrandIsExpected =(read.getFirstOfPairFlag() && !readHasForwardStrand) ||
+ (read.getSecondOfPairFlag() && readHasForwardStrand) ;
+ }
+
+ RegionOverlapLookupTable.OverlapResult r = regionOverlapLookupTable.overlaps( read.getAlignmentStart(),
+ read.getAlignmentEnd(), read.getReferenceName(), forwardTranscriptStrandIsExpected);
+
+ if (r.strandMatches()) {
+ ++numberOfCorrectStrandReads;
+ }
+
+ return r.intervalOverlaps();
+
+ }
+
+ }
+
+
+
+ public GenomeLocator getLocator() {
+ return locator;
+ }
+
+ public BamStats getBamStats() {
+ return bamStats;
+ }
+
+ public BamStats getOutsideBamStats() {
+ return outsideBamStats;
+ }
+
+ HashMap<Long,BamGenomeWindow> getOpenOutsideWindows() {
+ return openOutsideWindows;
+ }
+
+
+
+ ConcurrentMap<Long,BamGenomeWindow> getOpenWindows() {
+ return openWindows;
+ }
+
+ public boolean isPairedData() {
+ return isPairedData;
+ }
+
+ public boolean selectedRegionsAvailable() {
+ return selectedRegionsAvailable;
+ }
+
+ public void setNumberOfWindows(int windowsNum) {
+ numberOfWindows = windowsNum;
+ }
+
+ public void activeReporting(String outdir){
+ this.outdir = outdir;
+ this.activeReporting = true;
+ }
+
+ public void setSelectedRegions(String featureFile){
+ this.featureFile = featureFile;
+ selectedRegionsAvailable = true;
+ }
+
+ public void setComputeOutsideStats(boolean computeOutsideStats) {
+ this.computeOutsideStats = computeOutsideStats;
+ }
+
+ public boolean getComputeOutsideStats() {
+ return computeOutsideStats;
+ }
+
+ public void setNumberOfThreads(int threadNumber) {
+ this.threadNumber = threadNumber;
+ }
+
+ public void setNumberOfReadsInBunch(int bunchSize) {
+ numReadsInBunch = bunchSize;
+ }
+
+ public void setProtocol(LibraryProtocol protocol) {
+ this.protocol = protocol;
+ }
+
+ public int getMinHomopolymerSize() {
+ return minHomopolymerSize;
+ }
+
+ public void setMinHomopolymerSize(int size) {
+ minHomopolymerSize = size;
+ }
+
+ public void setPathToCoverageReport(String pathToCoverageReport) {
+ this.saveCoverage = true;
+ this.pathToCoverageReport = pathToCoverageReport;
+ }
+
+ private static String boolToStr(boolean yes) {
+ return yes ? "yes\n" : "no\n";
+ }
+
+ public String getQualimapCmdLine(boolean drawChromosomeLimits) {
+
+ CommandLineBuilder cmdBuilder = new CommandLineBuilder("qualimap " + Constants.TOOL_NAME_BAMQC);
+
+ cmdBuilder.append(Constants.BAMQC_OPTION_BAM_FILE, bamFile);
+
+ if (featureFile != null) {
+ cmdBuilder.append(Constants.BAMQC_OPTION_GFF_FILE, featureFile);
+ if (computeOutsideStats) {
+ cmdBuilder.append(Constants.BAMQC_OPTION_OUTSIDE_STATS);
+ }
+ }
+
+ if (drawChromosomeLimits) {
+ cmdBuilder.append(Constants.BAMQC_OPTION_PAINT_CHROMOSOMES);
+ }
+
+ cmdBuilder.append(Constants.BAMQC_OPTION_NUM_WINDOWS, numberOfWindows);
+ cmdBuilder.append(Constants.BAMQC_OPTION_MIN_HOMOPOLYMER_SIZE, minHomopolymerSize);
+
+ return cmdBuilder.getCmdLine();
+
+ }
+
+
+
+ public void prepareInputDescription(StatsReporter reporter, boolean drawChromosomeLimits) {
+
+ String[] qualimapCommand = { getQualimapCmdLine(drawChromosomeLimits) };
+ StatsKeeper.Section qualCommandSection = new StatsKeeper.Section(Constants.TABLE_SECTION_QUALIMAP_CMDLINE);
+ qualCommandSection.addRow(qualimapCommand);
+ reporter.getInputDataKeeper().addSection(qualCommandSection);
+
+
+ HashMap<String,String> alignParams = new HashMap<String, String>();
+ alignParams.put("BAM file: ", bamFile);
+ Date date = new Date();
+ alignParams.put("Analysis date: ", date.toString() );
+ alignParams.put("Number of windows: ", Integer.toString(numberOfWindows));
+ alignParams.put("Size of a homopolymer: ", Integer.toString(minHomopolymerSize));
+
+
+ Boolean.toString(true);
+ alignParams.put("Draw chromosome limits: ", boolToStr(drawChromosomeLimits));
+ if (!pgProgram.isEmpty()) {
+ alignParams.put("Program: ", pgProgram);
+ if (!pgCommandString.isEmpty()) {
+ alignParams.put("Command line: ", pgCommandString );
+ }
+ }
+ alignParams.put("Skip duplicated alignments: ", boolToStr(skipDuplicatedReads));
+ alignParams.put("Analyze overlapping paired-end reads:", boolToStr(collectIntersectingPairedEndReads));
+
+ reporter.addInputDataSection("Alignment", alignParams);
+
+ if ( selectedRegionsAvailable ) {
+ HashMap<String,String> regionParams = new HashMap<String, String>();
+ regionParams.put("GFF file: ", featureFile);
+ regionParams.put("Outside statistics: ", boolToStr(computeOutsideStats));
+ regionParams.put("Library protocol: ", protocol.toString() );
+ reporter.addInputDataSection("GFF region", regionParams);
+ }
+
+
+ }
+
+
+ public void setConfig(BamStatsAnalysisConfig cfg) {
+ if (cfg.gffFile != null) {
+ selectedRegionsAvailable = true;
+ featureFile = cfg.gffFile;
+ }
+ numberOfWindows = cfg.numberOfWindows;
+ minHomopolymerSize = cfg.minHomopolymerSize;
+
+ }
+
+ public void setLoggerThread(LoggerThread loggerThread) {
+ this.loggerThread = loggerThread;
+ }
+
+ public void incNumberOfReasWithStartGreatThenEnd() {
+ this.numberOfReadsWithStartGreatThenEnd++;
+ }
+
+
+ public void setSkipDuplicatedReads(boolean skipDuplications) {
+ this.skipDuplicatedReads = skipDuplications;
+ }
+
+
+ public void activateIntersectingPairedEndReadsStats() {
+ this.collectIntersectingPairedEndReads = true;
+ }
+
+
+}
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/process/BamStatsAnalysisConfig.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/process/BamStatsAnalysisConfig.java
new file mode 100644
index 0000000..b096e18
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/process/BamStatsAnalysisConfig.java
@@ -0,0 +1,48 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.process;
+
+import org.bioinfo.ngs.qc.qualimap.common.Constants;
+
+/**
+ * Created by kokonech
+ * Date: 8/20/14
+ * Time: 10:33 AM
+ */
+
+public class BamStatsAnalysisConfig {
+
+ public boolean drawChromosomeLimits;
+ public String gffFile;
+ public int numberOfWindows, bunchSize, minHomopolymerSize;
+ public BamStatsAnalysisConfig() {
+ this.drawChromosomeLimits = false;
+ this.numberOfWindows = Constants.DEFAULT_NUMBER_OF_WINDOWS;
+ this.bunchSize = Constants.DEFAULT_CHUNK_SIZE;
+ this.minHomopolymerSize = Constants.DEFAULT_HOMOPOLYMER_SIZE;
+
+ }
+
+ public boolean regionsAvailable() {
+ return gffFile != null;
+ }
+
+}
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/process/ComputeCountsTask.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/process/ComputeCountsTask.java
new file mode 100644
index 0000000..6d9efaa
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/process/ComputeCountsTask.java
@@ -0,0 +1,785 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.process;
+
+
+import net.sf.picard.io.IoUtil;
+import net.sf.picard.util.Interval;
+import net.sf.picard.util.IntervalTree;
+import net.sf.samtools.*;
+import net.sf.samtools.util.CoordMath;
+import org.apache.commons.collections15.MultiMap;
+import org.apache.commons.collections15.multimap.MultiHashMap;
+import org.apache.commons.io.FileUtils;
+import org.bioinfo.formats.exception.FileFormatException;
+import org.bioinfo.ngs.qc.qualimap.common.LibraryProtocol;
+import org.bioinfo.ngs.qc.qualimap.common.*;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.*;
+
+
+/**
+ * Created by kokonech
+ * Date: 12/12/11
+ * Time: 2:52 PM
+ */
+
+public class ComputeCountsTask {
+
+ Map<String,Double> readCounts;
+ Map<String, GenomicRegionSet> chromosomeRegionSetMap;
+ MultiMap<String, Interval> featureIntervalMap;
+ ArrayList<String> allowedFeatureList;
+ TranscriptDataHandler transcriptDataHandler;
+ LibraryProtocol protocol;
+ String countingAlgorithm;
+ String attrName;
+ LoggerThread logger;
+ boolean collectRnaSeqStats, skipSecondaryAlignments;
+ boolean loadGenericRegions;
+ boolean outputCoverage;
+ boolean strandSpecificAnalysis, pairedEndAnalysis, sortingRequired, cleanupRequired;
+
+ String pathToBamFile, pathToGffFile, sampleName;
+
+ long primaryAlignments, secondaryAlignments;
+ long notAligned, alignmentNotUnique, noFeature, ambiguous;
+ long readCount, fragmentCount, seqNotFoundCount;
+ long leftProperInPair, rightProperInPair, bothProperInPair;
+ long protocolCorrectlyMapped;
+
+ public static final String GENE_ID_ATTR = "gene_id";
+ public static final String EXON_TYPE_ATTR = "exon";
+ public static final String COUNTING_ALGORITHM_ONLY_UNIQUELY_MAPPED = "uniquely-mapped-reads";
+ public static final String COUNTING_ALGORITHM_PROPORTIONAL = "proportional";
+
+ public ComputeCountsTask(String pathToBamFile, String pathToGffFile) {
+ this.pathToBamFile = pathToBamFile;
+ this.pathToGffFile = pathToGffFile;
+ this.attrName = GENE_ID_ATTR;
+
+ protocol = LibraryProtocol.NON_STRAND_SPECIFIC;
+ countingAlgorithm = COUNTING_ALGORITHM_ONLY_UNIQUELY_MAPPED;
+ allowedFeatureList = new ArrayList<String>();
+ featureIntervalMap = new MultiHashMap<String, Interval>();
+ collectRnaSeqStats = false;
+ skipSecondaryAlignments = false;
+ loadGenericRegions = false;
+ outputCoverage = true;
+ pairedEndAnalysis = false;
+ sortingRequired = false;
+ cleanupRequired = false;
+
+ readCount = 0;
+ seqNotFoundCount = 0;
+
+ logger = new LoggerThread() {
+ @Override
+ public void logLine(String msg) {
+ System.out.println(msg);
+ }
+ };
+
+ sampleName = (new File(this.pathToBamFile)).getName();
+
+ }
+
+ public void addSupportedFeatureType(String featureName) {
+ allowedFeatureList.add(featureName);
+ }
+
+ public void setProtocol(LibraryProtocol protocol) {
+ this.protocol = protocol;
+ }
+
+ public void setLogger(LoggerThread thread) {
+ this.logger = thread;
+ }
+
+ public void skipSecondaryAlignments() {
+ this.skipSecondaryAlignments = true;
+ }
+
+ public void setCollectRnaSeqStats(boolean collectRnaSeqStats) {
+ this.collectRnaSeqStats = collectRnaSeqStats;
+ }
+
+ public static String getAlgorithmTypes() {
+ return ComputeCountsTask.COUNTING_ALGORITHM_ONLY_UNIQUELY_MAPPED + "(default) or " +
+ ComputeCountsTask.COUNTING_ALGORITHM_PROPORTIONAL;
+ }
+
+ String sortSamByName(String inputPath) throws IOException {
+
+ // bam file by name
+
+ long n = 0;
+ File targetFile = File.createTempFile("" + UniqueID.get(), ".bam");
+ String targetPath = targetFile.getAbsolutePath();
+
+ SAMFileReader reader = new SAMFileReader(IoUtil.openFileForReading(new File(inputPath)));
+ reader.getFileHeader().setSortOrder(SAMFileHeader.SortOrder.queryname);
+ final SAMFileWriter writer = new SAMFileWriterFactory().makeSAMOrBAMWriter(reader.getFileHeader(),
+ false,
+ targetFile);
+
+ for (SAMRecord record : reader) {
+ writer.addAlignment(record);
+ if (++n % 10000000 == 0) {
+ logger.logLine("Read " + n + " records.");
+ }
+ }
+
+ logger.logLine("Finished reading inputs, merging and writing to output now.");
+
+ reader.close();
+ writer.close();
+
+ logger.logLine("Sorting by name finished.");
+ cleanupRequired = true;
+
+ return targetPath;
+ }
+
+ boolean checkRead(SAMRecord read) {
+
+ if (read == null || read.getReadUnmappedFlag()) {
+ notAligned++;
+ return false;
+ }
+
+ if (read.getNotPrimaryAlignmentFlag() ) {
+ secondaryAlignments++;
+ if (skipSecondaryAlignments) {
+ return false;
+ }
+ } else {
+ primaryAlignments++;
+ if (read.getReadPairedFlag() ) {
+
+ if (read.getProperPairFlag()) {
+ bothProperInPair++;
+ }
+ if (read.getFirstOfPairFlag()) {
+ leftProperInPair++;
+ }
+ if (read.getSecondOfPairFlag()) {
+ rightProperInPair++;
+ }
+ }
+ }
+
+ String chrName = read.getReferenceName();
+ GenomicRegionSet regionSet = chromosomeRegionSetMap.get(chrName);
+
+ if (regionSet == null ) {
+ seqNotFoundCount++;
+ return false;
+ }
+
+ readCount++;
+
+ return true;
+
+ }
+
+ ArrayList<Interval> getReadIntervals(SAMRecord read) {
+
+ ArrayList<Interval> intervals = new ArrayList<Interval>();
+
+ String chrName = read.getReferenceName();
+ boolean pairedRead = read.getReadPairedFlag();
+ Cigar cigar = read.getCigar();
+ List<CigarElement> cigarElements = cigar.getCigarElements();
+ int offset = read.getAlignmentStart();
+ boolean strand = read.getReadNegativeStrandFlag();
+ if (pairedRead) {
+ boolean firstOfPair = read.getFirstOfPairFlag();
+ if ( (protocol == LibraryProtocol.STRAND_SPECIFIC_FORWARD && !firstOfPair) ||
+ (protocol == LibraryProtocol.STRAND_SPECIFIC_REVERSE && firstOfPair) ) {
+ strand = !strand;
+ }
+ } else {
+ if (protocol == LibraryProtocol.STRAND_SPECIFIC_REVERSE) {
+ strand = !strand;
+ }
+ }
+
+ int posInRead = 0;
+ for (CigarElement cigarElement : cigarElements) {
+ int length = cigarElement.getLength();
+
+ if ( cigarElement.getOperator().equals(CigarOperator.M) ) {
+ intervals.add(new Interval(chrName, offset, offset + length - 1, strand, "" ));
+ posInRead += length;
+ }
+
+ if (cigarElement.getOperator().equals(CigarOperator.I) ||
+ cigarElement.getOperator().equals(CigarOperator.EQ) ||
+ cigarElement.getOperator().equals(CigarOperator.S)) {
+ posInRead += length;
+ }
+
+ if (cigarElement.getOperator().equals(CigarOperator.N) && collectRnaSeqStats) {
+
+ transcriptDataHandler.collectJunctionInfo(read, posInRead, cigarElement.getLength());
+
+ }
+
+ offset += length;
+ }
+
+ return intervals;
+ }
+
+ Map<String,BitSet> findIntersectingFeatures(List<Interval> intervals) {
+
+ HashMap<String,BitSet> featureIntervalMap = new HashMap<String, BitSet>();
+ int intIndex = 0;
+ boolean readOverlaps = false;
+
+ for (Interval alignmentInterval : intervals) {
+ GenomicRegionSet regionSet = chromosomeRegionSetMap.get(alignmentInterval.getSequence());
+ Iterator<IntervalTree.Node<Set<GenomicRegionSet.Feature>>> overlapIter
+ = regionSet.overlappers(alignmentInterval.getStart(), alignmentInterval.getEnd() );
+ while (overlapIter.hasNext()) {
+ IntervalTree.Node<Set<GenomicRegionSet.Feature>> node = overlapIter.next();
+
+ boolean segmentEnclosed = CoordMath.encloses(node.getStart(), node.getEnd(),
+ alignmentInterval.getStart(), alignmentInterval.getEnd());
+
+ if ( segmentEnclosed) {
+
+ Set<GenomicRegionSet.Feature> features = node.getValue();
+ for (GenomicRegionSet.Feature feature : features) {
+ String featureName = feature.getName();
+
+ BitSet intervalBits = featureIntervalMap.get(featureName);
+ if (intervalBits == null) {
+ intervalBits = new BitSet(intervals.size());
+ featureIntervalMap.put(feature.getName(), intervalBits);
+ }
+
+ boolean includeInterval = true;
+ if (strandSpecificAnalysis) {
+ boolean featureStrand = feature.isPositiveStrand();
+ includeInterval = featureStrand == alignmentInterval.isPositiveStrand();
+ }
+
+ intervalBits.set(intIndex, includeInterval);
+ }
+ if (collectRnaSeqStats) {
+ for (GenomicRegionSet.Feature feature : features) {
+ transcriptDataHandler.addCoverage(feature.getName(),
+ alignmentInterval.getStart(), alignmentInterval.getEnd() );
+ }
+ }
+
+ } else {
+ if (collectRnaSeqStats && !readOverlaps) {
+ if (CoordMath.overlaps(node.getStart(), node.getEnd(),
+ alignmentInterval.getStart(), alignmentInterval.getEnd())) {
+ transcriptDataHandler.increaseNumReadsIntersectingExonRegion();
+ readOverlaps = true;
+ }
+ }
+ }
+
+ }
+
+ intIndex++;
+ }
+
+
+ return featureIntervalMap;
+ }
+
+ private void processFragment(ArrayList<SAMRecord> fragmentReads) {
+ int numReads = fragmentReads.size();
+ if (numReads == 0) {
+ return;
+ } else if (numReads == 1) {
+ String readName = fragmentReads.get(0).getReadName();
+ System.err.println("WARNING: The fragment " + readName + " has only 1 alignments," +
+ " however multiple segments are assumed!");
+ return;
+ } else if (numReads > 2) {
+ String readName = fragmentReads.get(0).getReadName();
+ System.err.println("WARNING: The fragment " + readName + " has more than 2 alignments!");
+ return;
+ }
+
+ fragmentCount++;
+
+ ArrayList<Interval> intervals = new ArrayList<Interval>();
+ float fragmentWeight = 0;
+ for (SAMRecord read : fragmentReads) {
+ intervals.addAll( getReadIntervals(read) );
+ fragmentWeight += read.getFloatAttribute(Constants.READ_WEIGHT_ATTR);
+ }
+ fragmentWeight /= numReads;
+ processAlignmentIntervals(intervals, fragmentWeight);
+
+
+ }
+
+
+ void processRead(SAMRecord read) {
+ List<Interval> intervals = getReadIntervals(read);
+ float readWeight = read.getFloatAttribute(Constants.READ_WEIGHT_ATTR);
+ fragmentCount++;
+ processAlignmentIntervals(intervals, readWeight);
+ }
+
+
+ void processAlignmentIntervals(List<Interval> intervals, float alnWeight) {
+
+ //Find intersections
+ Map<String,BitSet> featureIntervalMap = findIntersectingFeatures(intervals);
+
+
+ Set<String> features = new HashSet<String>();
+
+ /*if (featureIntervalMap.keySet().contains("ENSG00000214827")) {
+ System.out.println("AKALAI MAKALAI!" + featureIntervalMap.keySet() + read.getReadName());
+ }*/
+
+ for (Map.Entry<String,BitSet> entry : featureIntervalMap.entrySet() ) {
+ if (entry.getValue().cardinality() == intervals.size() ) {
+ features.add(entry.getKey());
+ }
+ }
+
+ if (features.size() == 0) {
+ noFeature++;
+ if (collectRnaSeqStats) {
+ transcriptDataHandler.collectNonFeatureMappedReadInfo(intervals);
+ }
+ } else if (features.size() == 1) {
+ //if (features.iterator().next().contains("ENSG00000124222")) {
+ // System.out.println(read.getReadName());
+ //}
+ String geneName = features.iterator().next();
+ double count = readCounts.get(geneName);
+ readCounts.put(geneName, count + alnWeight);
+
+ } else {
+ ambiguous++;
+ }
+
+ if (features.size() > 0 && strandSpecificAnalysis) {
+ protocolCorrectlyMapped++;
+ }
+
+ if (readCount % 500000 == 0) {
+ logger.logLine("Analyzed " + readCount + " reads...");
+ }
+
+ }
+
+
+ boolean computeReadWeight(SAMRecord read) {
+ float readWeight = 1.0f;
+ int nh = 1;
+ try {
+ nh = read.getIntegerAttribute("NH");
+ } catch (NullPointerException ex) {
+ //System.err.println("The read " + read.getReadName() + " doesn't have NH attribute");
+ }
+ if (nh > 1) {
+ if (countingAlgorithm.equals(COUNTING_ALGORITHM_ONLY_UNIQUELY_MAPPED)) {
+ alignmentNotUnique++;
+ return false;
+ } else if (countingAlgorithm.equals(COUNTING_ALGORITHM_PROPORTIONAL)) {
+ readWeight = 1.0f / nh;
+ }
+ }
+
+ read.setAttribute(Constants.READ_WEIGHT_ATTR, readWeight);
+ return true;
+ }
+
+
+ public void run() throws Exception {
+
+ initRegions();
+
+ logger.logLine("Starting BAM file analysis\n");
+
+ if (pairedEndAnalysis) {
+ if (sortingRequired) {
+ logger.logLine("Sorting BAM file by name...\n");
+ pathToBamFile = sortSamByName(pathToBamFile);
+ }
+ }
+
+ SAMFileReader reader = new SAMFileReader(new File(pathToBamFile));
+
+ SAMRecordIterator iter = reader.iterator();
+ strandSpecificAnalysis = protocol != LibraryProtocol.NON_STRAND_SPECIFIC;
+
+ ArrayList<SAMRecord> fragmentReads = new ArrayList<SAMRecord>();
+ ArrayList<String> chr_names = new ArrayList<String>();
+ HashSet<String> notFoundChrNames = new HashSet<String>();
+
+ String curReadName = null;
+
+ while (iter.hasNext()) {
+
+ SAMRecord read = iter.next();
+
+ if (!checkRead(read)) {
+ if (!chr_names.contains(read.getReferenceName())) {
+ notFoundChrNames.add(read.getReferenceName());
+ chr_names.add(read.getReferenceName());
+ }
+ continue;
+ }
+
+ if(!computeReadWeight(read) ) {
+ continue;
+ }
+
+ if (pairedEndAnalysis && read.getReadPairedFlag() && read.getProperPairFlag()) {
+ String readName = read.getReadName();
+ if (curReadName == null || readName.equals( curReadName ) ) {
+ fragmentReads.add(read);
+ } else {
+ processFragment(fragmentReads);
+ fragmentReads.clear();
+ fragmentReads.add(read);
+ }
+ curReadName = readName;
+ } else {
+ processRead(read);
+ }
+
+ }
+
+ if (pairedEndAnalysis && fragmentReads.size() > 0) {
+ processFragment(fragmentReads);
+ }
+
+ if (notFoundChrNames.size() > 0) {
+ System.err.println("\nWARNING! The following chromosomes from reads are not found in annotations:");
+ for (String notFoundChrName : notFoundChrNames) {
+ System.err.println(notFoundChrName);
+ }
+ }
+
+ if (readCount == 0) {
+ throw new RuntimeException("BAM file is empty.");
+ }
+
+ if (seqNotFoundCount + alignmentNotUnique == readCount) {
+ throw new RuntimeException("The BAM file and annotations file have no intersections. " +
+ "Check sequence names for consistency.");
+ }
+
+
+ if (collectRnaSeqStats) {
+ transcriptDataHandler.calculateCoverageBias();
+ }
+
+ logger.logLine("\nProcessed " + readCount + " reads in total");
+
+ if (cleanupRequired) {
+ logger.logLine("\nCleanup of temporary files");
+ FileUtils.deleteQuietly(new File(pathToBamFile));
+ }
+
+ logger.logLine("\nBAM file analysis finished");
+
+ }
+
+
+ void initRegions() throws Exception {
+
+ FeatureFileFormat format = DocumentUtils.guessFeaturesFileFormat(pathToGffFile);
+
+ if (format == FeatureFileFormat.UNKNOWN) {
+ throw new RuntimeException("Failed to detect annotations file format.");
+ }
+
+ if (format == FeatureFileFormat.GTF) {
+ loadRegionsFromGTF();
+ } else {
+ loadGenericRegions(format);
+ }
+
+ }
+
+ void loadGenericRegions(FeatureFileFormat format) throws Exception {
+
+ logger.logLine("Detected non-GTF annotations file. The counting will " +
+ "be performed based only on feature name");
+
+ if (collectRnaSeqStats) {
+ throw new RuntimeException("Calculating coverage bias is only available for GTF files. " +
+ "Please change your annotations file.");
+ }
+
+ GenomicFeatureStreamReader parser = new GenomicFeatureStreamReader(pathToGffFile, format);
+ logger.logLine("Initializing regions from " + pathToGffFile + "...\n");
+
+ chromosomeRegionSetMap = new HashMap<String, GenomicRegionSet>();
+ readCounts = new HashMap<String, Double>();
+
+ GenomicFeature record;
+ int recordCount = 0;
+ while((record = parser.readNextRecord())!=null){
+ recordCount++;
+ if (recordCount % 100000 == 0) {
+ logger.logLine("Initialized " + recordCount + " regions...");
+ }
+ addRegionToIntervalMap(record,false);
+
+ // init results map
+ readCounts.put(record.getFeatureName(), 0.0);
+}
+
+ if (chromosomeRegionSetMap.isEmpty()) {
+ throw new RuntimeException("Unable to load any regions from file.");
+ }
+
+ logger.logLine("\nInitialized " + recordCount + " regions it total\n\n");
+ loadGenericRegions = true;
+
+ parser.close();
+ }
+
+ void loadRegionsFromGTF() throws IOException, NoSuchMethodException, FileFormatException {
+
+ if (allowedFeatureList.isEmpty()) {
+ // default feature to consider
+ addSupportedFeatureType("exon");
+ }
+
+ GenomicFeatureStreamReader gtfParser = new GenomicFeatureStreamReader(pathToGffFile, FeatureFileFormat.GTF);
+ logger.logLine("Initializing regions from " + pathToGffFile + "...\n");
+
+ chromosomeRegionSetMap = new HashMap<String, GenomicRegionSet>();
+ readCounts = new HashMap<String, Double>();
+
+ if (collectRnaSeqStats) {
+ transcriptDataHandler = new TranscriptDataHandler();
+ transcriptDataHandler.validateAttributes(attrName, allowedFeatureList);
+ }
+
+ GenomicFeature record;
+ int recordCount = 0;
+ while((record = gtfParser.readNextRecord())!=null){
+
+ for (String featureType: allowedFeatureList) {
+ recordCount++;
+ if (recordCount % 100000 == 0) {
+ logger.logLine("Initialized " + recordCount + " regions...");
+ }
+ if (record.getFeatureName().equalsIgnoreCase(featureType)) {
+ addRegionToIntervalMap(record, true);
+ // init results map
+ readCounts.put(record.getAttribute(attrName), 0.0);
+ if (collectRnaSeqStats) {
+ transcriptDataHandler.addExonFeature(record);
+ }
+ break;
+ }
+
+ }
+ }
+
+ if (chromosomeRegionSetMap.isEmpty()) {
+ throw new RuntimeException("Unable to load any regions from file.");
+ }
+
+ logger.logLine("\nInitialized " + recordCount + " regions it total");
+
+ if (collectRnaSeqStats) {
+ logger.logLine("\nStarting constructing transcripts for RNA-seq stats...");
+ transcriptDataHandler.constructTranscriptsMap();
+ logger.logLine("Finished constructing transcripts\n");
+
+ }
+
+
+ gtfParser.close();
+
+ }
+
+
+
+ void addRegionToIntervalMap(GenomicFeature feature, boolean useAttributeForCounting) {
+
+ GenomicRegionSet regionSet = chromosomeRegionSetMap.get(feature.getSequenceName());
+ if (regionSet == null) {
+ regionSet = new GenomicRegionSet();
+ chromosomeRegionSetMap.put(feature.getSequenceName(), regionSet);
+ }
+
+ String featureName = useAttributeForCounting ? feature.getAttribute(attrName) : feature.getFeatureName();
+
+ regionSet.addRegion(feature, featureName);
+
+
+ }
+
+
+ public Map<String,Double> getReadCounts() {
+ return readCounts;
+ }
+
+ public long getNotAlignedNumber() {
+ return notAligned;
+ }
+
+ public long getPrimaryAlignmentsNumber() {
+ return primaryAlignments;
+ }
+
+ public long getLeftProperInPair() {
+ return leftProperInPair;
+ }
+
+ public long getRightProperInPair() {
+ return rightProperInPair;
+ }
+
+ public long getTotalAlignmentsNumber() {
+ return primaryAlignments + secondaryAlignments;
+ }
+
+ public long getSecondaryAlignmentsNumber() {
+ return secondaryAlignments;
+ }
+
+ public long getNoFeatureNumber() {
+ return noFeature;
+ }
+
+ public long getAlignmentNotUniqueNumber() {
+ return alignmentNotUnique;
+ }
+
+ public long getAmbiguousNumber() {
+ return ambiguous;
+ }
+
+ public long getNumberOfMappedPairs() {
+ return bothProperInPair / 2;
+ }
+
+
+ public StringBuilder getOutputStatsMessage() {
+ StringBuilder message = new StringBuilder();
+ message.append("Feature ");
+ if (!loadGenericRegions) {
+ message.append("\"").append(attrName).append("\" ");
+ }
+ message.append("counts: ").append(getTotalReadCounts()).append("\n");
+ message.append("No feature: ").append(noFeature).append("\n");
+ message.append("Not unique alignment: ");
+ if (countingAlgorithm.equals(COUNTING_ALGORITHM_ONLY_UNIQUELY_MAPPED)){
+ message.append(alignmentNotUnique).append("\n");
+ } else {
+ message.append("NA\n");
+ }
+ message.append("Ambiguous: ").append(ambiguous).append("\n");
+
+ if (loadGenericRegions) {
+ message.append("NOTE: features were computed based on feature name\n");
+ }
+
+ if (collectRnaSeqStats) {
+ message.append("Median 5' bias: ").append( transcriptDataHandler.getMedianFivePrimeBias() ).append("\n");
+ message.append("Median 3' bias: ").append( transcriptDataHandler.getMedianThreePrimeBias() ).append("\n");
+ message.append("Median 5' to 3' bias: ").append(transcriptDataHandler.getMedianFiveToThreeBias());
+ message.append("\n");
+ }
+
+
+ return message;
+ }
+
+ public long getTotalReadCounts() {
+ long totalCount = 0;
+ for ( Double count: readCounts.values()) {
+ totalCount += count;
+ }
+
+ return totalCount;
+ }
+
+
+ public void setAttrName(String attrName) {
+ this.attrName = attrName;
+ }
+
+ public void setCountingAlgorithm(String countingAlgorithm) {
+ this.countingAlgorithm = countingAlgorithm;
+ }
+
+ /*public void saveCoverage(String fileName) throws IOException {
+ if ( transcriptDataHandler != null ) {
+ transcriptDataHandler.outputTranscriptsCoverage(fileName);
+ }
+ }*/
+
+ public TranscriptDataHandler getTranscriptDataHandler() {
+ return transcriptDataHandler;
+ }
+
+ public void setPairedEndAnalysis() {
+ pairedEndAnalysis = true;
+ }
+
+ public static boolean supportedLibraryProtocol(String protocolName) {
+ return (protocolName.equals(LibraryProtocol.PROTOCOL_FORWARD_STRAND) ||
+ protocolName.equals(LibraryProtocol.PROTOCOL_REVERSE_STRAND) ||
+ protocolName.equals(LibraryProtocol.PROTOCOL_NON_STRAND_SPECIFIC) );
+ }
+
+
+ public void setSortingRequired() {
+ sortingRequired = true;
+ }
+
+ /*public LibraryProtocol getLibraryProtocol() {
+ return protocol;
+ }
+
+ public long getTotalFragmentCount() {
+ return fragmentCount;
+ }
+
+ public long getProtocolCorrectlyMapped() {
+ return protocolCorrectlyMapped;
+ }*/
+
+ public String getSampleName() {
+ return sampleName;
+ }
+
+ public LoggerThread getLogger() {
+ return logger;
+ }
+}
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/process/CountsQcAnalysis.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/process/CountsQcAnalysis.java
new file mode 100644
index 0000000..2f51b13
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/process/CountsQcAnalysis.java
@@ -0,0 +1,338 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.process;
+
+import org.bioinfo.ngs.qc.qualimap.beans.AnalysisResultManager;
+import org.bioinfo.ngs.qc.qualimap.beans.QChart;
+import org.bioinfo.ngs.qc.qualimap.beans.StatsReporter;
+import org.bioinfo.ngs.qc.qualimap.common.AppSettings;
+import org.bioinfo.ngs.qc.qualimap.common.LoggerThread;
+
+import javax.imageio.ImageIO;
+import java.awt.image.BufferedImage;
+import java.io.*;
+import java.util.*;
+
+
+/**
+ * Created by kokonech
+ * Date: 5/15/14
+ * Time: 4:03 PM
+ */
+public class CountsQcAnalysis extends AnalysisProcess{
+
+ List<CountsSampleInfo> samples;
+ Map<Integer,String> conditionNames;
+ boolean reportProgress, compareConditions;
+ String inputFilePath, infoFilePath;
+ int numSamples;
+
+ static final String COMPARISON_ANALYSIS = "Comparison";
+ private int countsThreshold;
+
+ public CountsQcAnalysis(AnalysisResultManager tabProperties,
+ String homePath,
+ List<CountsSampleInfo> samples) {
+ super(tabProperties, homePath);
+ this.samples = samples;
+ this.reportProgress = false;
+ this.compareConditions = false;
+ this.inputFilePath = "";
+ this.infoFilePath = "";
+ this.countsThreshold = 0;
+ this.numSamples = samples.size();
+ }
+
+
+ private void setupInputDataDescription(String workDir) throws IOException {
+
+ if (conditionNames.isEmpty()) {
+ throw new IOException("The condition names are not set! Can not setup input data description");
+ }
+
+ inputFilePath = workDir + File.separator + "input.txt";
+ PrintWriter outWriter = new PrintWriter(new FileWriter(inputFilePath));
+
+ outWriter.write("#Sample\tCondition\tPath\tColumn\n");
+
+ for (CountsSampleInfo sampleInfo : samples) {
+ outWriter.write(sampleInfo.name + "\t");
+ String conditionName = conditionNames.get(sampleInfo.conditionIndex);
+ outWriter.write(conditionName + "\t");
+ outWriter.write(sampleInfo.path + "\t");
+ outWriter.write(sampleInfo.columnNum + "\n");
+ }
+
+ outWriter.close();
+ }
+
+
+ @Override
+ public void run() throws Exception {
+
+ String workDir = tabProperties.createDirectory().toString();
+
+
+ removeSpacesFromNames();
+ setupInputDataDescription(workDir);
+
+ String commandString = createCommand(workDir);
+ if (loggerThread != null) {
+ loggerThread.logLine(commandString);
+ }
+
+ //reportProgress("Running R script");
+ Process p = Runtime.getRuntime().exec(commandString);
+
+ if (loggerThread != null) {
+ BufferedReader outputReader = new BufferedReader( new InputStreamReader(
+ new SequenceInputStream( p.getInputStream(), p.getErrorStream() )
+ ) );
+ loggerThread.start(outputReader);
+ }
+
+ int res = p.waitFor();
+
+ if (loggerThread != null) {
+ loggerThread.join();
+ }
+
+ if (res != 0) {
+ throw new RuntimeException("The RScript process finished with error.\n" +
+ " Check log for details.");
+ }
+
+ StatsReporter statsReporter = new StatsReporter();
+ statsReporter.setName("Global");
+ statsReporter.setFileName( "GlobalReport" );
+
+ if (!loadBufferedImages(statsReporter, workDir) ) {
+ throw new RuntimeException("No plots for global analysis generated.");
+ }
+
+ prepareInputDescription(statsReporter);
+ tabProperties.addReporter(statsReporter);
+
+
+ if (compareConditions) {
+ String compareDirPath = workDir + File.separator + COMPARISON_ANALYSIS;
+ StatsReporter reporter = new StatsReporter();
+ reporter.setName(COMPARISON_ANALYSIS);
+ reporter.setFileName( COMPARISON_ANALYSIS + "Report");
+ if (!loadBufferedImages(reporter, compareDirPath) ) {
+ throw new RuntimeException("No images generated for comparison of conditions!");
+ }
+ tabProperties.addReporter(reporter);
+ }
+
+
+ for (CountsSampleInfo sampleInfo : samples) {
+
+ String sampleDirPath = workDir + File.separator + sampleInfo.name;
+ StatsReporter reporter = new StatsReporter();
+ reporter.setName(sampleInfo.name);
+ reporter.setFileName( sampleInfo.name.replaceAll("\\s+","") + "Report");
+ if (!loadBufferedImages(reporter, sampleDirPath) ) {
+ throw new RuntimeException("No images generated for sample " + sampleInfo.name);
+ }
+ tabProperties.addReporter(reporter);
+
+ }
+
+
+
+
+ }
+
+ private void removeSpacesFromNames() {
+
+ //Replaces are performed because of the problem with NOISeq: "-" symbol or spaces should be removed
+
+ for (SampleInfo s : samples) {
+ s.name = s.name.replaceAll("\\s", "_");
+ s.name = s.name.replaceAll("-", "_");
+ if (Character.isDigit(s.name.charAt(0))) {
+ String novelName = "sample_" + s.name;
+ System.err.printf("WARNING: The sample name \"" + s.name + "\" will be replaced with name \""
+ + novelName + "\" due to NOISeq issues\n" );
+ s.name = novelName;
+ }
+
+ }
+
+
+
+ for (Integer index : conditionNames.keySet()) {
+ String cName = conditionNames.get(index);
+ conditionNames.put(index, cName.replaceAll("\\s", "_"));
+ }
+
+ }
+
+ private boolean loadBufferedImages(StatsReporter statsReporter, String outDir) throws IOException {
+
+ List<QChart> chartList = new ArrayList<QChart>();
+ int imageCount = 0;
+
+ File dir = new File(outDir);
+ if (!dir.exists() || !dir.isDirectory()) {
+ return false;
+ }
+
+ File[] children = dir.listFiles();
+ Arrays.sort(children);
+
+ for (File child : children ) {
+ String fileName = child.getName();
+ if (fileName.endsWith(".png")) {
+ String imageName = fileName.subSequence(3, fileName.length() - 4).toString().replace('_',' ');
+ BufferedImage image = ImageIO.read(new FileInputStream(child));
+ chartList.add(new QChart(imageName, imageName, image) );
+ imageCount++;
+ }
+ }
+
+ if (imageCount == 0) {
+ return false;
+ }
+
+ statsReporter.setChartList(chartList);
+
+ return true;
+
+ }
+
+ private String createCommand(String workDir) {
+ String pathToRscript = AppSettings.getGlobalSettings().getPathToRScript();
+ String commandString = pathToRscript + " " + homePath
+ + File.separator + "scripts"+ File.separator + "countsQC.r";
+
+ commandString += " --homedir " + homePath + File.separator + "scripts";
+ commandString += " --input " + inputFilePath;
+ commandString += " -k " + countsThreshold;
+ if (!infoFilePath.isEmpty()) {
+ commandString += " --info " + infoFilePath;
+ }
+
+ if (compareConditions) {
+ commandString += " --compare";
+ }
+ commandString += " -o " + workDir;
+
+ return commandString;
+ }
+
+ protected void prepareInputDescription(StatsReporter reporter) {
+
+ /*HashMap<String,String> locationParams = new HashMap<String, String>();
+ locationParams.put("Upstream offset (bp): ", Integer.toString(cfg.leftOffset) );
+ locationParams.put("Downstream offset (bp): ", Integer.toString( cfg.rightOffset) );
+ locationParams.put("Bin size: ", Integer.toString( cfg.binSize ));
+ reporter.addInputDataSection("Location: ", locationParams);*/
+
+
+ HashMap<String,String> sampleParams = new HashMap<String, String>();
+ for ( CountsSampleInfo info : samples ) {
+ String conditionName = conditionNames.get(info.conditionIndex);
+ sampleParams.put(info.name + " " + conditionName , info.path );
+ }
+ reporter.addInputDataSection("Samples", sampleParams);
+
+ HashMap<String,String> otherParams = new HashMap<String, String>();
+ otherParams.put("Species info: ", infoFilePath);
+ otherParams.put("Counts threshold: ", "" + countsThreshold );
+ reporter.addInputDataSection("Options", otherParams);
+
+
+
+ }
+
+ public void setConditionNames(Map<Integer,String> cMap) {
+ conditionNames = cMap;
+ }
+
+ public void setOutputParsingThread(LoggerThread outputParsingThread) {
+ this.loggerThread = outputParsingThread;
+ }
+
+ public void setInfoFilePath(String infoFilePath) {
+ this.infoFilePath = infoFilePath;
+ }
+
+ public static List<CountsSampleInfo> parseInputFile(String inputFilePath,
+ ArrayList<String> conditionsList) throws IOException {
+
+ ArrayList<CountsSampleInfo> res = new ArrayList<CountsSampleInfo>();
+
+ BufferedReader bufferedReader = new BufferedReader(new FileReader(inputFilePath));
+ String line;
+ while ( (line = bufferedReader.readLine()) != null) {
+ if (line.startsWith("#") || line.isEmpty()) {
+ continue;
+ }
+ String[] items = line.split("\\t+");
+ if (items.length < 4) {
+ throw new IOException("Failed to parse input file " + inputFilePath+
+ " not enough fields in line " + line);
+ }
+
+ CountsSampleInfo info = new CountsSampleInfo();
+ info.name = items[0];
+ String conditionName = items[1];
+ if (!conditionsList.contains(conditionName)) {
+ conditionsList.add(conditionName);
+ }
+ info.conditionIndex = conditionsList.indexOf(conditionName) + 1;
+ if (info.conditionIndex > 2) {
+ throw new IOException("More than 2 conditions detected in the input file!");
+ }
+
+ info.path = items[2];
+ if (! (new File(info.path)).exists() ) {
+ String absPath = new File(inputFilePath).getParent() + File.separator + info.path;
+ if (new File(absPath).exists()) {
+ info.path = absPath;
+ } else {
+ throw new IOException("Sample " + info.name + ": file " + info.path + " doesn't exist!");
+ }
+ }
+
+ info.columnNum = Integer.parseInt( items[3] );
+ res.add( info );
+
+ }
+
+ return res;
+
+ }
+
+ public void activateComparison() {
+ this.compareConditions = true;
+ }
+
+ public void setInputFilePath(String filePath) {
+ this.inputFilePath = filePath;
+ }
+
+ public void setThreshold(int k) {
+ this.countsThreshold = k;
+ }
+}
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/process/CountsSampleInfo.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/process/CountsSampleInfo.java
new file mode 100644
index 0000000..94ef706
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/process/CountsSampleInfo.java
@@ -0,0 +1,40 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.process;
+
+/**
+* Created by kokonech
+* Date: 5/15/14
+* Time: 4:25 PM
+*/
+public class CountsSampleInfo extends SampleInfo {
+
+ public int columnNum;
+ public int conditionIndex;
+
+ public static final int DEFAULT_COLUMN = 2;
+
+ public CountsSampleInfo() {
+ columnNum = DEFAULT_COLUMN;
+ conditionIndex = 1;
+ }
+
+}
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/process/EpiAnalysis.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/process/EpiAnalysis.java
new file mode 100644
index 0000000..5ececdc
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/process/EpiAnalysis.java
@@ -0,0 +1,430 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.process;
+
+import org.bioinfo.formats.core.feature.Gff;
+import org.bioinfo.formats.core.feature.io.GffReader;
+import org.bioinfo.ngs.qc.qualimap.beans.AnalysisResultManager;
+import org.bioinfo.ngs.qc.qualimap.beans.QChart;
+import org.bioinfo.ngs.qc.qualimap.beans.StatsReporter;
+import org.bioinfo.ngs.qc.qualimap.common.AppSettings;
+import org.bioinfo.ngs.qc.qualimap.common.Constants;
+import org.bioinfo.ngs.qc.qualimap.common.LoggerThread;
+
+import javax.imageio.ImageIO;
+import javax.swing.*;
+import javax.xml.stream.XMLOutputFactory;
+import javax.xml.stream.XMLStreamWriter;
+import java.awt.image.BufferedImage;
+import java.io.*;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+
+/**
+ * Created by kokonech
+ * Date: 3/9/12
+ * Time: 1:14 PM
+ */
+public class EpiAnalysis {
+
+
+ static final String TAG_PARAMETERS = "parameters";
+ static final String TAG_EXP_ID = "expID";
+ static final String TAG_REGIONS = "regions";
+ static final String TAG_LOCATION = "location";
+ static final String TAG_UP = "up";
+ static final String TAG_DOWN = "down";
+ static final String TAG_FREQ = "freq";
+ static final String TAG_SAMPLES = "samples";
+ static final String TAG_REPLICATE = "replicate";
+ static final String TAG_MEDIPS = "medips";
+ static final String TAG_NAME = "name";
+ static final String TAG_INPUT = "input";
+ //static final String TAG_MICROARRAY = "microarray";
+ //static final String TAG_THRESHOLD = "threshold";
+ static final String TAG_CLUSTERS = "clusters";
+ static final String TAG_NUM = "num";
+ static final String TAG_FRAGMENT = "fragment";
+ static final String TAG_DIR_OUT ="dirOut";
+
+
+
+ static public class ReplicateItem {
+ public String name;
+ public String medipPath;
+ public String inputPath;
+ }
+
+
+ static public class Config {
+
+ public List<ReplicateItem> replicates;
+ public String pathToRegions;
+ public int leftOffset, rightOffset, binSize;
+ public int fragmentLength;
+ public String clusters, vizType, experimentName;
+
+ public Config() {
+ replicates = new ArrayList<ReplicateItem>();
+ leftOffset = 2000;
+ rightOffset = 500;
+ binSize = 100;
+ fragmentLength = 300;
+ clusters = "10,15,20,25,30";
+ pathToRegions = "";
+ vizType = Constants.VIZ_TYPE_HEATMAP;
+ experimentName = "Experiment";
+ }
+ }
+
+ AnalysisResultManager tabProperties;
+ Config cfg;
+ LoggerThread outputParsingThread;
+ JLabel progressStream;
+ String homePath;
+
+
+ public EpiAnalysis(AnalysisResultManager tabProperties, String homePath, Config cfg) {
+ this.tabProperties = tabProperties;
+ this.cfg = cfg;
+ this.homePath = homePath;
+ this.outputParsingThread = null;
+ this.progressStream = null;
+ }
+
+
+ public void run() throws Exception {
+
+ String workDir = tabProperties.createDirectory().toString();
+
+ setupAnnotationsFile(workDir);
+
+
+ reportProgress("Generating configuration file...");
+ createConfigFile(workDir, "config.xml");
+
+ // Create the command to execute
+ String commandString = createCommand(workDir);
+ if (outputParsingThread != null) {
+ outputParsingThread.logLine(commandString);
+ }
+
+ reportProgress("Running R script");
+ Process p = Runtime.getRuntime().exec(commandString);
+
+ if (outputParsingThread != null) {
+ BufferedReader outputReader = new BufferedReader( new InputStreamReader(
+ new SequenceInputStream( p.getInputStream(), p.getErrorStream() )
+ ) );
+ outputParsingThread.start(outputReader);
+ }
+
+ int res = p.waitFor();
+
+ if (outputParsingThread != null) {
+ outputParsingThread.join();
+ }
+
+ if (res != 0) {
+ throw new RuntimeException("The RScript process finished with error.\n" +
+ " Check log for details.");
+ }
+
+ reportProgress("Loading images...");
+ StatsReporter statsReporter = new StatsReporter();
+ if (!loadBufferedImages(statsReporter, workDir) ) {
+ throw new RuntimeException("No images generated.");
+ }
+
+ prepareInputDescription(statsReporter);
+
+ tabProperties.addReporter(statsReporter);
+
+ }
+
+ private void setupAnnotationsFile(String workDir) throws Exception {
+ if (cfg.pathToRegions.endsWith("gff")) {
+ // we have gff file -> convert it to BED
+ String bedFile = workDir + "/file.bed";
+ PrintWriter outWriter = new PrintWriter( new FileWriter(bedFile) );
+
+ GffReader gffReader = new GffReader(cfg.pathToRegions);
+ Gff region;
+
+ int numLines = 0;
+
+ while((region = gffReader.read())!=null){
+ StringBuilder buf = new StringBuilder();
+ buf.append(region.getSequenceName()).append("\t");
+ buf.append(region.getStart()).append("\t");
+ buf.append(region.getEnd()).append("\t");
+ buf.append(region.getFeature()).append("\t");
+ buf.append(region.getScore()).append("\t");
+ buf.append(region.getStrand()).append("\n");
+ outWriter.print(buf.toString());
+ numLines++;
+ }
+
+ outWriter.close();
+ if (numLines == 0) {
+ throw new RuntimeException("Failed to process GFF file, make sure it is correctly formatted");
+ }
+
+ cfg.pathToRegions = bedFile;
+ }
+ }
+
+ String createCommand(String outputDir) {
+ String pathToRscript = AppSettings.getGlobalSettings().getPathToRScript();
+ String commandString = pathToRscript + " " + homePath
+ + File.separator + "scripts"+ File.separator + "paintLocation.r";
+
+ commandString += " --fileConfig=" + outputDir + "config.xml";
+ commandString += " --homedir=" + homePath + File.separator + "scripts";
+ commandString += " --vizType=" + cfg.vizType;
+
+ return commandString;
+ }
+
+ void createConfigFile(String outDir, String configFileName) throws Exception {
+
+ FileOutputStream stream = new FileOutputStream(outDir + configFileName);
+
+ XMLOutputFactory outputFactory = XMLOutputFactory.newInstance();
+ XMLStreamWriter xmlWriter = outputFactory.createXMLStreamWriter(stream);
+
+ xmlWriter.writeStartDocument();
+ xmlWriter.writeCharacters("\n");
+
+ xmlWriter.writeStartElement(TAG_PARAMETERS);
+ xmlWriter.writeCharacters("\n\n\t");
+
+
+ // dirOut
+ xmlWriter.writeStartElement(TAG_DIR_OUT);
+ xmlWriter.writeCharacters(outDir);
+ xmlWriter.writeEndElement();
+ xmlWriter.writeCharacters("\n\n\t");
+
+ // expId
+ xmlWriter.writeStartElement(TAG_EXP_ID);
+ xmlWriter.writeCharacters(cfg.experimentName);
+ xmlWriter.writeEndElement();
+ xmlWriter.writeCharacters("\n\n\t");
+
+
+ // gene selection
+ xmlWriter.writeStartElement(TAG_REGIONS);
+ xmlWriter.writeCharacters("\n\t\t");
+ xmlWriter.writeCharacters(cfg.pathToRegions);
+ xmlWriter.writeEndElement();
+ xmlWriter.writeCharacters("\n\n\t");
+
+ //location
+ xmlWriter.writeStartElement(TAG_LOCATION);
+ xmlWriter.writeCharacters("\n\t\t");
+ xmlWriter.writeStartElement(TAG_UP);
+ xmlWriter.writeCharacters(Integer.toString(cfg.leftOffset));
+ xmlWriter.writeEndElement();
+ xmlWriter.writeCharacters("\n\t\t");
+ xmlWriter.writeStartElement(TAG_DOWN);
+ xmlWriter.writeCharacters(Integer.toString(cfg.rightOffset));
+ xmlWriter.writeEndElement();
+ xmlWriter.writeCharacters("\n\t\t");
+ xmlWriter.writeStartElement(TAG_FREQ);
+ xmlWriter.writeCharacters(Integer.toString(cfg.binSize));
+ xmlWriter.writeEndElement();
+ xmlWriter.writeCharacters("\n\t");
+ xmlWriter.writeEndElement();
+ xmlWriter.writeCharacters("\n\n\t");
+
+ // samples
+ xmlWriter.writeStartElement(TAG_SAMPLES);
+
+ xmlWriter.writeCharacters("\n\t\t");
+ xmlWriter.writeStartElement("sample1");
+ List<EpiAnalysis.ReplicateItem> sampleItems = cfg.replicates;
+ for (EpiAnalysis.ReplicateItem item : sampleItems) {
+ xmlWriter.writeCharacters("\n\t\t\t");
+ xmlWriter.writeStartElement(TAG_REPLICATE);
+
+ xmlWriter.writeCharacters("\n\t\t\t\t");
+ xmlWriter.writeStartElement(TAG_MEDIPS);
+ xmlWriter.writeCharacters(item.medipPath);
+ xmlWriter.writeEndElement();
+ xmlWriter.writeCharacters("\n\t\t\t\t");
+ xmlWriter.writeStartElement(TAG_INPUT);
+ xmlWriter.writeCharacters(item.inputPath);
+ xmlWriter.writeEndElement();
+ xmlWriter.writeCharacters("\n\t\t\t\t");
+ xmlWriter.writeStartElement(TAG_NAME);
+ xmlWriter.writeCharacters(item.name);
+ xmlWriter.writeEndElement();
+ xmlWriter.writeCharacters("\n\t\t\t");
+ xmlWriter.writeEndElement();
+ }
+ xmlWriter.writeCharacters("\n\t\t");
+ xmlWriter.writeEndElement();
+
+
+
+ xmlWriter.writeCharacters("\n\t");
+ xmlWriter.writeEndElement();
+
+ // MAYBE WILL BE INCLUDED IN FUTURE VERSIONS
+ /*if (settingsDialog.microArrayDataAvailable()) {
+ xmlWriter.writeCharacters("\n\n\t");
+ xmlWriter.writeStartElement(TAG_MICROARRAY);
+
+ xmlWriter.writeCharacters("\n\t\t");
+ xmlWriter.writeStartElement(TAG_FILE);
+ xmlWriter.writeCharacters(settingsDialog.getMicroArrayDataPath());
+ xmlWriter.writeEndElement();
+
+ String[] thresholds = settingsDialog.getMicroArrayThresholds();
+
+ for (String threshold : thresholds) {
+ xmlWriter.writeCharacters("\n\t\t");
+ xmlWriter.writeStartElement(TAG_THRESHOLD);
+ xmlWriter.writeCharacters(threshold);
+ xmlWriter.writeEndElement();
+ }
+ xmlWriter.writeCharacters("\n\t");
+ xmlWriter.writeEndElement();
+ }*/
+
+ xmlWriter.writeCharacters("\n\n\t");
+ xmlWriter.writeStartElement(TAG_CLUSTERS);
+
+ String[] clusters = cfg.clusters.split(",");
+
+ for (String numClusters : clusters) {
+ xmlWriter.writeCharacters("\n\t\t");
+ xmlWriter.writeStartElement(TAG_NUM);
+ xmlWriter.writeCharacters(numClusters);
+ xmlWriter.writeEndElement();
+ }
+ xmlWriter.writeCharacters("\n\t");
+ xmlWriter.writeEndElement();
+
+ xmlWriter.writeCharacters("\n\n\t");
+ xmlWriter.writeStartElement(TAG_FRAGMENT);
+ xmlWriter.writeCharacters(Integer.toString(cfg.fragmentLength));
+
+ xmlWriter.writeEndElement();
+
+ xmlWriter.writeCharacters("\n\n");
+ xmlWriter.writeEndElement(); // parameters
+ xmlWriter.writeCharacters("\n");
+
+
+ xmlWriter.writeEndDocument();
+
+ xmlWriter.close();
+
+ stream.close();
+
+
+
+ }
+
+
+ void reportProgress(String msg) {
+ if (progressStream == null) {
+ System.out.println(msg);
+ } else {
+ progressStream.setText(msg);
+ }
+
+ }
+
+
+ public static boolean loadBufferedImages(StatsReporter reporter, String outDir) throws IOException {
+
+ List<QChart> chartList = new ArrayList<QChart>();
+ int imageCount = 0;
+
+ File dir = new File(outDir);
+ if (!dir.exists() || !dir.isDirectory()) {
+ return false;
+ }
+ for (File child : dir.listFiles()) {
+ String fileName = child.getName();
+ if (fileName.endsWith(".jpg")) {
+ String imageName = fileName.subSequence(0, fileName.length() - 4).toString();
+ BufferedImage image = ImageIO.read(new FileInputStream(child));
+ chartList.add(new QChart(imageName, imageName, image) );
+ imageCount++;
+ }
+ }
+
+ if (imageCount == 0) {
+ return false;
+ }
+
+ reporter.setChartList(chartList);
+
+ return true;
+
+ }
+
+ private void prepareInputDescription(StatsReporter reporter) {
+
+ HashMap<String,String> selectionParams = new HashMap<String, String>();
+ selectionParams.put("Name: ", cfg.experimentName);
+ selectionParams.put("Path to regions file: ", cfg.pathToRegions);
+ reporter.addInputDataSection("Experiment", selectionParams);
+
+ HashMap<String,String> locationParams = new HashMap<String, String>();
+ locationParams.put("Upstream offset (bp): ", Integer.toString(cfg.leftOffset) );
+ locationParams.put("Downstream offset (bp): ", Integer.toString( cfg.rightOffset) );
+ locationParams.put("Bin size: ", Integer.toString( cfg.binSize ));
+ reporter.addInputDataSection("Location: ", locationParams);
+
+ List<EpiAnalysis.ReplicateItem> items = cfg.replicates;
+
+ for ( EpiAnalysis.ReplicateItem item : items ) {
+ HashMap<String,String> sampleParams = new HashMap<String, String>();
+ sampleParams.put("Sample file: ", item.medipPath );
+ sampleParams.put("Control file: ", item.inputPath );
+ reporter.addInputDataSection("Sample " + item.name, sampleParams);
+ }
+
+ HashMap<String,String> otherParams = new HashMap<String, String>();
+ otherParams.put("Thresholds: ", cfg.clusters );
+ otherParams.put("Smoothing length: ", Integer.toString(cfg.fragmentLength));
+ otherParams.put("Visualization: ", cfg.vizType );
+ reporter.addInputDataSection("Options", otherParams);
+
+ }
+
+ public void setOutputParsingThread(LoggerThread outputParsingThread) {
+ this.outputParsingThread = outputParsingThread;
+ }
+
+ public void setProgressStream(JLabel progressStream) {
+ this.progressStream = progressStream;
+ }
+
+
+
+}
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/process/FinalizeWindowTask.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/process/FinalizeWindowTask.java
new file mode 100644
index 0000000..2831958
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/process/FinalizeWindowTask.java
@@ -0,0 +1,59 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.process;
+
+import org.bioinfo.ngs.qc.qualimap.beans.BamGenomeWindow;
+import org.bioinfo.ngs.qc.qualimap.beans.BamStats;
+
+import java.util.concurrent.Callable;
+
+/**
+ * Created by kokonech
+ * Date: 11/7/11
+ * Time: 6:12 PM
+ */
+
+public class FinalizeWindowTask implements Callable<Integer> {
+
+
+ BamStats bamStats;
+ BamGenomeWindow window;
+
+ public FinalizeWindowTask(BamStats bamStats, BamGenomeWindow windowToFinalize) {
+ this.bamStats = bamStats;
+ this.window = windowToFinalize;
+ }
+
+ public Integer call() {
+
+ try {
+ window.computeDescriptors();
+ bamStats.addWindowInformation(window);
+ } catch (CloneNotSupportedException e) {
+ e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates.
+ return -1;
+ }
+
+ return 0;
+ }
+
+
+}
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/process/MultisampleBamQcAnalysis.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/process/MultisampleBamQcAnalysis.java
new file mode 100644
index 0000000..4d733c4
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/process/MultisampleBamQcAnalysis.java
@@ -0,0 +1,613 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.process;
+
+import org.apache.commons.io.FilenameUtils;
+import org.apache.commons.math.stat.descriptive.DescriptiveStatistics;
+import org.bioinfo.ngs.qc.qualimap.beans.*;
+import org.bioinfo.ngs.qc.qualimap.common.AnalysisType;
+import org.bioinfo.ngs.qc.qualimap.common.LoggerThread;
+import org.bioinfo.ngs.qc.qualimap.gui.threads.ExportHtmlThread;
+import org.bioinfo.ngs.qc.qualimap.gui.utils.StatsKeeper;
+import org.jfree.chart.ChartColor;
+
+import java.awt.*;
+import java.io.*;
+import java.util.*;
+import java.util.List;
+
+/**
+ * Created by kokonech
+ * Date: 6/5/14
+ * Time: 12:45 PM
+ */
+public class MultisampleBamQcAnalysis extends AnalysisProcess{
+
+
+ List<SampleInfo> bamQCResults;
+ List<double[]> sampleData;
+ LoggerThread loggerThread;
+ Paint[] palette;
+ Map<SampleInfo,String> rawDataDirs;
+ boolean runBamQcFirst;
+ BamStatsAnalysisConfig bamQcConfig;
+
+ static final int NUM_FEATURES = 5;
+
+ public MultisampleBamQcAnalysis(AnalysisResultManager tabProperties,
+ String homePath,
+ List<SampleInfo> bamQCResults) {
+ super(tabProperties, homePath);
+ this.bamQCResults = bamQCResults;
+ this.palette = ChartColor.createDefaultPaintArray();
+ this.rawDataDirs = new HashMap<SampleInfo, String>();
+ sampleData = new ArrayList<double[]>();
+
+ }
+
+ @Override
+ public void run() throws Exception {
+
+ if (runBamQcFirst) {
+ runBamQcOnSamples();
+ }
+
+ loggerThread.logLine("Running multi-sample BAM QC\n");
+
+ loggerThread.logLine("Checking input paths");
+ checkInputPaths();
+
+ StatsReporter reporter = new StatsReporter();
+ reporter.setFileName( "multisampleBamQcReport" );
+
+
+ prepareInputDescription(reporter);
+ loggerThread.logLine("Loading sample data");
+ createSummaryTable(reporter);
+ loggerThread.logLine("Creating charts");
+ createCharts(reporter);
+
+
+ tabProperties.addReporter(reporter);
+
+ }
+
+
+ public void setRunBamQcFirst(BamStatsAnalysisConfig cfg) {
+ this.runBamQcFirst = true;
+ this.bamQcConfig = cfg;
+ }
+
+
+ void initOutputDir(String outdir){
+
+ if(!outdir.isEmpty()){
+ if(new File(outdir).exists()){
+ loggerThread.logLine("Output directory already exists.");
+ } else {
+ boolean ok = new File(outdir).mkdirs();
+ if (!ok) {
+ loggerThread.logLine("Failed to create output directory.");
+ }
+ }
+ }
+ }
+
+
+ private void runBamQcOnSamples() throws Exception {
+
+ loggerThread.logLine("Running BAM QC on given samples\n");
+
+ for (SampleInfo s : bamQCResults) {
+
+ String bamFilePath = s.path;
+ loggerThread.logLine("Started processing " + bamFilePath + "\n\n");
+
+ String sampleOutdir = FilenameUtils.removeExtension(new File(bamFilePath).getAbsolutePath()) + "_stats";
+ initOutputDir(sampleOutdir);
+
+ loggerThread.updateProgress(0);
+ BamStatsAnalysis bamQC = new BamStatsAnalysis(bamFilePath);
+ bamQC.setConfig(bamQcConfig);
+ bamQC.setLoggerThread(loggerThread);
+ bamQC.run();
+
+ BamQCRegionReporter reporter = new BamQCRegionReporter(bamQcConfig.regionsAvailable(),false);
+ reporter.setPaintChromosomeLimits(bamQcConfig.drawChromosomeLimits);
+ reporter.writeReport(bamQC.getBamStats(),sampleOutdir);
+ reporter.loadReportData(bamQC.getBamStats());
+ reporter.computeChartsBuffers(bamQC.getBamStats(), bamQC.getLocator(), bamQC.isPairedData());
+
+ AnalysisResultManager resultManager = new AnalysisResultManager(AnalysisType.BAM_QC);
+ resultManager.addReporter(reporter);
+
+ Thread exportReportThread = new ExportHtmlThread(resultManager,sampleOutdir);
+ exportReportThread.run();
+ loggerThread.updateProgress(100);
+ loggerThread.logLine("Finished processing " + bamFilePath + "\n");
+ loggerThread.logLine("BAM QC results are saved to " + sampleOutdir + "\n");
+
+ s.path = sampleOutdir;
+
+ }
+ }
+
+
+ private BamStats loadSummaryStats(String inputFilePath) throws IOException {
+ BamStats bamStats = new BamStats(null,null, 0,0);
+
+ BufferedReader bufferedReader = new BufferedReader(new FileReader(inputFilePath));
+ String line;
+ while ( (line = bufferedReader.readLine()) != null) {
+ if (line.startsWith("#") || line.isEmpty()) {
+ continue;
+ }
+ if (line.contains("mean coverageData =")) {
+ double meanCoverage = Double.parseDouble( line.split("=")[1].trim().replaceAll("[X\\,]", "") );
+ bamStats.setCoverageMean(meanCoverage);
+ } else if (line.contains("std coverageData =")) {
+ double stdCoverage = Double.parseDouble(line.split("=")[1].trim().replaceAll("[X\\,]", ""));
+ bamStats.setCoverageStd(stdCoverage);
+ } else if (line.contains("mean mapping quality =")) {
+ double mappingQuality = Double.parseDouble(line.split("=")[1].trim().replaceAll("\\,",""));
+ bamStats.setMeanMappingQuality(mappingQuality);
+ } else if (line.contains("GC percentage =")) {
+ // This is actually in percents already - only should be used in the context of Multiple BAM QC
+ double gcPercentage = Double.parseDouble(line.split("=")[1].trim().replace("%", ""));
+ bamStats.setMeanGcContent(gcPercentage);
+ } else if (line.contains("median insert size =")) {
+ int insertSize = Integer.parseInt(line.split("=")[1].trim().replaceAll("\\,",""));
+ bamStats.setMedianInsertSize(insertSize);
+ }
+
+
+
+
+ }
+
+ return bamStats;
+
+ }
+
+
+ private void createSummaryTable(StatsReporter reporter) throws IOException {
+
+ logLine("Creating summary...\n");
+
+ StatsKeeper summaryKeeper = reporter.getSummaryStatsKeeper();
+
+ StatsKeeper.Section section = new StatsKeeper.Section("Globals");
+ section.addRow("Number of samples", Integer.toString( bamQCResults.size() ));
+ summaryKeeper.addSection(section);
+
+ StatsKeeper tableDataKeeper = reporter.getTableDataStatsKeeper();
+
+ StatsKeeper.Section headerSection = new StatsKeeper.Section("header");
+ String[] header = {"Sample name", "Coverage mean", "Coverage std",
+ "GC percentage", "Mapping quality mean", "Insert size median" };
+ headerSection.addRow( header );
+ tableDataKeeper.addSection(headerSection);
+
+ StatsKeeper.Section dataSection = new StatsKeeper.Section("data");
+
+ for (SampleInfo bamQcResult : bamQCResults) {
+ String path = bamQcResult.path + File.separator + "genome_results.txt";
+ BamStats stats = loadSummaryStats(path);
+
+ String[] row = new String[header.length];
+ row[0] = bamQcResult.name;
+ row[1] = Double.toString( stats.getMeanCoverage() );
+ row[2] = Double.toString( stats.getStdCoverage() );
+ row[3] = Double.toString( stats.getMeanGcRelativeContent() );
+ row[4] = Double.toString( stats.getMeanMappingQualityPerWindow() );
+ row[5] = Double.toString( stats.getMedianInsertSize() );
+ dataSection.addRow(row);
+
+ double[] sample = new double[NUM_FEATURES];
+ sample[0] = stats.getMeanCoverage();
+ sample[1] = stats.getStdCoverage();
+ sample[2] = stats.getMeanGcRelativeContent();
+ sample[3] = stats.getMeanMappingQualityPerWindow();
+ sample[4] = stats.getMedianInsertSize();
+ sampleData.add(sample);
+
+
+ }
+ tableDataKeeper.addSection(dataSection);
+
+
+
+ }
+
+
+ XYVector loadColumnData(File inputFile, double minX, double maxX, int dataColumn) throws IOException {
+ XYVector data = new XYVector();
+
+ BufferedReader bufferedReader = new BufferedReader(new FileReader(inputFile));
+ String line;
+ while ( (line = bufferedReader.readLine()) != null) {
+ if (line.startsWith("#") || line.isEmpty()) {
+ continue;
+ }
+
+ String[] items = line.split("\t");
+ if (items.length < dataColumn + 1) {
+ continue;
+ }
+
+ double d1 = Double.parseDouble(items[0]);
+ if (d1 < minX || d1 >= maxX) {
+ continue;
+ }
+ double d2 = Double.parseDouble(items[dataColumn]);
+
+ data.addItem( new XYItem(d1,d2));
+
+ }
+ return data;
+ }
+
+
+ Color getSampleColor(int idx) {
+ return (Color) palette[idx % palette.length];
+ }
+
+ QChart createHistogramBasedChart(String chartName, String dataPath, String xTitle, String yTitle) throws IOException {
+ return createHistogramBasedChart(chartName, dataPath, xTitle, yTitle, 0);
+ }
+
+
+ QChart createHistogramBasedChart(String chartName, String dataPath, String xTitle, String yTitle, int minXValue) throws IOException {
+ BamQCChart baseChart = new BamQCChart(chartName,
+ "Multi-sample BAM QC", xTitle, yTitle);
+
+ int i = 0;
+ for (SampleInfo bamQcResult : bamQCResults) {
+ String path = rawDataDirs.get(bamQcResult) + File.separator + dataPath;
+ File inputFile = new File(path);
+ if (!inputFile.exists()) {
+ continue;
+ }
+ XYVector histData = loadColumnData(inputFile, minXValue, Double.MAX_VALUE, 1);
+ if (histData.getSize() == 0) {
+ continue;
+ }
+ baseChart.addSeries(bamQcResult.name, histData, getSampleColor(i) );
+ ++i;
+ }
+
+ baseChart.render();
+
+ return new QChart(chartName, baseChart.getChart());
+ }
+
+ QChart createReadsGcContentChart(String chartName, String dataPath, String xTitle, String yTitle) throws IOException {
+ BamQCChart baseChart = new BamQCChart(chartName,
+ "Multi-sample BAM QC", xTitle, yTitle);
+
+ int i = 0;
+ for (SampleInfo bamQcResult : bamQCResults) {
+
+ File inputFile = new File( rawDataDirs.get(bamQcResult) + File.separator + dataPath );
+
+ if (!inputFile.exists()) {
+ continue;
+ }
+
+ XYVector cData = loadColumnData(inputFile, 0, Double.MAX_VALUE, 2);
+ XYVector gData = loadColumnData(inputFile, 0, Double.MAX_VALUE, 3);
+
+ if (cData.getSize() != gData.getSize()) {
+ continue;
+ }
+
+ XYVector gcData = new XYVector();
+ for (int j = 0; j < cData.getSize(); ++j) {
+ double pos = cData.get(j).getX();
+ double gc = cData.get(j).getY() + gData.get(j).getY();
+ gcData.addItem( new XYItem(pos,gc));
+ }
+
+ baseChart.addSeries(bamQcResult.name, gcData, getSampleColor(i));
+ ++i;
+ }
+
+ baseChart.render();
+
+ return new QChart(chartName, baseChart.getChart());
+ }
+
+
+
+ XYVector scaleXAxis(XYVector raw) {
+ XYVector scaled = new XYVector();
+
+
+ double scaleFactor = 1./raw.getSize();
+
+ for (int i = 0; i < raw.getSize(); ++i) {
+ XYItem item = raw.get(i);
+ XYItem newItem = new XYItem(scaleFactor*i, item.getY());
+ scaled.addItem(newItem);
+ }
+
+ return scaled;
+
+ }
+
+
+
+ QChart createCoverageAcrossReferenceChart() throws IOException {
+ BamQCChart baseChart = new BamQCChart("Coverage Across Reference",
+ "Multi-sample BAM QC", "Position in reference (relative)", "Coverage");
+
+ DescriptiveStatistics stats = new DescriptiveStatistics();
+ int k = 0;
+ for (SampleInfo bamQcResult : bamQCResults) {
+ String path = rawDataDirs.get(bamQcResult) + File.separator + "coverage_across_reference.txt";
+ XYVector rawData = loadColumnData(new File(path), 0, Double.MAX_VALUE, 1);
+ XYVector scaledData = scaleXAxis(rawData);
+ for (int i = 0; i < scaledData.getSize(); ++i) {
+ stats.addValue( scaledData.get(i).getY() );
+ }
+
+ baseChart.addSeries(bamQcResult.name, scaledData, getSampleColor(k) );
+ ++k;
+ }
+ baseChart.setDomainAxisIntegerTicks(false);
+
+ baseChart.render();
+ double p75 = stats.getPercentile(75);
+ if (p75 > 0) {
+ baseChart.getChart().getXYPlot().getRangeAxis().setRange(0, 2*p75);
+ }
+ stats.clear();
+
+ return new QChart("Coverage across reference", baseChart.getChart());
+ }
+
+ QChart createAcrossReferenceChart(String chartName, String dataPath, String yTitle) throws IOException {
+ BamQCChart baseChart = new BamQCChart(chartName,
+ "Multi-sample BAM QC", "Position in reference (relative)", yTitle);
+
+ int k = 0;
+ for (SampleInfo bamQcResult : bamQCResults) {
+ File dataFile = new File( rawDataDirs.get(bamQcResult) + File.separator + dataPath );
+ if (!dataFile.exists()) {
+ continue;
+ }
+ XYVector rawData = loadColumnData(dataFile, 0, Double.MAX_VALUE, 1);
+ XYVector scaledData = scaleXAxis(rawData);
+
+ baseChart.addSeries(bamQcResult.name, scaledData, getSampleColor(k) );
+ ++k;
+ }
+ baseChart.setDomainAxisIntegerTicks(false);
+
+ baseChart.render();
+
+
+ return new QChart(chartName, baseChart.getChart());
+ }
+
+
+
+
+ QChart createCoverageProfileChart(String chartName, String dataPath, String xTitle, String yTitle) throws IOException {
+ BamQCChart baseChart = new BamQCChart(chartName,
+ "Multi-sample BAM QC", xTitle, yTitle);
+
+ int i = 0;
+ int maxCoverage = 50;
+ for (SampleInfo bamQcResult : bamQCResults) {
+ String path = rawDataDirs.get(bamQcResult) + File.separator + dataPath;
+ XYVector histData = loadColumnData(new File(path), 0, 1000000,1);
+ int coverage = (int) histData.getXVector()[histData.getSize() - 1];
+ maxCoverage = coverage > maxCoverage ? coverage : maxCoverage;
+ baseChart.addSeries(bamQcResult.name, histData, getSampleColor(i) );
+
+ ++i;
+ }
+
+ chartName += " (0 - " + maxCoverage + "X)";
+ baseChart.setTitle(chartName);
+
+ baseChart.render();
+
+ return new QChart(chartName, baseChart.getChart());
+ }
+
+ private QChart createPCABiPlot() {
+
+ PrincipleComponentAnalysis pca = new PrincipleComponentAnalysis();
+ pca.setup(bamQCResults.size(), NUM_FEATURES);
+
+ for (double[] sample : sampleData) {
+ pca.addSample( sample );
+ }
+
+ logLine("Running PCA...\n");
+ pca.computeBasis(2);
+
+ String chartName = "PCA";
+
+ BamQCPointChart baseChart = new BamQCPointChart(chartName,
+ "Multi-sample BAM QC", "PC1", "PC2");
+
+ for (int i = 0; i < sampleData.size(); ++i) {
+ double[] transformedSample = pca.sampleToEigenSpace(sampleData.get(i));
+ baseChart.addPoint(bamQCResults.get(i).name, transformedSample[0],transformedSample[1], getSampleColor(i) );
+ }
+
+ baseChart.render();
+
+ return new QChart(chartName, baseChart.getChart());
+ }
+
+ private void createCharts(StatsReporter reporter) throws Exception {
+
+ ArrayList<QChart> charts = new ArrayList<QChart>();
+
+ QChart pcaBiPlot = createPCABiPlot();
+ charts.add(pcaBiPlot);
+
+ logLine("Creating charts...\n");
+
+ QChart coverageAcrossRefChart = createCoverageAcrossReferenceChart();
+ charts.add(coverageAcrossRefChart);
+
+ QChart coverageChart = createCoverageProfileChart("Coverage Histogram", "coverage_histogram.txt",
+ "Coverage", "Number of genomic locations");
+ charts.add(coverageChart);
+
+ QChart genomeFractionCoverage = createHistogramBasedChart("Genome Fraction Coverage",
+ "genome_fraction_coverage.txt", "Coverage", "Fraction of genome (%)");
+ charts.add(genomeFractionCoverage);
+
+ QChart duplicationRate = createHistogramBasedChart("Duplication Rate Histogram",
+ "duplication_rate_histogram.txt", "Duplication rate", "Number of genomic locations");
+ charts.add(duplicationRate);
+
+
+ QChart readsGcContent = createReadsGcContentChart("Mapped reads GC-content",
+ "mapped_reads_nucleotide_content.txt", "Read position (bp)", "GC-content (%)" );
+ charts.add(readsGcContent);
+
+ QChart readsClippingProfile = createHistogramBasedChart("Mapped Reads Clipping Profile",
+ "mapped_reads_clipping_profile.txt", "Read position (bp)", "Clipped bases (%)");
+ charts.add(readsClippingProfile);
+
+
+ QChart readsGCContentDistr = createHistogramBasedChart("Mapped Reads GC-content Distribution",
+ "mapped_reads_gc-content_distribution.txt", "GC Content (%)", "Fraction of reads");
+ charts.add(readsGCContentDistr);
+
+ QChart mappingQualityAcrossRef = createAcrossReferenceChart("Mapping Quality Across Reference",
+ "mapping_quality_across_reference.txt", "Mapping Quality");
+ charts.add(mappingQualityAcrossRef);
+
+ QChart mappingQualityHist = createHistogramBasedChart("Mapping Quality Histogram",
+ "mapping_quality_histogram.txt", "Mapping quality", "Number of genomic locations");
+ charts.add(mappingQualityHist);
+
+ QChart insertSizeAcrossRef = createAcrossReferenceChart("Insert Size Across Reference",
+ "insert_size_across_reference.txt", "Insert Size");
+ charts.add(insertSizeAcrossRef);
+
+ QChart insertSizeHist = createHistogramBasedChart("Insert Size Histogram",
+ "insert_size_histogram.txt", "Insert Size", "Number of reads", 1);
+ charts.add(insertSizeHist);
+
+ reporter.setChartList(charts);
+
+ }
+
+
+ private void prepareInputDescription(StatsReporter reporter) {
+ HashMap<String,String> sampleParams = new HashMap<String, String>();
+ for ( SampleInfo info : bamQCResults ) {
+ sampleParams.put(info.name, info.path );
+ }
+ reporter.addInputDataSection("Samples", sampleParams);
+
+
+ }
+
+
+ private String findRawDataPath(String targetDir) {
+
+ File dir = new File(targetDir);
+
+ if (!dir.exists() || !dir.isDirectory()) {
+ return null;
+ }
+
+ File[] children = dir.listFiles();
+ Arrays.sort(children);
+
+ for (File child : children ) {
+ String fileName = child.getName();
+ if (child.isDirectory() && fileName.startsWith("raw_data")) {
+ return child.getAbsolutePath();
+ }
+ }
+
+ return null;
+
+ }
+
+
+ private void checkInputPaths() throws RuntimeException {
+ for (SampleInfo sampleInfo : bamQCResults) {
+
+ if (! new File(sampleInfo.path).isDirectory()) {
+ sampleInfo.path = (new File(sampleInfo.path).getParent() );
+ }
+ String rawDataDir = findRawDataPath(sampleInfo.path);
+
+
+ if (rawDataDir == null) {
+ throw new RuntimeException("The raw data doesn't exist for sample: " + sampleInfo.name +
+ "\nFolder path:" + sampleInfo.path +
+ "\nPlease check raw data directory is present.\n");
+ }
+
+ rawDataDirs.put(sampleInfo, rawDataDir);
+
+ }
+ }
+
+ public void setOutputParsingThread(LoggerThread loggerThread) {
+ this.loggerThread = loggerThread;
+ }
+
+ public static List<SampleInfo> parseInputFile(String inputFilePath) throws IOException {
+ ArrayList<SampleInfo> paths = new ArrayList<SampleInfo>();
+
+ BufferedReader bufferedReader = new BufferedReader(new FileReader(inputFilePath));
+ String line;
+ while ( (line = bufferedReader.readLine()) != null) {
+ if (line.startsWith("#") || line.isEmpty()) {
+ continue;
+ }
+
+ String[] items = line.trim().split("\\s+");
+
+ if (items.length != 2) {
+ continue;
+ }
+
+ String path = items[1];
+ File sampleFile = new File(path);
+ if (!sampleFile.exists()) {
+ // Try relative path
+ path = new File(inputFilePath).getParent() + File.separator + path;
+ }
+
+ paths.add( new SampleInfo(items[0], path ) );
+
+ }
+
+ return paths;
+
+ }
+
+}
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/process/ProcessBunchOfReadsTask.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/process/ProcessBunchOfReadsTask.java
new file mode 100644
index 0000000..c266487
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/process/ProcessBunchOfReadsTask.java
@@ -0,0 +1,568 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.process;
+
+import net.sf.samtools.*;
+import org.bioinfo.ngs.qc.qualimap.beans.BamGenomeWindow;
+import org.bioinfo.ngs.qc.qualimap.beans.BamStats;
+import org.bioinfo.ngs.qc.qualimap.beans.SingleReadData;
+import org.bioinfo.ngs.qc.qualimap.common.Constants;
+
+import java.util.*;
+import java.util.concurrent.Callable;
+import java.util.concurrent.ConcurrentMap;
+
+/**
+ * Created by kokonech
+ * Date: 11/15/11
+ * Time: 5:04 PM
+ */
+public class ProcessBunchOfReadsTask implements Callable<ProcessBunchOfReadsTask.Result> {
+ List<SAMRecord> reads;
+ BamStatsAnalysis ctx;
+ BamGenomeWindow currentWindow;
+ boolean computeInsertSize;
+ boolean isPairedData;
+ boolean analyzeRegions, computeOutsideStats;
+ private static final Object lock = new Object();
+ HashMap<Long, SingleReadData> analysisResults;
+ HashMap<Long, SingleReadData> outOfRegionsResults;
+ ArrayList<Float> readsGcContent;
+ ReadStatsCollector readStatsCollector;
+ ArrayList<Float> outOfRegionsReadsGCContent;
+ ReadStatsCollector outOfRegionsReadStatsCollector;
+
+ static final char CIGAR_M = CigarOperator.MATCH_OR_MISMATCH.name().charAt(0);
+ static final char CIGAR_EQ = CigarOperator.EQ.name().charAt(0);
+ //TODO: use variables instead of magic constants in computeAlignment()
+ //static final char CIGAR_X = CigarOperator.X.name().charAt(0);
+
+ public static class Result {
+ Collection<SingleReadData> readsData;
+ Collection<SingleReadData> outRegionReadsData;
+ ReadStatsCollector readStatsCollector;
+ ReadStatsCollector outRegionReadStatsCollector;
+
+ public ReadStatsCollector getReadStatsCollector() {
+ return readStatsCollector;
+ }
+
+ public ReadStatsCollector getOutRegionReadStatsCollector() {
+ return outRegionReadStatsCollector;
+ }
+
+ public void setReadStatsCollector(ReadStatsCollector readStatsCollector) {
+ this.readStatsCollector = readStatsCollector;
+ }
+
+ public void setOutRegionReadStatsCollector(ReadStatsCollector readsStatsCollector) {
+ this.outRegionReadStatsCollector = readsStatsCollector;
+ }
+
+ public void setGlobalReadsData(Collection<SingleReadData> readsData) {
+ this.readsData = readsData;
+ }
+
+ public Collection<SingleReadData> getReadAlignmentData() {
+ return readsData;
+ }
+
+ public void setOutOfRegionReadsData(Collection<SingleReadData> inRegionReadsData) {
+ this.outRegionReadsData = inRegionReadsData;
+ }
+
+ public Collection<SingleReadData> getOutOfRegionReadsData() {
+ return outRegionReadsData;
+ }
+
+ }
+
+ public ProcessBunchOfReadsTask(List<SAMRecord> reads, BamGenomeWindow window, BamStatsAnalysis ctx) {
+ this.reads = reads;
+ this.ctx = ctx;
+ this.analyzeRegions = ctx.selectedRegionsAvailable();
+ computeInsertSize = true;
+ isPairedData = true;
+ currentWindow = window;
+ analysisResults = new HashMap<Long, SingleReadData>();
+ computeOutsideStats = ctx.getComputeOutsideStats();
+ readsGcContent = new ArrayList<Float>();
+ readStatsCollector = new ReadStatsCollector(ctx.getMinHomopolymerSize());
+ if ( analyzeRegions && computeOutsideStats ) {
+ outOfRegionsResults = new HashMap<Long, SingleReadData>();
+ outOfRegionsReadsGCContent = new ArrayList<Float>();
+ outOfRegionsReadStatsCollector = new ReadStatsCollector(ctx.getMinHomopolymerSize());
+ }
+
+ }
+
+
+ static private SingleReadData getWindowData(Long windowStart, HashMap<Long,SingleReadData> resultsMap) {
+ if (resultsMap.containsKey(windowStart)) {
+ return resultsMap.get(windowStart);
+ } else {
+ SingleReadData data = new SingleReadData(windowStart);
+ resultsMap.put(windowStart, data);
+ return data;
+ }
+ }
+
+
+ ReadStatsCollector getReadStatsCollector(SAMRecord read) {
+ if (read.getAttribute(Constants.READ_IN_REGION).equals(1) ) {
+ return readStatsCollector;
+ } else if (analyzeRegions && computeOutsideStats) {
+ return outOfRegionsReadStatsCollector;
+ }
+
+ return null;
+ }
+
+
+ public Result call() {
+
+ //long startTime = System.currentTimeMillis();
+ //System.out.println("Started bunch of read analysis. The first read is" + reads.get(0).getReadName());
+
+ Result taskResult = new Result();
+
+ for (SAMRecord read : reads) {
+
+ long position = ctx.getLocator().getAbsoluteCoordinates(read.getReferenceName(), read.getAlignmentStart());
+
+ char[] alignment = null;
+ // compute alignment
+ try {
+ ReadStatsCollector statsCollector = getReadStatsCollector(read);
+ if (statsCollector != null) {
+ // compute alignment and collect read stats
+ alignment = computeReadAlignment(read, statsCollector);
+ } else {
+ // only compute alignment
+ alignment = computeReadAlignment(read);
+ }
+ } catch (SAMFormatException e) {
+ System.err.println("WARNING! Problematic read alignment skipped: " + read.getReadName());
+ System.err.println(e.getMessage());
+ e.printStackTrace();
+ } catch (ArrayIndexOutOfBoundsException e) {
+ System.err.println("WARNING! Incorrect read alignment skipped: " + read.getReadName());
+ //e.printStackTrace();
+ }
+
+ if (alignment == null ) {
+ continue;
+ }
+
+ //System.out.println("From ProcessReadTask: computed alignment for read" + read.getHeader().toString());
+
+ // insert size
+
+ try {
+ if(computeInsertSize && read.getProperPairFlag()){
+ long insertSize = read.getInferredInsertSize();
+ currentWindow.acumInsertSize(insertSize);
+ }
+ } catch(IllegalStateException ise){
+ isPairedData = false;
+ }
+
+ int mappingQuality = read.getMappingQuality();
+ long readEnd = position + alignment.length - 1;
+
+ // acum read
+
+ //regionOverlapLookupTable = createRegionLookupTable(position, readEnd, ctx.getRegionsTree());
+ boolean outOfBounds = processReadAlignment(currentWindow, alignment, position, readEnd,
+ mappingQuality);
+
+ if(outOfBounds) {
+ //System.out.println("From ProcessReadTask: propogating read" + read.getHeader().toString());
+ propagateRead(alignment, position, readEnd, mappingQuality);
+ }
+
+ }
+
+ readStatsCollector.saveGC();
+ taskResult.setGlobalReadsData(analysisResults.values());
+ taskResult.setReadStatsCollector(readStatsCollector);
+
+ if (analyzeRegions && computeOutsideStats) {
+ outOfRegionsReadStatsCollector.saveGC();
+ taskResult.setOutOfRegionReadsData(outOfRegionsResults.values());
+ taskResult.setOutRegionReadStatsCollector(outOfRegionsReadStatsCollector);
+ }
+
+
+ //long endTime = System.currentTimeMillis();
+ //System.out.println("Analyze bunch of reads time: " + (endTime - startTime));
+
+ return taskResult;
+ }
+
+ static private int computeNumMismatches(SAMRecord read) {
+
+ int numMismatches = 0;
+ String mdAttr = read.getStringAttribute("MD");
+
+ if (mdAttr == null) {
+ return numMismatches;
+ }
+
+ for (int i = 0; i < mdAttr.length(); i++){
+ char c = mdAttr.charAt(i);
+
+ if (c == 'A' || c== 'C' || c == 'G' || c == 'T') {
+ numMismatches += 1;
+ }
+ }
+
+ return numMismatches;
+ }
+
+ /**
+ * This method computes read to reference alignment vector along with collecting read's stats
+ * @param read The record being analyzed
+ * @param statsCollector Read stats collector
+ * @return Alignment vector, which includes extended issues
+ */
+
+ public static char[] computeReadAlignment(SAMRecord read, ReadStatsCollector statsCollector){
+ // init read params
+ int alignmentLength = (read.getAlignmentEnd()-read.getAlignmentStart()+1);
+
+ //TODO: analyze alignment when read length is zero
+ int readLength = read.getReadLength();
+
+ if (alignmentLength < 0 || readLength == 0) {
+ return null;
+ }
+
+ /* This is to check the status
+ if (read.getReadName().equals("M_AHSTEUER006:166:C5UJMANXX:8:1113:11295:78610B")
+ System.err.println("Detected strange alignment");
+ System.err.println("Read length: " + read.getReadLength());
+ System.err.println("Read bases:" + read.getReadString());
+ }*/
+
+
+ //System.err.println("Computing alignment for read " + read.getReadName());
+ Cigar cigar = read.getCigar();
+
+ // precompute total size of alignment
+ int totalSize = 0;
+ List<CigarElement> elementList = cigar.getCigarElements();
+ //int numCigarElements = cigar.numCigarElements();
+ boolean readIsClipped = false;
+ boolean readHasDeletions = false;
+ boolean readHasInsertions = false;
+ for(CigarElement element : elementList){
+ totalSize += element.getLength();
+ if (element.getOperator() == CigarOperator.H || element.getOperator() == CigarOperator.S) {
+ readIsClipped = true;
+ } else if (element.getOperator() == CigarOperator.I) {
+ statsCollector.incNumInsertions();
+ if (!readHasInsertions) {
+ statsCollector.incNumReadsWithInsertion();
+ }
+ readHasInsertions = true;
+
+ } else if (element.getOperator() == CigarOperator.D) {
+ statsCollector.incNumDeletions();
+ if (!readHasDeletions) {
+ statsCollector.incNumReadsWithDeletion();
+ }
+ readHasDeletions = true;
+ }
+ }
+
+ // compute extended cigar
+ char[] extendedCigarVector = new char[totalSize];
+ int mpos = 0;
+ int npos;
+ for(CigarElement element : elementList){
+ npos = mpos + element.getLength();
+ Arrays.fill(extendedCigarVector, mpos, npos, element.getOperator().name().charAt(0));
+ mpos = npos;
+ }
+
+ char[] alignmentVector = new char[alignmentLength];
+
+ int readPos = 0;
+ int alignmentPos = 0;
+ byte[] readBases = read.getReadBases();
+ statsCollector.resetCounters();
+
+ for( int pos = 0; pos < extendedCigarVector.length; ++pos){
+ char cigarChar = extendedCigarVector[pos];
+ // M
+ if(cigarChar == CIGAR_M || cigarChar == CIGAR_EQ){
+ // get base
+ byte base = readBases[readPos];
+ statsCollector.collectBase(readPos, base, false);
+ readPos++;
+ alignmentVector[alignmentPos] = (char) base;
+ alignmentPos++;
+ }
+ // I
+ else if(cigarChar == 'I'){
+ byte base = readBases[readPos];
+ statsCollector.collectBase(readPos, base, true);
+ readPos++;
+ }
+ // D
+ else if(cigarChar == 'D'){
+ int nextCigarPos = pos + 1;
+ if (nextCigarPos < extendedCigarVector.length && extendedCigarVector[nextCigarPos] != 'D' ) {
+ byte nextBase = readPos + 1 < readBases.length ? readBases[readPos + 1] : -1;
+ statsCollector.collectDeletedBase(nextBase);
+ }
+ alignmentVector[alignmentPos] = '-';
+ alignmentPos++;
+ }
+ // N
+ else if(cigarChar == 'N'){
+ alignmentVector[alignmentPos] = 'N';
+ alignmentPos++;
+ }
+ // S
+ else if(cigarChar == 'S'){
+ statsCollector.incClippingContent(readPos);
+ readPos++;
+ }
+ // H
+ else if(cigarChar =='H'){
+ statsCollector.incClippingContent(readPos);
+ }
+ // P
+ else if(cigarChar == 'P'){
+ alignmentVector[alignmentPos] = '-';
+ alignmentPos++;
+ }
+ }
+
+ if (readIsClipped) {
+ statsCollector.incNumClippedReads();
+ }
+
+ int numMismatches = computeNumMismatches(read);
+ statsCollector.incNumMismatches(numMismatches);
+
+ Integer editDist = read.getIntegerAttribute("NM");
+ if (editDist != null) {
+ statsCollector.incEditDistance(editDist);
+ }
+
+
+
+
+ return alignmentVector;
+ }
+
+
+ public static char[] computeReadAlignment(SAMRecord read){
+ // init read params
+ int alignmentLength = (read.getAlignmentEnd()-read.getAlignmentStart()+1);
+
+ if (alignmentLength < 0) {
+ return null;
+ }
+
+ Cigar cigar = read.getCigar();
+
+ // precompute total size of alignment
+ int totalSize = 0;
+ List<CigarElement> elementList = cigar.getCigarElements();
+ //int numCigarElements = cigar.numCigarElements();
+ for(CigarElement element : elementList){
+ totalSize += element.getLength();
+ }
+
+ // compute extended cigar
+ char[] extendedCigarVector = new char[totalSize];
+ int mpos = 0;
+ int npos;
+ for(CigarElement element : elementList){
+ npos = mpos + element.getLength();
+ Arrays.fill(extendedCigarVector, mpos, npos, element.getOperator().name().charAt(0));
+ mpos = npos;
+ }
+
+ // init extended cigar portion
+ //char[] extendedCigarVector = extended; // Arrays.copyOfRange(extended,0,mpos);
+
+ char[] alignmentVector = new char[alignmentLength];
+
+ int readPos = 0;
+ int alignmentPos = 0;
+ byte[] readBases = read.getReadBases();
+
+ for(char cigarChar : extendedCigarVector){
+ // M
+ if(cigarChar == CIGAR_M || cigarChar == CIGAR_EQ){
+ // get base
+ byte base = readBases[readPos];
+ readPos++;
+ // set base
+ alignmentVector[alignmentPos] = (char) base;
+ alignmentPos++;
+ }
+ // I
+ else if(cigarChar == 'I'){
+ readPos++;
+ }
+ // D
+ else if(cigarChar == 'D'){
+ alignmentVector[alignmentPos] = '-';
+ alignmentPos++;
+ }
+ // N
+ else if(cigarChar == 'N'){
+ alignmentVector[alignmentPos] = 'N';
+ alignmentPos++;
+ }
+ // S
+ else if(cigarChar == 'S'){
+ readPos++;
+ }
+ // H
+ else if(cigarChar =='H'){
+
+ }
+ // P
+ else if(cigarChar == 'P'){
+ alignmentVector[alignmentPos] = '-';
+ alignmentPos++;
+ }
+ }
+
+ return alignmentVector;
+ }
+
+ private boolean processReadAlignment(BamGenomeWindow window, char[] alignment, long readStart, long readEnd,
+ int mappingQuality) {
+
+ long windowSize = window.getWindowSize();
+ long windowStart = window.getStart();
+
+ SingleReadData readData = getWindowData(windowStart, analysisResults);
+
+ // working variables
+ boolean outOfBounds = false;
+ long relative;
+ int pos;
+
+ if(readEnd < readStart){
+ ctx.incNumberOfReasWithStartGreatThenEnd();
+ }
+
+ //readData.numberOfProcessedReads++;
+ if(readEnd> window.getEnd()){
+ outOfBounds = true;
+ //readData.numberOfOutOfBoundsReads++;
+ }
+
+
+ // run read
+ for(long j=readStart; j<=readEnd; j++){
+ relative = (int)(j - windowStart);
+ pos = (int)(j-readStart);
+
+ if(relative<0){
+
+ } else if(relative >= windowSize){
+ break;
+ } else {
+
+ if (analyzeRegions) {
+ boolean insideOfRegion = window.getSelectedRegions().get((int)relative);
+ if (insideOfRegion) {
+ if (computeOutsideStats) {
+ readData =getWindowData(windowStart, analysisResults);
+ //statsCollector = insideCollector;
+ }
+ } else {
+ if (computeOutsideStats) {
+ readData = getWindowData(windowStart, outOfRegionsResults);
+ //statsCollector = outsideCollector;
+ } else {
+ continue;
+ }
+ }
+ }
+
+ char nucleotide = alignment[pos];
+
+ // aligned bases
+ readData.numberOfMappedBases++;
+
+ if (nucleotide != '-' && nucleotide != 'N') {
+ // mapping quality
+ readData.acumMappingQuality(relative, mappingQuality);
+ // base stats
+ readData.acumBase(relative, nucleotide);
+ }
+
+ }
+
+
+
+ }
+
+
+ return outOfBounds;
+ }
+
+ private void propagateRead(char[] alignment,long readStart, long readEnd,
+ int mappingQuality ){
+ // init covering stat
+ BamStats bamStats = ctx.getBamStats();
+ int index = bamStats.getNumberOfProcessedWindows()+1;
+
+ BamGenomeWindow adjacentWindow;
+ boolean outOfBounds = true;
+ while(outOfBounds && index < bamStats.getNumberOfWindows()){
+
+ // next currentWindow
+ long ws = bamStats.getWindowStart(index);
+
+ synchronized (lock) {
+ ConcurrentMap<Long,BamGenomeWindow> openWindows = ctx.getOpenWindows();
+ adjacentWindow = ctx.getOpenWindow(ws, bamStats, openWindows);
+ if (computeOutsideStats) {
+ Map<Long,BamGenomeWindow> openOutsideWindows = ctx.getOpenOutsideWindows();
+ ctx.getOpenWindow(ws, ctx.getOutsideBamStats(), openOutsideWindows);
+ }
+ }
+
+ // acum read
+ outOfBounds = processReadAlignment(adjacentWindow, alignment, readStart, readEnd,
+ mappingQuality);
+
+ index++;
+ }
+ }
+
+
+
+
+
+}
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/process/RNASeqQCAnalysis.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/process/RNASeqQCAnalysis.java
new file mode 100644
index 0000000..b02d978
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/process/RNASeqQCAnalysis.java
@@ -0,0 +1,320 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.process;
+
+
+import org.bioinfo.ngs.qc.qualimap.beans.AnalysisResultManager;
+import org.bioinfo.ngs.qc.qualimap.beans.QChart;
+import org.bioinfo.ngs.qc.qualimap.beans.StatsReporter;
+import org.bioinfo.ngs.qc.qualimap.common.JunctionInfo;
+import org.bioinfo.ngs.qc.qualimap.common.LoggerThread;
+import org.bioinfo.ngs.qc.qualimap.common.TranscriptDataHandler;
+import org.bioinfo.ngs.qc.qualimap.gui.utils.StatsKeeper;
+import org.bioinfo.ngs.qc.qualimap.gui.utils.StringUtilsSwing;
+
+import java.io.FileWriter;
+import java.io.IOException;
+import java.io.PrintWriter;
+import java.util.*;
+
+/**
+ * Created by kokonech
+ * Date: 12/12/11
+ * Time: 2:52 PM
+ */
+
+public class RNASeqQCAnalysis {
+
+
+ ComputeCountsTask computeCountsTask;
+ private AnalysisResultManager resultManager;
+ LoggerThread loggerThread;
+ String countsFilePath,reportFilePath;
+
+
+ boolean outputCounts;
+
+ public RNASeqQCAnalysis(AnalysisResultManager resultManager, ComputeCountsTask task) {
+ this.resultManager = resultManager;
+ this.computeCountsTask = task;
+ this.loggerThread = task.getLogger();
+ computeCountsTask.setCollectRnaSeqStats(true);
+ countsFilePath = "";
+ reportFilePath = "";
+
+ outputCounts = false;
+
+ }
+
+ public void run() throws Exception {
+ computeCountsTask.run();
+
+ createResultReport();
+
+ if (reportFilePath.length() > 0 ) {
+ writeReport();
+ }
+
+ if (countsFilePath.length() > 0) {
+ writeGeneCounts();
+ }
+
+ }
+
+
+ public void writeReport() throws IOException{
+
+ // init report
+ PrintWriter report = new PrintWriter(new FileWriter(reportFilePath));
+ StringUtilsSwing sdf = new StringUtilsSwing();
+ TranscriptDataHandler th = computeCountsTask.getTranscriptDataHandler();
+
+ report.println("RNA-Seq QC report");
+ report.println("-----------------------------------");
+ report.println("");
+
+ report.println(">>>>>>> Input");
+ report.println("");
+ report.println(" bam file = " + computeCountsTask.pathToBamFile );
+ report.println(" gff file = " + computeCountsTask.pathToGffFile );
+ report.println(" counting algorithm = " + computeCountsTask.countingAlgorithm);
+ report.println(" protocol = " + computeCountsTask.protocol.toString());
+ report.println("");
+ report.println("");
+
+ report.println(">>>>>>> Reads alignment");
+ report.println("");
+ if (computeCountsTask.pairedEndAnalysis) {
+ report.println(" reads aligned (left/right) = " +
+ sdf.formatLong(computeCountsTask.getLeftProperInPair()) + " / " +
+ sdf.formatLong(computeCountsTask.getRightProperInPair())
+ );
+ report.println(" read pairs aligned = " +
+ sdf.formatLong(computeCountsTask.getNumberOfMappedPairs()));
+ } else {
+ report.println(" reads aligned = " + sdf.formatLong(computeCountsTask.getPrimaryAlignmentsNumber()));
+ }
+ report.println(" total alignments = " + sdf.formatLong(computeCountsTask.getTotalAlignmentsNumber()));
+ report.println(" secondary alignments = " + sdf.formatLong(computeCountsTask.getSecondaryAlignmentsNumber()));
+ report.println(" non-unique alignments = " + sdf.formatLong(computeCountsTask.getAlignmentNotUniqueNumber()));
+ report.println(" aligned to genes = " + sdf.formatLong(computeCountsTask.getTotalReadCounts()));
+ report.println(" ambiguous alignments = " + sdf.formatLong(computeCountsTask.getAmbiguousNumber()));
+ report.println(" no feature assigned = " + sdf.formatLong(computeCountsTask.getNoFeatureNumber()));
+ report.println(" not aligned = " + sdf.formatLong(computeCountsTask.getNotAlignedNumber()));
+ report.println("");
+ report.println("");
+
+ report.println(">>>>>>> Reads genomic origin");
+ report.println("");
+ long totalReadCount = computeCountsTask.getTotalReadCounts() + computeCountsTask.getNoFeatureNumber();
+ long exonicReadCount = totalReadCount - computeCountsTask.getNoFeatureNumber();
+ long intronicReadCount = th.getNumIntronicReads();
+ long intergenicReadCount = th.getNumIntergenicReads();
+ long intersectingExonReadCount = th.getNumReadsIntersectingExonRegion();
+ report.println(" exonic = " + sdf.formatLong(exonicReadCount) + " (" +
+ sdf.formatPercentage( (100.*exonicReadCount) / totalReadCount ) + ")");
+ report.println(" intronic = " + sdf.formatLong(intronicReadCount) + " (" +
+ sdf.formatPercentage( (100.*intronicReadCount) / totalReadCount ) + ")");
+ report.println(" intergenic = " + sdf.formatLong(intergenicReadCount) + " (" +
+ sdf.formatPercentage( (100.*intergenicReadCount) / totalReadCount ) + ")");
+
+ report.println(" overlapping exon = " + sdf.formatLong(intersectingExonReadCount) +
+ " (" + sdf.formatPercentage( (100.*intersectingExonReadCount) / totalReadCount) + ")");
+
+
+ report.println("");
+ report.println("");
+
+ report.println(">>>>>>> Transcript coverage profile");
+ report.println("");
+ report.println(" 5' bias = " + sdf.formatDecimal(th.getMedianFivePrimeBias()));
+ report.println(" 3' bias = " + sdf.formatDecimal(th.getMedianThreePrimeBias()));
+ report.println(" 5'-3' bias = " + sdf.formatDecimal(th.getMedianFiveToThreeBias()));
+ report.println("");
+ report.println("");
+
+ report.println(">>>>>>> Junction analysis");
+ report.println("");
+ long numReadsWithJunctions = th.getNumReadsWithJunctions();
+ report.println(" reads at junctions = " + sdf.formatLong(numReadsWithJunctions));
+ report.println("");
+ if (numReadsWithJunctions > 0) {
+ List<JunctionInfo> junctionList = th.computeSortedJunctionsMap();
+
+ int count = 0;
+ for(int i = junctionList.size() -1; i >= 0 && count <= 10; i--){
+ JunctionInfo info = junctionList.get(i);
+ report.println(" " + info.getJunctionString() + " : " + sdf.formatPercentage(info.getPercentage()));
+ count += 1;
+ }
+
+ }
+
+ report.close();
+ }
+
+
+ private void writeGeneCounts() throws IOException {
+ PrintWriter outWriter = new PrintWriter(new FileWriter(countsFilePath));
+ Map<String,Double> counts = computeCountsTask.getReadCounts();
+ for (Map.Entry<String,Double> entry: counts.entrySet()) {
+ long roundedValue = entry.getValue().longValue();
+ String str = entry.getKey() + "\t" + roundedValue;
+ outWriter.println(str);
+ }
+ outWriter.flush();
+ }
+
+ private void createResultReport() throws IOException {
+ StatsReporter reporter = new StatsReporter();
+ prepareHtmlSummary(reporter);
+ prepareInputDescription(reporter);
+ createCharts(reporter);
+
+ resultManager.addReporter(reporter);
+
+
+ }
+
+ private void createCharts(StatsReporter reporter) throws IOException {
+
+ TranscriptDataHandler th = computeCountsTask.getTranscriptDataHandler();
+
+ loggerThread.logLine("Creating plots");
+ th.setNumTotalReads(computeCountsTask.getTotalReadCounts() + computeCountsTask.getNoFeatureNumber());
+ List<QChart> plots = th.createPlots(computeCountsTask.getSampleName());
+
+ reporter.setChartList(plots);
+
+ }
+
+ private void prepareHtmlSummary(StatsReporter reporter) {
+
+
+ StatsKeeper summaryKeeper = reporter.getSummaryStatsKeeper();
+ StringUtilsSwing sdf = new StringUtilsSwing();
+ TranscriptDataHandler th = computeCountsTask.getTranscriptDataHandler();
+
+ StatsKeeper.Section readsAlignment = new StatsKeeper.Section("Reads alignment");
+
+ if (computeCountsTask.pairedEndAnalysis) {
+ readsAlignment.addRow("Number of mapped reads (left/right):",
+ sdf.formatLong(computeCountsTask.getLeftProperInPair()) + " / " +
+ sdf.formatLong(computeCountsTask.getRightProperInPair())
+ );
+ readsAlignment.addRow("Number of aligned pairs (without duplicates):",
+ sdf.formatLong(computeCountsTask.getNumberOfMappedPairs()));
+ } else {
+ readsAlignment.addRow("Number of mapped reads:", sdf.formatLong(computeCountsTask.getPrimaryAlignmentsNumber()));
+ }
+ readsAlignment.addRow("Total number of alignments:", sdf.formatLong(computeCountsTask.getTotalAlignmentsNumber()));
+ readsAlignment.addRow("Number of secondary alignments:", sdf.formatLong(computeCountsTask.getSecondaryAlignmentsNumber()));
+ readsAlignment.addRow("Number of non-unique alignments:", sdf.formatLong(computeCountsTask.getAlignmentNotUniqueNumber()));
+ readsAlignment.addRow("Aligned to genes:", sdf.formatLong(computeCountsTask.getTotalReadCounts()));
+ readsAlignment.addRow("Ambiguous alignments:", sdf.formatLong(computeCountsTask.getAmbiguousNumber()));
+ readsAlignment.addRow("No feature assigned:", sdf.formatLong(computeCountsTask.getNoFeatureNumber()));
+ readsAlignment.addRow("Not aligned:", sdf.formatLong(computeCountsTask.getNotAlignedNumber()));
+
+ summaryKeeper.addSection(readsAlignment);
+
+ StatsKeeper.Section readsOrigin = new StatsKeeper.Section("Reads genomic origin");
+ long totalReadCount = computeCountsTask.getTotalReadCounts() + computeCountsTask.getNoFeatureNumber();
+ long exonicReadCount = totalReadCount - computeCountsTask.getNoFeatureNumber();
+ long intronicReadCount = th.getNumIntronicReads();
+ long intergenicReadCount = th.getNumIntergenicReads();
+ long intersectingExonReadCount = th.getNumReadsIntersectingExonRegion();
+ readsOrigin.addRow("Exonic: ", sdf.formatLong(exonicReadCount) + " / " +
+ sdf.formatPercentage( (100.*exonicReadCount) / totalReadCount ));
+ readsOrigin.addRow("Intronic: ", sdf.formatLong(intronicReadCount) + " / " +
+ sdf.formatPercentage( (100.*intronicReadCount) / totalReadCount ));
+ readsOrigin.addRow("Intergenic: ", sdf.formatLong(intergenicReadCount) + " / " +
+ sdf.formatPercentage( (100.*intergenicReadCount) / totalReadCount ));
+ readsOrigin.addRow("Intronic/intergenic overlapping exon: ", sdf.formatLong(intersectingExonReadCount)
+ + " / " + sdf.formatPercentage( (100.*intersectingExonReadCount) / totalReadCount));
+ summaryKeeper.addSection(readsOrigin);
+
+ //TODO: fix this in case of SE reads
+ /*if (computeCountsTask.getLibraryProtocol() != LibraryProtocol.NON_STRAND_SPECIFIC) {
+ StatsKeeper.Section libraryProtocol = new StatsKeeper.Section("Library protocol");
+ double correctlyMappedPercentage =
+ (100.*computeCountsTask.getProtocolCorrectlyMapped()) / computeCountsTask.getTotalFragmentCount() ;
+ libraryProtocol.addRow("Concordant fragments: ",
+ sdf.formatLong(computeCountsTask.getProtocolCorrectlyMapped()) + " / " +
+ sdf.formatPercentage(correctlyMappedPercentage));
+ }*/
+
+
+ StatsKeeper.Section transcriptCoverage = new StatsKeeper.Section("Transcript coverage profile");
+ transcriptCoverage.addRow("5' bias:", sdf.formatDecimal(th.getMedianFivePrimeBias()));
+ transcriptCoverage.addRow("3' bias:", sdf.formatDecimal(th.getMedianThreePrimeBias()));
+ transcriptCoverage.addRow("5'-3' bias:", sdf.formatDecimal(th.getMedianFiveToThreeBias()));
+
+ summaryKeeper.addSection(transcriptCoverage);
+
+ StatsKeeper.Section junctionAnalysisSection = new StatsKeeper.Section("Junction analysis");
+ long numReadsWithJunctions = th.getNumReadsWithJunctions();
+ junctionAnalysisSection.addRow("Reads at junctions:", sdf.formatLong(numReadsWithJunctions));
+ if (numReadsWithJunctions > 0) {
+ List<JunctionInfo> junctionList = th.computeSortedJunctionsMap();
+
+ int count = 0;
+ for(int i = junctionList.size() -1; i >= 0 && count <= 10; i--){
+ JunctionInfo info = junctionList.get(i);
+ junctionAnalysisSection.addRow(info.getJunctionString(), sdf.formatPercentage(info.getPercentage()));
+ count += 1;
+ }
+
+ }
+ summaryKeeper.addSection(junctionAnalysisSection);
+
+
+
+
+ }
+
+ private void prepareInputDescription(StatsReporter reporter) {
+
+ Map<String,String> inputParams = new TreeMap<String, String>();
+ inputParams.put("BAM file: ", computeCountsTask.pathToBamFile);
+ inputParams.put("GTF file: ", computeCountsTask.pathToGffFile);
+ inputParams.put("Protocol: ", computeCountsTask.protocol.toString());
+ inputParams.put("Counting algorithm:", computeCountsTask.countingAlgorithm);
+ inputParams.put("Paired-end sequencing:", computeCountsTask.pairedEndAnalysis ? "yes" : "no");
+ inputParams.put("Sorting performed:", computeCountsTask.sortingRequired ? "yes" : "no");
+
+
+ Date date = new Date();
+ inputParams.put("Analysis date: ", date.toString());
+
+ reporter.addInputDataSection("Input", inputParams);
+
+ }
+
+
+ public void setCountsFilePath(String path) {
+ countsFilePath = path;
+ }
+
+
+ public void setReportFilePath(String path) {
+ reportFilePath = path;
+ }
+}
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/process/ReadStatsCollector.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/process/ReadStatsCollector.java
new file mode 100644
index 0000000..4f3c5b6
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/process/ReadStatsCollector.java
@@ -0,0 +1,300 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.process;
+
+import java.util.ArrayList;
+
+/**
+ * Created by kokonech
+ * Date: 6/15/12
+ * Time: 11:58 AM
+ */
+public class ReadStatsCollector {
+
+ private static int[] ensureArraySize(int[] array, int pos) {
+ int size = array.length;
+ if (pos >= size) {
+ int new_size = size*2 < pos + 1 ? pos + 1 : size*2;
+ int[] new_array = new int[new_size];
+ System.arraycopy(array, 0, new_array, 0, array.length);
+ return new_array;
+ }
+ return array;
+ }
+
+ private static final int INITIAL_SIZE = 64;
+
+ int[] readsAContent;
+ int[] readsCContent;
+ int[] readsGContent;
+ int[] readsTContent;
+ int[] readsNContent;
+ int[] readsClippingContent;
+ ArrayList<Float> readsGcContent;
+ int[] homopolymerIndels;
+
+ int numClippedReads;
+ int numReadsWithInsertion;
+ int numReadsWithDeletion;
+ int numInsertions;
+ int numDeletions;
+ int numMismatches;
+ int editDistance;
+
+ int numBases;
+ int numGC;
+ int minHomopolymerSize;
+ boolean prevBaseInsideIndelRegion, homopolymerStartsInsideIndelRegion;
+
+ // per read counters
+ byte prevBase;
+ int homopolymerSize;
+
+ public int[] getReadsAContent() {
+ return readsAContent;
+ }
+
+ public int[] getReadsCContent() {
+ return readsCContent;
+ }
+
+ public int[] getReadsGContent() {
+ return readsGContent;
+ }
+
+ public int[] getReadsTContent() {
+ return readsTContent;
+ }
+
+ public int[] getReadsNContent() {
+ return readsNContent;
+ }
+
+ public ArrayList<Float> getReadsGcContent() {
+ return readsGcContent;
+ }
+
+ public int[] getReadsClippingInfo() {
+ return readsClippingContent;
+ }
+
+ ReadStatsCollector(int homopolymerSize) {
+ readsGcContent = new ArrayList<Float>();
+ readsAContent = new int[INITIAL_SIZE];
+ readsCContent = new int[INITIAL_SIZE];
+ readsGContent = new int[INITIAL_SIZE];
+ readsTContent = new int[INITIAL_SIZE];
+ readsNContent = new int[INITIAL_SIZE];
+ readsClippingContent = new int[INITIAL_SIZE];
+ homopolymerIndels = new int[5];
+ minHomopolymerSize = homopolymerSize;
+ }
+
+ void saveGC() {
+ if (numGC != 0) {
+ float gcContent = (float)numGC / (float)numBases;
+ readsGcContent.add(gcContent);
+ }
+
+ numBases = 0;
+ numGC = 0;
+ }
+
+
+ public void collectBase(int pos, byte base, boolean insideIndelRegion) {
+ if (base == 'A') {
+ incAsContent(pos);
+ numBases++;
+ } else if (base == 'C') {
+ incCsContent(pos);
+ numGC++;
+ numBases++;
+ } else if (base == 'G') {
+ incGsContent(pos);
+ numGC++;
+ numBases++;
+ } else if (base == 'T') {
+ incTsContent(pos);
+ numBases++;
+ } else if (base == 'N') {
+ incNsContent(pos);
+ }
+
+ if (numBases >= 1000) {
+ saveGC();
+ }
+
+ updateHomopolymerStats(base, insideIndelRegion);
+ }
+
+
+ void updateHomopolymerStats(byte base, boolean insideIndelRegion) {
+
+ if (base == prevBase) {
+ homopolymerSize ++;
+ } else {
+ if ( prevBaseInsideIndelRegion || homopolymerStartsInsideIndelRegion ) {
+ if (homopolymerSize >= minHomopolymerSize) {
+ saveHomopolymerData();
+ }
+ }
+ homopolymerSize = 1;
+ homopolymerStartsInsideIndelRegion = insideIndelRegion;
+ }
+
+ prevBase = base;
+ prevBaseInsideIndelRegion = insideIndelRegion;
+ }
+
+
+ private void saveHomopolymerData() {
+ if (prevBase == 'A') {
+ homopolymerIndels[0]++;
+ } else if (prevBase == 'C') {
+ homopolymerIndels[1]++;
+ } else if (prevBase == 'G') {
+ homopolymerIndels[2]++;
+ } else if (prevBase == 'T') {
+ homopolymerIndels[3]++;
+ } else if (prevBase == 'N') {
+ homopolymerIndels[4]++;
+ }
+ }
+
+ public void collectDeletedBase( byte nextBase) {
+ if (nextBase != prevBase) {
+ if (homopolymerSize + 1 >= minHomopolymerSize ) {
+ saveHomopolymerData();
+ homopolymerStartsInsideIndelRegion = false;
+ } else {
+ homopolymerStartsInsideIndelRegion = true;
+ }
+ prevBase = nextBase;
+ homopolymerSize = 1;
+ } else {
+ homopolymerSize += 1;
+ }
+ }
+
+ public void resetCounters() {
+ prevBase = 'X';
+ homopolymerSize = 1;
+ prevBaseInsideIndelRegion = false;
+ homopolymerStartsInsideIndelRegion = false;
+ }
+
+ private void incAsContent(int pos) {
+ readsAContent = ensureArraySize(readsAContent, pos);
+ readsAContent[pos]++;
+ }
+
+ private void incGsContent(int pos) {
+ readsGContent = ensureArraySize(readsGContent, pos);
+ readsGContent[pos]++;
+ }
+
+ private void incCsContent(int pos) {
+ readsCContent = ensureArraySize(readsCContent, pos);
+ readsCContent[pos]++;
+ }
+
+ private void incTsContent(int pos) {
+ readsTContent = ensureArraySize(readsTContent, pos);
+ readsTContent[pos]++;
+ }
+
+ private void incNsContent(int pos) {
+ readsNContent = ensureArraySize(readsNContent, pos);
+ readsNContent[pos]++;
+ }
+
+ public void incClippingContent(int pos){
+ readsClippingContent = ensureArraySize(readsClippingContent, pos);
+ readsClippingContent[pos]++;
+ }
+
+ public void incNumClippedReads() {
+ ++numClippedReads;
+ }
+
+ public void incNumInsertions() {
+ ++numInsertions;
+ }
+
+ public void incNumDeletions() {
+ ++numDeletions;
+ }
+
+ public void incNumReadsWithInsertion() {
+ ++numReadsWithInsertion;
+ }
+
+ public void incNumReadsWithDeletion() {
+ ++numReadsWithDeletion;
+ }
+
+ public int getNumClippedReads() {
+ return numClippedReads;
+ }
+
+ public int getNumReadsWithDeletion() {
+ return numReadsWithDeletion;
+ }
+
+ public int getNumReadsWithInsertion() {
+ return numReadsWithInsertion;
+ }
+
+ public int[] getHomopolymerIndels() {
+ return homopolymerIndels;
+ }
+
+ public int getNumIndels() {
+ return numInsertions + numDeletions;
+ }
+
+ public int getNumInsertions() {
+ return numInsertions;
+ }
+
+ public int getNumDeletions() {
+ return numDeletions;
+ }
+
+ public void incNumMismatches(int mismatches) {
+ numMismatches += mismatches;
+ }
+
+ public int getNumMismatches() {
+ return numMismatches;
+ }
+
+ public void incEditDistance(int dist) {
+ editDistance += dist;
+ }
+
+ public int getEditDistance() {
+ return editDistance;
+ }
+
+
+
+}
diff --git a/src/main/java/org/bioinfo/ngs/qc/qualimap/process/SampleInfo.java b/src/main/java/org/bioinfo/ngs/qc/qualimap/process/SampleInfo.java
new file mode 100644
index 0000000..5f79b30
--- /dev/null
+++ b/src/main/java/org/bioinfo/ngs/qc/qualimap/process/SampleInfo.java
@@ -0,0 +1,41 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.process;
+
+/**
+ * Created by kokonech
+ * Date: 6/5/14
+ * Time: 2:59 PM
+ */
+public class SampleInfo{
+
+ public String name;
+ public String path;
+
+ public SampleInfo() {}
+
+ public SampleInfo(String name, String path) {
+ this.name = name;
+ this.path = path;
+ }
+
+
+}
diff --git a/src/main/resources/app.properties b/src/main/resources/app.properties
new file mode 100644
index 0000000..b18e050
--- /dev/null
+++ b/src/main/resources/app.properties
@@ -0,0 +1,4 @@
+# app.properties
+app.name=${pom.name}
+app.version=${pom.version}
+app.buildTime=${buildTime}
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diff --git a/src/main/resources/org/bioinfo/ngs/qc/qualimap/help/main-help.txt b/src/main/resources/org/bioinfo/ngs/qc/qualimap/help/main-help.txt
new file mode 100644
index 0000000..ae7314e
--- /dev/null
+++ b/src/main/resources/org/bioinfo/ngs/qc/qualimap/help/main-help.txt
@@ -0,0 +1,15 @@
+
+usage: qualimap <tool> [options]
+
+To launch GUI leave <tool> empty.
+
+Available tools:
+
+ bamqc Evaluate NGS mapping to a reference genome
+ rnaseq Evaluate RNA-seq alignment data
+ counts Counts data analysis (further RNA-seq data evaluation)
+ multi-bamqc Compare QC reports from multiple NGS mappings
+ clustering Cluster epigenomic signals
+ comp-counts Compute feature counts
+
+
diff --git a/src/main/resources/org/bioinfo/ngs/qc/qualimap/scripts/qualimapRfunctions.r b/src/main/resources/org/bioinfo/ngs/qc/qualimap/scripts/qualimapRfunctions.r
new file mode 100644
index 0000000..f19cc30
--- /dev/null
+++ b/src/main/resources/org/bioinfo/ngs/qc/qualimap/scripts/qualimapRfunctions.r
@@ -0,0 +1,1419 @@
+####################################################################
+################### Qualimap R Functions ####################
+####################################################################
+
+# By Sonia Tarazona
+# Last modified: 29-VI-2011
+#
+
+
+#****************************************************************************#
+
+
+## Function to intersect multiple sets
+
+int.mult <- function(lista, todos = NULL) {
+
+ if(is.null(todos)) {
+ todos <- unlist(lista)
+ }
+
+ comunes <- todos
+
+ for(i in 1:length(lista)) {
+ comunes <- intersect(comunes, lista[[i]])
+ }
+
+ comunes
+}
+
+
+
+
+#****************************************************************************#
+
+
+
+
+## To count number of non-zero elements
+
+noceros <- function (x, num = TRUE, k = 0) {
+
+ nn <- length(which(x > k))
+
+ if (num) {
+ nn
+
+ } else {
+ if(nn > 0) { which(x > k) } else { NULL }
+ }
+}
+
+
+
+
+#***************************************************************************#
+
+
+
+
+
+## Saturation Plot (GLOBAL)
+
+
+satur.plot <- function (datos1, datos2, ylim = NULL, k = 0, tit = "Saturation",
+ cex.main = cex.main, cex.lab = cex.lab,
+ cex.axis = cex.axis, cex = cex,
+ legend = c(deparse(substitute(datos1)),
+ deparse(substitute(datos2)))) {
+
+
+# For datos1
+ n1 <- ncol(as.matrix(datos1))
+
+
+ if (n1 > 1) {
+
+ muestra1 <- as.list(1:n1)
+ for (i in 2:n1) {
+
+ combi1 <- combn(n1, i, simplify = FALSE)
+
+ if( length(combi1) > 20 ) {
+ sub20 <- sample(1:length(combi1), size = 20, replace = FALSE)
+ combi1 <- combi1[sub20]
+ }
+
+ muestra1 <- append(muestra1, combi1)
+ }
+
+ varias1 <- vector("list", length = length(muestra1))
+ names(varias1) <- sapply(muestra1, function(x) {
+ paste("C1.", x, collapse = "", sep = "")})
+
+ for (i in 1:length(muestra1)) {
+ varias1[[i]] <- apply(as.matrix(datos1[,muestra1[[i]]]), 1, sum)
+ }
+
+ satura1 <- data.frame("muestra" = names(varias1),
+ "seq.depth" = sapply(varias1, sum),
+ "noceros" = sapply(varias1, noceros, k = k))
+ }
+
+
+
+ if (n1 == 1) {
+
+ total1 <- sum(datos1)
+ satura1 <- NULL
+
+ for (i in 1:9) { # 10%, 20%, ..., 90% reads (apart 100% is calculated)
+ muestra1 <- rmultinom(10, size = round(total1*i/10,0), prob = datos1)
+ detec1 <- mean(apply(muestra1, 2, noceros, k = k))
+ satura1 <- rbind(satura1, c(round(total1*i/10,0), detec1))
+ }
+ satura1 <- rbind(satura1, c(total1, noceros(datos1, k = k)))
+ colnames(satura1) <- c("seq.depth", "noceros")
+ satura1 <- as.data.frame(satura1)
+ }
+
+
+
+
+# For datos2
+
+ if (!is.null(datos2)) {
+
+ n2 <- ncol(as.matrix(datos2))
+
+ if (n2 > 1) {
+
+ if (n1 == n2) {
+ muestra2 <- muestra1
+
+ } else {
+
+ muestra2 <- as.list(1:n2)
+
+ for (i in 2:n2) {
+
+ combi2 <- combn(n2, i, simplify = FALSE)
+
+ if (length(combi2) > 20) {
+ sub20 <- sample(1:length(combi2), size = 20, replace = FALSE)
+ combi2 <- combi2[sub20]
+ }
+
+ muestra2 <- append(muestra2, combi2)
+
+ }
+ }
+
+ varias2 <- vector("list", length = length(muestra2))
+ names(varias2) <- sapply(muestra2, function(x) {
+ paste("C2.", x, collapse = "", sep = "")})
+
+ for (i in 1:length(muestra2)) {
+ varias2[[i]] <- apply(as.matrix(datos2[,muestra2[[i]]]), 1, sum)
+ }
+
+ satura2 <- data.frame("muestra" = names(varias2),
+ "seq.depth" = sapply(varias2, sum),
+ "noceros" = sapply(varias2, noceros, k = k))
+ }
+
+
+ if (n2 == 1) {
+
+ total2 <- sum(datos2)
+ satura2 <- NULL
+
+ for (i in 1:9) { # 10%, 20%, ..., 90% reads (apart 100% is calculated)
+
+ muestra2 <- rmultinom(10, size = round(total2*i/10,0), prob = datos2)
+ detec2 <- mean(apply(muestra2, 2, noceros, k = k))
+ satura2 <- rbind(satura2, c(round(total2*i/10,0), detec2))
+ }
+
+ satura2 <- rbind(satura2, c(total2, noceros(datos2, k = k)))
+ colnames(satura2) <- c("seq.depth", "noceros")
+ satura2 <- as.data.frame(satura2)
+ }
+
+
+ if (is.null(ylim)) {
+ ylim <- c(0, NROW(datos1))
+ }
+
+ SS1 <- range(satura1$seq.depth/10^6)
+ SS2 <- range(satura2$seq.depth/10^6)
+
+ xM <- max(SS1[2], SS2[2])
+ xm <- min(SS1[1], SS2[1])
+
+ par(xpd=TRUE, mar=par()$mar+c(0,0,2,0), bg = "#e6e6e6")
+
+ plot(satura1$seq.depth/10^6, satura1$noceros, pch = 16, col = 2,
+ ylim = ylim, xlim = c(xm, xM), main = tit, type = "o",
+ xlab = "Sequencing Depth (million reads)",
+ ylab = paste("Number of features with reads >", k), cex = 1.5, las = 1,
+ cex.main = cex.main, cex.lab = cex.lab, cex.axis = cex.axis)
+
+ rect(par("usr")[1], par("usr")[3], par("usr")[2], par("usr")[4],
+ col = "white")
+
+ points(satura1$seq.depth/10^6, satura1$noceros, pch = 16, col = 2,
+ type = "o", cex = 1.5)
+
+ points(satura2$seq.depth/10^6, satura2$noceros, pch = 16, col = 4,
+ type = "o", cex = 1.5)
+
+ legend(x = (xm+xM)/2, y = ylim[2]+0.15*diff(ylim),
+ legend = legend, text.col = c(2,4), bty = "n", xjust = 0.5,
+ lty = 1, lwd = 2, col = c(2, 4), cex = cex, horiz = TRUE)
+
+ par(mar=c(5, 4, 4, 2) + 0.1)
+
+
+ } else {
+
+ if (is.null(ylim)) {
+ ylim <- c(0, NROW(datos1))
+ }
+
+ xlim <- range(satura1$seq.depth/10^6)
+
+ par(bg = "#e6e6e6")
+
+ plot(satura1$seq.depth/10^6, satura1$noceros, pch = 16, col = 2,
+ ylim = ylim, xlim = xlim, main = tit, type = "o",
+ xlab = "Sequencing Depth (million reads)",
+ ylab = paste("Number of features with reads >", k), cex = 1.5, las = 1,
+ cex.main = cex.main, cex.lab = cex.lab, cex.axis = cex.axis)
+
+ rect(par("usr")[1], par("usr")[3], par("usr")[2], par("usr")[4],
+ col = "white")
+
+ points(satura1$seq.depth/10^6, satura1$noceros, pch = 16, col = 2,
+ type = "o", cex = 1.5)
+
+ }
+
+}
+
+
+
+
+
+#***************************************************************************#
+
+
+
+
+
+
+
+###############################################################################
+###############################################################################
+
+
+## Data for saturation plot with different biotypes
+
+
+saturbio.dat <- function (datos1, datos2, k = 0, infobio, biotypes, nsim = 5) {
+
+ # infobio = vector containing biotype for each gene in "datos"
+ # biotypes = list containing groups of biotypes to be studied
+
+ biog <- lapply(biotypes, function(x) { which(is.element(infobio, x)) })
+
+ satura1 <- satura2 <- vector("list", length = length(biotypes))
+ names(satura1) <- names(satura2) <- names(biotypes)
+
+ newdet1 <- newdet2 <- vector("list", length = length(biotypes))
+ names(newdet1) <- names(newdet2) <- names(biotypes)
+
+
+ # datos1
+ n1 <- NCOL(datos1)
+
+
+ if (n1 > 1) { # when replicates are available in condition 1
+
+ varias1 <- vector("list", length = n1) # counts for each sequencing depth
+ names(varias1) <- paste(1:n1, "rep", sep = "")
+
+ for(i in 1:n1) {
+
+ muestra1 <- combn(n1, i, simplify = FALSE)
+
+ if (length(muestra1) > 20) {
+ sub20 <- sample(1:length(muestra1), size = 20, replace = FALSE)
+ muestra1 <- muestra1[sub20]
+ }
+
+ sumrepli <- NULL
+
+ for (com in 1:length(muestra1)) {
+ sumrepli <- cbind(sumrepli, rowSums(as.matrix(datos1[,muestra1[[com]]])))
+ }
+
+ varias1[[i]] <- as.matrix(sumrepli)
+
+ }
+ }
+
+
+ if (n1 == 1) { # simulating replicates for datos1
+
+ varias1 <- vector("list", length = nsim) # counts for each sequencing depth
+ names(varias1) <- paste("dp", 1:nsim, sep = "")
+
+ total1 <- sum(datos1)
+
+ for (i in 1:(nsim-1)) { # total1*i/nbox reads (100% is calculated apart)
+
+ muestra1 <- rmultinom(10, size = round(total1*i/nsim,0), prob = datos1)
+
+ varias1[[i]] <- muestra1
+ }
+
+ varias1[[nsim]] <- as.matrix(datos1)
+ }
+
+ seq.depth1 <- sapply(varias1, function(x) { mean(colSums(x)) })
+
+ # computing saturation for each biotype (datos1)
+ for (j in 1:length(satura1)) {
+
+ conbio1 <- lapply(varias1, function(x) { as.matrix(x[biog[[j]],]) })
+
+ satura1[[j]] <- sapply(conbio1,
+ function(x) { mean(apply(x, 2, noceros, k = k)) })
+ }
+
+
+ ## computing detection increasing per million reads: condition 1
+ for (j in 1:length(newdet1)) {
+
+ puntos1 <- data.frame("x" = seq.depth1, "y" = satura1[[j]])
+
+ pendi <- NULL
+
+ for(i in 2:nrow(puntos1)) {
+
+ nuevo <- max(0, (puntos1$y[i]-puntos1$y[i-1])/
+ (puntos1$x[i]-puntos1$x[i-1]))
+
+ pendi <- c(pendi, nuevo)
+ }
+
+ pendimil1 <- c(NA, pendi)*1000000
+
+ newdet1[[j]] <- pendimil1
+
+ }
+
+
+
+
+ #### datos2
+ if (!is.null(datos2)) {
+
+ n2 <- NCOL(datos2)
+
+ if (n2 > 1) { # when replicates are available in condition 2
+
+ varias2 <- vector("list", length = n2) # counts for each sequencing depth
+ names(varias2) <- paste(1:n2, "rep", sep = "")
+
+ for(i in 1:n2) {
+
+ muestra2 <- combn(n2, i, simplify = FALSE)
+
+ if (length(muestra2) > 20) {
+ sub20 <- sample(1:length(muestra2), size = 20, replace = FALSE)
+ muestra2 <- muestra2[sub20]
+ }
+
+ sumrepli <- NULL
+
+ for (com in 1:length(muestra2)) {
+ sumrepli <- cbind(sumrepli,
+ rowSums(as.matrix(datos2[,muestra2[[com]]])))
+ }
+
+ varias2[[i]] <- as.matrix(sumrepli)
+
+ }
+ }
+
+
+ if (n2 == 1) { # replicates have to be simulated
+
+ varias2 <- vector("list", length = nsim) # counts for each seq depth
+ names(varias2) <- paste("dp", 1:nsim, sep = "")
+
+ total2 <- sum(datos2)
+
+ for (i in 1:(nsim-1)) { # total1*i/nbox reads (100% is calculated apart)
+
+ muestra2 <- rmultinom(10, size = round(total2*i/nsim,0), prob = datos2)
+
+ varias2[[i]] <- muestra2
+ }
+
+ varias2[[nsim]] <- as.matrix(datos2)
+ }
+
+ seq.depth2 <- sapply(varias2, function(x) { mean(colSums(x)) })
+
+ # computing saturation for each biotype (datos2)
+ for (j in 1:length(satura2)) {
+
+ conbio2 <- lapply(varias2, function(x) { as.matrix(x[biog[[j]]]) })
+
+ satura2[[j]] <- sapply(conbio2,
+ function(x) { mean(apply(x, 2, noceros, k = k)) })
+ }
+
+
+ # computing detection increasing per million reads: condition 2
+ for (j in 1:length(newdet2)) {
+
+ puntos2 <- data.frame("x" = seq.depth2, "y" = satura2[[j]])
+
+ pendi <- NULL
+
+ for(i in 2:nrow(puntos2)) {
+
+ nuevo <- max(0, (puntos2$y[i]-puntos2$y[i-1])/
+ (puntos2$x[i]-puntos2$x[i-1]))
+
+ pendi <- c(pendi, nuevo)
+ }
+
+ pendimil2 <- c(NA, pendi)*1000000
+
+ newdet2[[j]] <- pendimil2
+ }
+
+ satura <- list("cond1" = satura1, "cond2" = satura2,
+ "bionum" = sapply(biog, length),
+ "depth1" = seq.depth1, "depth2" = seq.depth2,
+ "newdet1" = newdet1, "newdet2" = newdet2)
+
+
+ } else {
+
+ satura <- list("cond1" = satura1, "cond2" = satura2,
+ "bionum" = sapply(biog, length),
+ "depth1" = seq.depth1, "depth2" = NULL,
+ "newdet1" = newdet1, "newdet2" = NULL)
+ }
+
+
+ ### Results
+
+ satura
+
+}
+
+
+
+
+
+#*****************************************************************************#
+
+
+
+
+
+
+## Saturation plot with different biotypes
+
+saturbio.plot <- function(depth1, depth2 = NULL, sat1, sat2 = NULL, bionum,
+ newdet1 = NULL, newdet2 = NULL,
+ xlim = NULL, yleftlim = NULL, yrightlim = NULL,
+ main = "Saturation per biotype", lwdL = 2, lwdR = 20,
+ legend = c("sample1", "sample2"),
+ ylabL = "Number of detected features",
+ ylabR = "New detections per million reads",
+ cex.main = 1, cex.lab = 1, cex.axis = 1, cex = 1) {
+
+
+ if (bionum > 0) {
+
+ if (!is.null(depth2)) {
+
+ # yleftlim for plot and plot.y2
+ if (is.null(yleftlim)) {
+ yleftlim <- c(min(c(sat1, sat2)), max(c(sat1, sat2)))
+ }
+
+ # xlim for plot
+ if (is.null(xlim)) {
+ SS1 <- range(depth1/10^6)
+ SS2 <- range(depth2/10^6)
+
+ xM <- max(SS1[2], SS2[2])
+ xm <- min(SS1[1], SS2[1])
+
+ xlim <- c(xm, xM)
+ }
+
+ percen1 <- round(100*max(sat1)/bionum, 1)
+ percen2 <- round(100*max(sat2)/bionum, 1)
+
+
+ if(is.null(newdet1)) {
+
+ # PLOT for detections
+ #par(bg = "#e6e6e6")
+
+ plot(depth1/10^6, sat1, pch = 16, col = 2, ylim = yleftlim, lwd = lwdL,
+ xlim = xlim, main = main, type = "o",
+ xlab = "Sequencing Depth (million reads)",
+ ylab = ylabL, cex.main = cex.main, cex.lab = cex.lab, las = 1,
+ cex.axis = cex.axis, cex = 1.5)
+
+ rect(par("usr")[1], par("usr")[3], par("usr")[2], par("usr")[4],
+ col = "white")
+
+ points(depth1/10^6, sat1, pch = 16, col = 2, lwd = lwdL,
+ type = "o", cex = 1.5)
+
+ points(depth2/10^6, sat2, pch = 16, col = 4, lwd = lwdL,
+ type = "o", cex = 1.5)
+
+ legend("top",
+ legend = paste(legend, ": ",
+ c(percen1, percen2), "% detected", sep = ""),
+ text.col = c(2,4), bty = "n", lty = 1, lwd = lwdL,
+ col = c(2, 4), cex = 0.9)
+
+ } else {
+
+ # yrightlim for plot.y2
+ if (is.null(yrightlim)) {
+ maxi <- max(na.omit(c(newdet1, newdet2)))
+ if (maxi < 10) {
+ yrightlim <- c(0, max(10,maxi))
+ } else {
+ yrightlim <- c(0, maxi*1.1)
+ }
+ }
+
+ # PLOT with 2 axis
+ plot.y2(x = depth1/10^6, yright = newdet1, yleft = sat1,
+ type = c("h", "o"), lwd = c(lwdR, lwdL),
+ xlab = "Sequencing depth (million reads)", xlim = xlim,
+ yrightlim = yrightlim, yleftlim = yleftlim,
+ yylab = c(ylabR, ylabL), pch = c(1,19), col = c("pink",2),
+ main = main, x2 = depth2/10^6, yright2 = newdet2, yleft2 = sat2,
+ col2 = c("lightblue1",4), cex.main = cex.main,
+ cex.lab = cex.lab, cex.axis = cex.axis, cex2 = c(1.5,1.5))
+
+ legend.text <- c(paste(legend[1], "(left)"),
+ paste(legend[2], "(left)"),
+ paste(legend[1], "(right)"),
+ paste(legend[2], "(right)"),
+ paste(percen1,"% detected"),
+ paste(percen2,"% detected"))
+
+ legend.pch <- c(16, 16, 15, 15, 1, 1)
+
+ legend.col <- c(2, 4, "pink", "lightblue1", 0, 0)
+
+ legend("top",
+ legend = legend.text, pch = legend.pch,
+ col = legend.col, ncol = 3, bty = "n", cex = 0.9)
+ }
+
+ } else {
+
+
+
+
+ ### Only for 1 sample
+
+ # yleftlim for plot and plot.y2
+ if (is.null(yleftlim)) {
+ yleftlim <- range(sat1)
+ }
+
+ # xlim for plot
+ if (is.null(xlim)) {
+ xlim <- range(depth1/10^6)
+ }
+
+ percen1 <- round(100*max(sat1)/bionum, 1)
+
+
+ if(is.null(newdet1)) {
+
+ # PLOT for detections
+ #par(bg = "#e6e6e6")
+
+ plot(depth1/10^6, sat1, pch = 16, col = 4, ylim = yleftlim, lwd = lwdL,
+ xlim = xlim, main = main, type = "o",
+ xlab = "Sequencing Depth (million reads)",
+ ylab = ylabL, cex.main = cex.main, cex.lab = cex.lab, las = 1,
+ cex.axis = cex.axis, cex = 1.5)
+
+ rect(par("usr")[1], par("usr")[3], par("usr")[2], par("usr")[4],
+ col = "white")
+
+ points(depth1/10^6, sat1, pch = 16, col = 2, lwd = lwdL,
+ type = "o", cex = 1.5)
+
+ legend("top",
+ legend = paste(legend, ": ", percen1, "% detected", sep = ""),
+ text.col = 2, bty = "n", lty = 1, lwd = lwdL,
+ col = 4, cex = 0.9)
+
+ } else {
+
+ # yrightlim for plot.y2
+ if (is.null(yrightlim)) {
+ maxi <- max(na.omit(newdet1))
+ if (maxi < 10) {
+ yrightlim <- c(0, max(10,maxi))
+ } else {
+ yrightlim <- c(0, maxi*1.1)
+ }
+ }
+
+ # PLOT with 2 axis
+ plot.y2(x = depth1/10^6, yright = newdet1, yleft = sat1,
+ type = c("h", "o"),
+ lwd = c(lwdR, lwdL),
+ xlab = "Sequencing depth (million reads)", xlim = xlim,
+ yrightlim = yrightlim, yleftlim = yleftlim,
+ yylab = c(ylabR, ylabL), pch = c(1,19),
+ main = main, col = c("pink",2), cex.main = cex.main,
+ cex.lab = cex.lab, cex.axis = cex.axis, cex2 = c(1.5,1.5))
+
+ legend.text <- c("Left axis", "Right axis",
+ paste(percen1,"%detected"))
+
+ legend.pch = c(16, 15, 1)
+
+ legend.col = c(2, "pink", 0)
+
+ legend("top",
+ legend = legend.text, pch = legend.pch,
+ col = legend.col, ncol = 3, cex = 0.9)
+ }
+ }
+
+ } else {
+
+ print("Biotype not found in this dataset")
+ }
+}
+
+
+
+
+
+
+
+#*****************************************************************************#
+
+
+
+
+
+
+
+## Counts for detected genes Plot according to BIOTYPES
+
+
+countsbio.dat <- function (datos1, datos2, k = 0, infobio, biotypes, nbox = 5)
+ {
+
+ # infobio = vector containing biotype for each gene in "datos"
+ # biotypes = list containing groups of biotypes to be studied
+ # nbox = number of different depths to be plotted (only for simulated data)
+
+
+ biog <- lapply(biotypes, function(x) { which(is.element(infobio, x)) })
+ # which genes belong to each biotype
+
+ satura1 <- satura2 <- vector("list", length = length(biotypes))
+ names(satura1) <- names(satura2) <- names(biotypes)
+
+
+ ### DATOS 1
+ n1 <- NCOL(datos1)
+
+ ## replicates available for condition 1
+ if (n1 > 1) {
+
+ varias1 <- vector("list", length = n1) # counts for each sequencing depth
+ names(varias1) <- paste(1:n1, "rep", sep = "")
+
+ for(i in 1:n1) {
+
+ muestra1 <- combn(n1, i, simplify = FALSE)
+
+ if (length(muestra1) > 20) {
+ sub20 <- sample(1:length(muestra1), size = 20, replace = FALSE)
+ muestra1 <- muestra1[sub20]
+ }
+
+ sumrepli <- NULL
+
+ for (com in 1:length(muestra1)) {
+ sumrepli <- cbind(sumrepli, rowSums(as.matrix(datos1[,muestra1[[com]]])))
+ }
+
+ varias1[[i]] <- rowMeans(sumrepli)
+ }
+ }
+
+
+ ## replicates simulated for condition 1
+ if (n1 == 1) { # replicates have to be simulated
+
+ varias1 <- vector("list", length = nbox) # counts for each sequencing depth
+ names(varias1) <- paste("dp", 1:nbox, sep = "")
+
+ total1 <- sum(datos1)
+
+ if (nbox > 1) {
+
+ for (i in 1:(nbox-1)) { # total1*i/nbox reads (100% is calculated apart)
+
+ muestra1 <- rmultinom(10, size = round(total1*i/nbox,0), prob = datos1)
+
+ varias1[[i]] <- rowMeans(muestra1)
+ }
+ }
+
+ varias1[[nbox]] <- datos1
+ }
+
+ seq.depth1 <- sapply(varias1, sum) # sequencing depth for each new sample
+
+
+
+ ## selecting detected genes for each biotype (datos1)
+ for (j in 1:length(satura1)) {
+
+ satura1[[j]] <- vector("list", length = length(varias1))
+ names(satura1[[j]]) <- names(varias1)
+
+ # selecting genes in bioclass j for each sample
+ conbio1 <- lapply(varias1, function(x) { x[biog[[j]]] })
+
+ for (i in 1:length(conbio1)) {
+
+ # selecting the genes with counts > k
+ noK <- noceros(conbio1[[i]], k = k, num = FALSE)
+
+ if (is.null(noK)) {
+ satura1[[j]][[i]] <- NA
+ } else {
+ satura1[[j]][[i]] <- conbio1[[i]][noK]
+ }
+ }
+ }
+
+
+
+ #### DATOS 2
+
+ if (!is.null(datos2)) {
+
+ n2 <- NCOL(datos2)
+
+ ## replicates available for condition 2
+ if (n2 > 1) {
+
+ varias2 <- vector("list", length = n2)
+ names(varias2) <- paste(1:n2, "rep", sep = "")
+
+ for (i in 1:n2) {
+
+ muestra2 <- combn(n2, i, simplify = FALSE)
+
+ if (length(muestra2) > 20) {
+ sub20 <- sample(1:length(muestra2), size = 20, replace = FALSE)
+ muestra2 <- muestra2[sub20]
+ }
+
+ sumrepli2 <- NULL
+
+ for (com in 1:length(muestra2)) {
+ sumrepli2 <- cbind(sumrepli2,
+ rowSums(as.matrix(datos2[,muestra2[[com]]])))
+ }
+
+ varias2[[i]] <- rowMeans(sumrepli2)
+ }
+ }
+
+
+ ## replicates simulated for condition 2
+ if (n2 == 1) { # replicates have to be simulated
+
+ varias2 <- vector("list", length = nbox) # counts for each seq depth
+ names(varias2) <- paste("dp", 1:nbox, sep = "")
+
+ total2 <- sum(datos2)
+
+ if (nbox > 1) {
+
+ for (i in 1:(nbox-1)) { # total1*i/nbox reads (100% is calculated apart)
+
+ muestra2 <- rmultinom(10,
+ size = round(total2*i/nbox,0), prob = datos2)
+
+ varias2[[i]] <- rowMeans(muestra2)
+ }
+ }
+
+ varias2[[nbox]] <- datos2
+ }
+
+ seq.depth2 <- sapply(varias2, sum) # sequencing depth for each new sample
+
+
+ ## selecting detected genes for each biotype (datos2)
+ for (j in 1:length(satura2)) {
+
+ satura2[[j]] <- vector("list", length = length(varias2))
+ names(satura2[[j]]) <- names(varias2)
+
+ # selecting genes in bioclass j for each sample
+ conbio2 <- lapply(varias2, function(x) { x[biog[[j]]] })
+
+ for (i in 1:length(conbio2)) {
+
+ # selecting the genes with counts > k
+ noK <- noceros(conbio2[[i]], k = k, num = FALSE)
+
+ if (is.null(noK)) {
+ satura2[[j]][[i]] <- NA
+ } else {
+ satura2[[j]][[i]] <- conbio2[[i]][noK]
+ }
+ }
+ }
+
+ ## results
+ satura <- list("cond1" = satura1, "cond2" = satura2,
+ "bionum" = sapply(biog, length),
+ "depth1" = seq.depth1, "depth2" = seq.depth2)
+ } else {
+
+ ## results
+ satura <- list("cond1" = satura1, "cond2" = satura2,
+ "bionum" = sapply(biog, length),
+ "depth1" = seq.depth1, "depth2" = NULL)
+
+ }
+
+ satura
+
+}
+
+
+
+
+#****************************************************************************#
+
+
+
+
+
+## PLOT: Mean length for detected genes Plot according to BIOTYPES
+
+countbio.plot <- function (depth1, depth2, sat1, sat2, bionum,
+ legend = c("sample1", "sample2"), main = "",
+ ylab = "# counts of detected features",
+ xlab = "Sequencing Depth", ylim = NULL, las = 0,
+ cex.main = 1, cex.lab = 1, cex.axis = 1, cex = 1) {
+
+ if (bionum == 0) {
+
+ print("Biotype not found in this dataset")
+
+ } else {
+
+ if (!is.null(depth2)) {
+
+ # ylim for plot
+ if (is.null(ylim)) {
+
+ #maxi <- sapply(c(sat1,sat2), max, na.rm = TRUE)
+ q75 <- sapply(c(sat1,sat2), quantile, probs = 0.75, na.rm = TRUE)
+
+ #limis <- q75 + 0.2*(maxi - q75)
+
+ #ylim <- c(0, max(limis, na.rm = TRUE))
+ ylim <- c(0, suppressWarnings(max(q75, na.rm = TRUE))*1.3)
+ }
+
+ # boxplots data
+
+ depth <- c(depth1, depth2)
+ depth <- round(depth/10^6, 1)
+ d.sort <- sort(depth)
+ d.order <- order(depth)
+
+ n1 <- length(depth1)
+ n2 <- length(depth2)
+
+ databox <- vector("list", length = n1+n2)
+ names(databox) <- d.sort
+
+ colo <- NULL
+
+ for (i in 1:(n1+n2)) {
+
+ if ( d.order[i] > n1 ) {
+
+ dd <- d.order[i] - n1
+ databox[[i]] <- sat2[[dd]]
+ colo <- c(colo, 4)
+
+ } else {
+
+ dd <- d.order[i]
+ databox[[i]] <- sat1[[dd]]
+ colo <- c(colo, 2)
+ }
+ }
+ } else {
+
+ #### only DATOS1
+
+ # ylim for plot
+ if (is.null(ylim)) {
+
+ #maxi <- sapply(sat1, max, na.rm = TRUE)
+ q75 <- sapply(sat1, quantile, probs = 0.75, na.rm = TRUE)
+
+ #limis <- q75 + 0.001*(maxi - q75)
+
+ #ylim <- c(0, max(limis, na.rm = TRUE))
+ ylim <- c(0, suppressWarnings(max(q75, na.rm = TRUE))*1.3)
+ }
+
+ # boxplots data
+
+ depth <- round(depth1/10^6,1)
+
+ n1 <- length(depth1)
+
+ databox <- sat1
+
+ colo <- rep(2, n1)
+
+ }
+
+ numNA <- sapply(databox, function(x) { length(which(is.na(x))) })
+ cuantos <- sapply(databox, length)
+
+ if (sum(cuantos-numNA) != 0) {
+
+ # BOXPLOT
+ par(bg = "#e6e6e6")
+
+ boxplot(databox, col = colo, ylim = ylim, main = main,
+ type = "b", xlab = xlab, ylab = ylab, names = depth,
+ cex.main = cex.main, cex.lab = cex.lab, cex.axis = cex.axis)
+
+ rect(par("usr")[1], par("usr")[3], par("usr")[2], par("usr")[4], col = "white")
+
+ boxplot(databox, col = colo, ylim = ylim, main = main,
+ type = "b", xlab = xlab, ylab = ylab, names = depth,
+ cex.main = cex.main, cex.lab = cex.lab, cex.axis = cex.axis, add = TRUE)
+
+
+ if (!is.null(depth2)) {
+
+ legend("top",
+ legend = legend, text.col = c(2,4), bty = "o",
+ bg = "white", fill = c(2, 4), cex = cex, horiz = TRUE)
+ }
+
+ cuantos1 <- which(cuantos == 1)
+ sumant <- sapply(databox, sum, na.rm = TRUE)
+ sumant0 <- which(sumant == 0)
+ cuantosNA <- intersect(cuantos1, sumant0)
+
+ cuantos[cuantosNA] <- 0
+
+ mtext(cuantos, 3, at = 1:length(databox), cex = 0.7*cex, las = las)
+
+ } else {
+ mismar <- par()$mar
+ par(mar = c(2,2,4,2), bg = "#e6e6e6")
+ plot(1,1, col = "white", xlab = "", ylab = "", xaxt = "n", yaxt = "n", main = main)
+ rect(par("usr")[1], par("usr")[3], par("usr")[2], par("usr")[4], col = "white")
+ text(1,1, "No counts found for this class")
+ par(mar = mismar)
+ #print("No features detected for this biotype")
+ }
+ }
+}
+
+
+
+
+
+#*************************************************************************#
+
+
+
+#############################################################################
+############## Plot with 2 different Y axis (left and right) ############
+#############################################################################
+
+
+# By Ajay Shah (taken from [R] Plot 2 time series with different y axes
+# (left and right),
+# in https://stat.ethz.ch/pipermail/r-help/2004-March/047775.html)
+
+# Modified by: Sonia Tarazona
+
+### PARAMETERS (default):
+# x: data to be drawn on X-axis
+# yright: data to be drawn on Y right axis
+# yleft: data to be drawn on Y left axis
+# yrightlim (range(yright, na.rm = TRUE)): ylim for rigth Y-axis
+# yleftlim (range(yleft, na.rm = TRUE)): ylim for left Y-axis
+# xlab (NULL): Label for X-axis
+# yylab (c("","")): Labels for right and left Y-axis
+# pch (c(1,2)): Type of symbol for rigth and left data
+# col (c(1,2)): Color for rigth and left data
+# linky (TRUE): If TRUE, points are connected by lines.
+# smooth (0): Friedman's super smoothing
+# lwds (1): Line width for smoothed line
+# length (10): Number of tick-marks to be drawn on axis
+# ...: Other graphical parameters to be added by user (such as main, font, etc.)
+###
+
+
+
+plot.y2 <- function(x, yright, yleft, yrightlim = range(yright, na.rm = TRUE),
+ yleftlim = range(yleft, na.rm = TRUE),
+ xlim = range(x, na.rm = TRUE),
+ xlab = NULL, yylab = c("",""), lwd = c(2,2),
+ pch = c(1,2), col = c(1,2), type = c("o","o"),
+ linky = TRUE, smooth = 0, cex2 = c(1,1),
+ lwds = 1, length = 10, ...,
+ x2 = NULL, yright2 = NULL, yleft2 = NULL, col2 = c(3,4))
+{
+ #par(mar = c(5,2,4+2,2), oma = c(0,3,0,3))
+ #par(mar = c(5,4,4+2,4))
+
+ ## Plotting RIGHT axis data
+
+ #par(bg = "#e6e6e6")
+
+ plot(x, yright, ylim = yrightlim, axes = FALSE, ylab = "", xlab = xlab,
+ xlim = xlim,
+ pch = pch[1], type = type[1], lwd = lwd[1], col = col[1], ...)
+
+ rect(par("usr")[1], par("usr")[3], par("usr")[2], par("usr")[4],
+ col = "white")
+
+ points(x, yright, pch = pch[1], type = type[1], lwd = lwd[1],
+ col = col[1], cex = cex2[1], ...)
+
+ axis(4, pretty(yrightlim, length), col = 1, col.axis = 1, las = 1)
+
+ if (!is.null(yright2)) {
+ points(x2, yright2, type = type[1], pch = pch[1], lwd = lwd[1],
+ col = col2[1], cex = cex2[1], ...)
+ }
+
+ #if (linky) lines(x, yright, col = col[1], ...)
+
+ if (smooth != 0) lines(supsmu(x, yright, span = smooth), col = col[1],
+ lwd = lwds, ...)
+
+ if(yylab[1]=="") {
+ mtext(deparse(substitute(yright)), side = 4, outer = FALSE, line = 4,
+ col = 1, las = 3, ...)
+ } else {
+ mtext(yylab[1], side = 4, outer = FALSE, line = 4, col = 1, las = 3, ...)
+ }
+
+
+ par(new = TRUE)#, xpd = TRUE, mar = c(5,2,4+2,2), oma = c(0,3,0,3))
+
+ ## Plotting LEFT axis data
+
+ plot(x, yleft, ylim = yleftlim, axes = FALSE, ylab = "" , xlab = xlab,
+ xlim = xlim, cex = cex2[2],
+ pch = pch[2], type = type[2], lwd = lwd[2], col = col[2], ...)
+
+ box()
+
+ axis(2, pretty(yleftlim, length), col = 1, col.axis = 1, las = 1)
+
+ if (!is.null(yleft2)) {
+ points(x2, yleft2, type = type[2], pch = pch[2], lwd = lwd[2],
+ col = col2[2], cex = cex2[2], ...)
+ }
+
+
+ #if (linky) lines(x, yleft, col = col[2], ...)
+
+ if (smooth != 0) lines(supsmu(x, yleft, span = smooth), col = col[2],
+ lwd=lwds, ...)
+
+ if(yylab[2] == "") {
+ mtext(deparse(substitute(yleft)), side = 2, outer = FALSE, line = 4,
+ col = 1, las = 3,...)
+ } else {
+ mtext(yylab[2], side = 2, outer = FALSE, line = 4, col = 1, las = 3,...)
+ }
+
+
+ ## X-axis
+ axis(1, at = pretty(xlim, length))
+
+
+}
+
+
+
+
+
+
+###############################################################################
+###############################################################################
+
+
+
+
+
+## Global Saturation Plot including new detection per million reads
+
+
+satur.plot2 <- function (datos1, datos2, yleftlim = NULL, yrightlim = NULL,
+ k = 0, tit = "Saturation", cex.main = cex.main,
+ cex.lab = cex.lab, cex.axis = cex.axis, cex = cex,
+ legend = c(deparse(substitute(datos1)),
+ deparse(substitute(datos2)))) {
+
+
+# For datos1
+ n1 <- ncol(as.matrix(datos1))
+
+
+ if (n1 > 1) {
+
+ muestra1 <- as.list(1:n1)
+ for (i in 2:n1) {
+
+ combi1 <- combn(n1, i, simplify = FALSE)
+
+ if( length(combi1) > 20 ) {
+ sub20 <- sample(1:length(combi1), size = 20, replace = FALSE)
+ combi1 <- combi1[sub20]
+ }
+
+ muestra1 <- append(muestra1, combi1)
+ }
+
+ varias1 <- vector("list", length = length(muestra1))
+ names(varias1) <- sapply(muestra1, function(x) {
+ paste("C1.", x, collapse = "", sep = "")})
+
+ for (i in 1:length(muestra1)) {
+ varias1[[i]] <- apply(as.matrix(datos1[,muestra1[[i]]]), 1, sum)
+ }
+
+ satura1 <- data.frame("muestra" = names(varias1),
+ "seq.depth" = sapply(varias1, sum),
+ "noceros" = sapply(varias1, noceros, k = k))
+ }
+
+
+
+ if (n1 == 1) {
+
+ total1 <- sum(datos1)
+ satura1 <- NULL
+
+ for (i in 1:9) { # 10%, 20%, ..., 90% reads (apart 100% is calculated)
+ muestra1 <- rmultinom(10, size = round(total1*i/10,0), prob = datos1)
+ detec1 <- mean(apply(muestra1, 2, noceros, k = k))
+ satura1 <- rbind(satura1, c(round(total1*i/10,0), detec1))
+ }
+ satura1 <- rbind(satura1, c(total1, noceros(datos1, k = k)))
+ colnames(satura1) <- c("seq.depth", "noceros")
+ satura1 <- as.data.frame(satura1)
+ }
+
+
+ # new detections (sample 1)
+
+ puntos1 <- data.frame("x" = satura1$seq.depth, "y" = satura1$noceros)
+
+ pendi <- NULL
+
+ for (i in 2:nrow(puntos1)) {
+
+ nuevo <- max(0, (puntos1$y[i]-puntos1$y[i-1])/
+ (puntos1$x[i]-puntos1$x[i-1]))
+
+ pendi <- c(pendi, nuevo)
+ }
+
+ newdet1 <- c(NA, pendi)*1000000
+
+
+
+
+
+# For datos2
+
+ if (!is.null(datos2)) {
+
+ n2 <- ncol(as.matrix(datos2))
+
+ if (n2 > 1) {
+
+ if (n1 == n2) {
+ muestra2 <- muestra1
+
+ } else {
+
+ muestra2 <- as.list(1:n2)
+
+ for (i in 2:n2) {
+
+ combi2 <- combn(n2, i, simplify = FALSE)
+
+ if (length(combi2) > 20) {
+ sub20 <- sample(1:length(combi2), size = 20, replace = FALSE)
+ combi2 <- combi2[sub20]
+ }
+
+ muestra2 <- append(muestra2, combi2)
+
+ }
+ }
+
+ varias2 <- vector("list", length = length(muestra2))
+ names(varias2) <- sapply(muestra2, function(x) {
+ paste("C2.", x, collapse = "", sep = "")})
+
+ for (i in 1:length(muestra2)) {
+ varias2[[i]] <- apply(as.matrix(datos2[,muestra2[[i]]]), 1, sum)
+ }
+
+ satura2 <- data.frame("muestra" = names(varias2),
+ "seq.depth" = sapply(varias2, sum),
+ "noceros" = sapply(varias2, noceros, k = k))
+ }
+
+
+ if (n2 == 1) {
+
+ total2 <- sum(datos2)
+ satura2 <- NULL
+
+ for (i in 1:9) { # 10%, 20%, ..., 90% reads (apart 100% is calculated)
+
+ muestra2 <- rmultinom(10, size = round(total2*i/10,0), prob = datos2)
+ detec2 <- mean(apply(muestra2, 2, noceros, k = k))
+ satura2 <- rbind(satura2, c(round(total2*i/10,0), detec2))
+ }
+
+ satura2 <- rbind(satura2, c(total2, noceros(datos2, k = k)))
+ colnames(satura2) <- c("seq.depth", "noceros")
+ satura2 <- as.data.frame(satura2)
+ }
+
+
+ # new detections (sample 2)
+
+ puntos2 <- data.frame("x" = satura2$seq.depth, "y" = satura2$noceros)
+
+ pendi <- NULL
+
+ for (i in 2:nrow(puntos2)) {
+
+ nuevo <- max(0, (puntos2$y[i]-puntos2$y[i-1])/
+ (puntos2$x[i]-puntos2$x[i-1]))
+
+ pendi <- c(pendi, nuevo)
+ }
+
+ newdet2 <- c(NA, pendi)*1000000
+
+
+
+
+ ## PLOT LIMITS
+
+ # yleftlim for plot.y2
+ if (is.null(yleftlim)) {
+ yleftlim <- c(0, NROW(datos1))
+ }
+
+
+ # xlim
+ SS1 <- range(satura1$seq.depth/10^6)
+ SS2 <- range(satura2$seq.depth/10^6)
+
+ xM <- max(SS1[2], SS2[2])
+ xm <- min(SS1[1], SS2[1])
+
+
+ # yrightlim for plot.y2
+ if (is.null(yrightlim)) {
+ maxi <- max(na.omit(c(newdet1, newdet2)))
+ if (maxi < 10) {
+ yrightlim <- c(0, max(10,maxi))
+ } else {
+ yrightlim <- c(0, maxi*1.1)
+ }
+ }
+
+
+
+ ## PLOT for SAMPLES 1 and 2
+
+ #par(xpd=TRUE, mar=par()$mar+c(0,0,2,0))
+
+ plot.y2(x = satura1$seq.depth/10^6, yright = newdet1,
+ yleft = satura1$noceros,
+ type = c("h", "o"), lwd = c(20,2), pch = c(1, 19),
+ yrightlim = yrightlim, yleftlim = yleftlim,
+ xlim = c(xm, xM), main = tit,
+ xlab = "Sequencing Depth (million reads)", col = c("pink", 2),
+ yylab = c("New detections per million reads",
+ paste("Number of features with reads >", k)),
+ cex2 = c(1.5,1.5),
+ cex.main = cex.main, cex.lab = cex.lab, cex.axis = cex.axis,
+ x2 = satura2$seq.depth/10^6, yright2 = newdet2,
+ yleft2 = satura2$noceros, col2 = c("lightblue1", 4))
+
+ legend.text <- c(paste(legend[1], "(left axis)"),
+ paste(legend[2], "(left axis)"),
+ paste(legend[1], "(right axis)"),
+ paste(legend[2], "(right axis)"))
+
+ legend.pch <- c(16, 16, 15, 15)
+
+ legend.col <- c(2, 4, "pink", "lightblue1")
+
+ legend("top",
+ legend = legend.text, pch = legend.pch,
+ col = legend.col, ncol = 2, bty = "n")
+
+ par(mar=c(5, 4, 4, 2) + 0.1)
+
+
+ } else {
+
+ ## PLOT LIMITS
+
+ # yleftlim for plot.y2
+ if (is.null(yleftlim)) {
+ yleftlim <- c(0, NROW(datos1))
+ }
+
+
+ # xlim
+ xlim <- range(satura1$seq.depth/10^6)
+
+
+ # yrightlim for plot.y2
+ if (is.null(yrightlim)) {
+ maxi <- max(na.omit(newdet1))
+ if (maxi < 10) {
+ yrightlim <- c(0, max(10,maxi))
+ } else {
+ yrightlim <- c(0, maxi*1.1)
+ }
+ }
+
+
+ ## PLOT for SAMPLE 1
+
+ plot.y2(x = satura1$seq.depth/10^6, yright = newdet1,
+ yleft = satura1$noceros,
+ type = c("h", "o"), lwd = c(20,2), pch = c(1, 19),
+ yrightlim = yrightlim, yleftlim = yleftlim,
+ xlim = xlim, main = tit,
+ xlab = "Sequencing Depth (million reads)", col = c("pink", 2),
+ yylab = c("New detections per million reads",
+ paste("Number of features with reads >", k)),
+ cex = c(1.5,1.5),
+ cex.main = cex.main, cex.lab = cex.lab, cex.axis = cex.axis)
+
+ legend.text <- c("Left axis", "Right axis")
+
+ legend.pch <- c(16, 15)
+
+ legend.col <- c(2, "pink")
+
+ legend("top",
+ legend = legend.text, pch = legend.pch,
+ col = legend.col, ncol = 2, bty = "n")
+
+ par(mar=c(5, 4, 4, 2) + 0.1)
+
+ }
+
+}
+
+
+
+
+
+#***************************************************************************#
+
+
diff --git a/src/main/resources/org/bioinfo/ngs/qc/qualimap/scripts/qualimapRscript.r b/src/main/resources/org/bioinfo/ngs/qc/qualimap/scripts/qualimapRscript.r
new file mode 100644
index 0000000..84f0c72
--- /dev/null
+++ b/src/main/resources/org/bioinfo/ngs/qc/qualimap/scripts/qualimapRscript.r
@@ -0,0 +1,609 @@
+#!/usr/bin/env Rscript
+if(!require("optparse")) { install.packages("optparse", repos = "http://cran.r-project.org") }
+suppressPackageStartupMessages(library("optparse"))
+
+# Last modified: 29-VI-2011
+
+option_list <- list(
+ make_option(c("-v", "--verbose"), action="store_true", default=TRUE,
+ help="Print extra output [default]"),
+ make_option(c("-q", "--quietly"), action="store_false",
+ dest="verbose", help="Print little output"),
+ make_option(c("--data1"), type="character", action="store",
+ help="REQUIRED. First file with counts.",default=NULL,
+ metavar="file_counts"),
+ make_option(c("--data2"), type="character", action="store",
+ help="Optional. Second file with counts.",default=NULL,
+ metavar="file_counts"),
+ make_option(c("--name1"), type="character", action="store",
+ help="Optional. Name for the first sample",default="Sample 1",
+ metavar="sample_name"),
+ make_option(c("--name2"), type="character", action="store",
+ help="Optional. Name for the second sample.",default="Sample 2",
+ metavar="sample_name"),
+ make_option(c("--info"), type="character", action="store",
+ help="Optional. Info file.",default=NULL, metavar="file_info"),
+ make_option(c("--groups"), type="character", action="store",
+ help="Optional. File with groups for the --info file." , default=NULL, metavar="file_groups"),
+ make_option(c("-k", "--threshold"), type="integer", action="store",
+ help="Optional. Threshold for the number of counts.",default=5,
+ metavar="counts_threshold"),
+ make_option(c("-o", "--dirOut"), type="character", action="store",
+ help="Optional. Output folder.",default="./",
+ metavar="folder_output"),
+ make_option("--homesrc", type="character", action="store",
+ help="DEVELOPMENTAL. NOT TO BE USED IN THIS VERSION", default="./",
+ metavar="home_src folder")
+ )
+
+opt <- parse_args(OptionParser(option_list=option_list))
+
+#HOMESRC <- "/home/fdgarcia/qualimap/sonia"
+HOMESRC <- opt$homesrc
+source(file.path(HOMESRC, "qualimapRfunctions.r"))
+
+#datos1 <- "counts1.txt"
+datos1 <- opt$data1
+if(is.null(datos1)){
+ stop("--data1 is a REQUIRED argument")
+}
+datos2 <- opt$data2 # with the same features than datos1 and in the same order
+
+
+if(!file.exists(opt$dirOut)){
+ dir.create(opt$dirOut, recursive=TRUE)
+}
+
+# cutoff for the number of counts to consider a biological feature as detected
+k <- opt$threshold
+
+
+cm <- 1.5 # cex.main
+cl <- 1.2 # cex.lab
+ca <- 1 # cex.axis
+cc <- 1.2 # cex
+
+
+nom1 <- opt$name1
+nom2 <- opt$name2
+
+#agru.vari <- "biotype"
+
+
+if (!is.null(opt$info)){
+#file including features ID in "datos1" and biotypes or other classification
+ infobio <- opt$info # NO header
+ if (!is.null(opt$groups)){
+ agru.biotype <- TRUE
+ # two columns file: 1) all biotypes in infobio 2) group for biotypes
+ file.agru <- opt$groups # NO header
+ }else{
+ file.agru <- NULL
+ agru.biotype <- FALSE
+ }
+
+
+}
+
+
+
+
+###########################################################################
+
+
+#### DATA
+
+fichero1 <- read.delim(datos1, header = FALSE, sep = "\t", as.is = TRUE)
+
+misdatos1 <- fichero1[,2]
+names(misdatos1) <- fichero1[,1]
+
+if (is.null(datos2)) {
+
+ misdatos2 <- NULL
+
+} else {
+
+ fichero2 <- read.delim(datos2, header = FALSE, sep = "\t", as.is = TRUE)
+
+ misdatos2 <- fichero2[,2]
+ names(misdatos2) <- fichero2[,1]
+}
+
+
+
+#### BIOTYPES
+if (!is.null(opt$info)) {
+
+ infofile <- read.delim(infobio, header = FALSE, sep = "\t", as.is = TRUE)
+ info <- infofile[,2]
+ names(info) <- infofile[,1]
+ myinfo <- info
+ #myinfo[which(is.na(myinfo))] <- "unknown"
+
+
+ ## Completing files: data & info
+
+ genes1 <- as.character(names(misdatos1))
+ genes2 <- as.character(names(misdatos2))
+ genesI <- as.character(names(myinfo))
+
+ if (length(genes2) > 0) {
+ allgenes <- union(genes1, genes2)
+ } else { allgenes <- genes1 }
+
+
+ # Completing myinfo
+ unknown <- setdiff(allgenes, genesI) # genes in data without biotype
+
+ if(length(unknown) > 0) {
+ unk <- rep("unknown", length(unknown))
+ names(unk) <- unknown
+ myinfo <- c(myinfo, unk) # adding unknown genes (without biotype)
+ write.table(unknown, file = file.path(opt$dirOut, "nogroup.txt"),
+ sep = "\t", row.names = FALSE,
+ col.names = FALSE, quote = FALSE) # file for unknown genes
+ }
+
+ genesII <- names(myinfo)
+
+
+ # Completing my data
+ notdet1 <- setdiff(genesII, genes1) # genes1 not in complete info -> counts=0
+ if (length(genes2) > 0) {
+ notdet2 <- setdiff(genesII, genes2)
+ # genes2 not in complete info -> counts=0
+ } else { notdet2 <- NULL }
+
+ if(length(notdet1) > 0) {
+ ceros1 <- rep(0, length(notdet1))
+ names(ceros1) <- notdet1
+ misdatos1 <- c(misdatos1, ceros1) # adding genes with 0s to data
+ nom <- paste(nom1, "nocounts.txt", sep = ".")
+ write.table(notdet1, file = file.path(opt$dirOut, nom),
+ sep = "\t", row.names = FALSE,
+ col.names = FALSE, quote = FALSE) # file for added genes
+ }
+
+ if(length(notdet2) > 0) {
+ ceros2 <- rep(0, length(notdet2))
+ names(ceros2) <- notdet2
+ misdatos2 <- c(misdatos2, ceros2) # adding genes with 0s to data
+ nom <- paste(nom2, "nocounts.txt", sep = ".")
+ write.table(notdet2, file = file.path(opt$dirOut, nom),
+ sep = "\t", row.names = FALSE,
+ col.names = FALSE, quote = FALSE) # file for added genes
+ }
+
+
+ # OK files
+ ok1 <- intersect(genes1, genesII) # genes1 with counts and biotype
+
+ nom <- paste(nom1, "OK.txt", sep = ".")
+ write.table(ok1, file = file.path(opt$dirOut, nom),
+ sep = "\t", row.names = FALSE,
+ col.names = FALSE, quote = FALSE) # file for added genes
+
+ if (!is.null(notdet2)) {
+
+ ok2 <- intersect(genes2, genesII) # genes2 with counts and biotype
+
+ nom <- paste(nom2, "OK.txt", sep = ".")
+ write.table(ok2, file = file.path(opt$dirOut, nom),
+ sep = "\t", row.names = FALSE,
+ col.names = FALSE, quote = FALSE) # file for added genes
+ }
+
+
+
+ ## Sorting files according to genes (all with the same genes)
+ misdatos1 <- misdatos1[genesII]
+
+ if(!is.null(misdatos2)) {
+ misdatos2 <- misdatos2[genesII]
+ }
+
+
+
+
+ ## Preparing biotype files
+
+ if (agru.biotype) { # If you want to group biotypes
+
+ biogroups <- read.delim(file.agru, header = FALSE, sep = "\t", as.is = TRUE)
+ biogrupos <- unique(biogroups)
+
+ # Creating a list for groupes of biotypes
+ bio.agru <- vector("list", length = length(table(biogrupos[,2])))
+ names(bio.agru) <- names(table(biogrupos[,2]))
+
+ for (i in 1:length(bio.agru)) {
+
+ bio.agru[[i]] <- biogrupos[is.element(biogrupos[,2],
+ names(bio.agru)[i]),1]
+ }
+
+ biotipus <- bio.agru
+
+ bio.agru2 <- NULL
+
+ for (i in 1:length(bio.agru)) {
+ bio.agru2 <- c(bio.agru2, rep(names(bio.agru)[i], length(bio.agru[[i]])))
+ }
+ names(bio.agru2) <- unlist(bio.agru)
+
+ } else { # No grouping
+
+ biotipus <- as.list(names(table(myinfo)))
+ names(biotipus) <- names(table(myinfo))
+
+ bio.agru2 <- names(table(myinfo))
+ names(bio.agru2) <- bio.agru2
+
+ }
+
+
+
+
+
+###########################################################################
+###########################################################################
+
+
+#### FEATURES DETECTION per BIOTYPE
+
+ if (agru.biotype) {
+
+ mybioagru <- bio.agru2[myinfo]
+
+ } else { mybioagru <- myinfo }
+
+ detect <- misdatos1 > k
+
+ genome <- 100*table(bio.agru2[myinfo])/sum(table(bio.agru2[myinfo]))
+
+ ordre <- order(genome, decreasing = TRUE)
+
+ perdet1 <- genome*table(mybioagru, detect)[,2]/
+ table(bio.agru2[myinfo])[rownames(table(mybioagru, detect))]
+ perdet2 <- 100*table(mybioagru, detect)[,2]/sum(table(mybioagru, detect)[,2])
+
+ ceros <- rep(0, length(genome))
+
+ biotable <- as.matrix(rbind(genome[ordre], perdet1[ordre],
+ perdet2[ordre], ceros))
+ rownames(biotable) <- c("genome", "detectionVSgenome", "detectionVSsample",
+ "ceros")
+
+ if (is.null(misdatos2)) {
+
+ # Plot (1 sample)
+ png(filename = file.path(opt$dirOut, "DetectionPerGroup.png"),
+ width = 3*480*2, height = 3*480, units = "px", pointsize = 3*12)
+
+ par(mar = c(11, 4, 2, 2), bg = "#e6e6e6")
+
+ barplot(biotable[c(1,3),], main = "Detection per group",
+ xlab = "", ylab = "%features", axis.lty = 1, legend = FALSE,
+ beside = TRUE, col = c("grey", 2), las = 2,
+ ylim = c(0, 100), border = c("grey", 2))
+
+ rect(par("usr")[1], par("usr")[3], par("usr")[2], par("usr")[4],
+ col = "white")
+
+ barplot(biotable[c(1,3),], main = "Detection per group",
+ xlab = "", ylab = "%features", axis.lty = 1, legend = FALSE,
+ beside = TRUE, col = c("grey", 2), las = 2, add = TRUE,
+ ylim = c(0, 100), border = c("grey", 2))
+
+ barplot(biotable[c(2,4),], main = "Detection per group",
+ xlab = "", ylab = "%features", axis.lty = 1, legend = FALSE,
+ beside = TRUE, col = c(2, 1), las = 2, density = 30,
+ ylim = c(0, 100), border = 2, add = TRUE)
+
+ legend(x = "top", bty = "n", horiz = TRUE,
+ fill = c("grey", 2, 2), density = c(NA,30,NA),
+ border = c("grey", 2, 2),
+ legend = c("% in genome", "detected", "% in sample"))
+
+ garbage <- dev.off()
+
+ } else {
+
+ # Plot (2 samples)
+
+ detect2 <- misdatos2>k
+
+ perdet3 <- genome*table(mybioagru, detect2)[names(genome),2]/
+ table(bio.agru2[info])[names(genome)]
+ perdet4 <- 100*table(mybioagru, detect2)[,2]/
+ sum(table(mybioagru, detect2)[,2])
+
+ biotable2 <- as.matrix(rbind(genome[ordre], perdet3[ordre],
+ perdet4[ordre], ceros))
+ rownames(biotable2) <- c("genome", "detectionVSgenome", "detectionVSsample",
+ "ceros")
+
+ png(filename = file.path(opt$dirOut, "DetectionPerGroup.png"),
+ width = 3*480*2, height = 3*480*2, units = "px", pointsize = 3*12)
+# pdf(file = file.path(opt$dirOut, "DetectionPerGroup.pdf"),
+# width = 7*2, height = 7*2)
+
+ par(mar = c(11, 4, 2, 2), mfrow = c(2,1), bg = "#e6e6e6")
+
+ # Datos1
+ barplot(biotable[c(1,3),],
+ main = paste("Detection per group:", nom1),
+ xlab = "", ylab = "%features", axis.lty = 1, legend = FALSE,
+ beside = TRUE, col = c("grey", 2), las = 2,
+ ylim = c(0, 100), border = c("grey", 2))
+
+ rect(par("usr")[1], par("usr")[3], par("usr")[2], par("usr")[4],
+ col = "white")
+
+ barplot(biotable[c(1,3),],
+ main = paste("Detection per group:", nom1),
+ xlab = "", ylab = "%features", axis.lty = 1, legend = FALSE,
+ beside = TRUE, col = c("grey", 2), las = 2, add = TRUE,
+ ylim = c(0, 100), border = c("grey", 2))
+
+ barplot(biotable[c(2,4),],
+ main = paste("Detection per group:", nom1),
+ xlab = "", ylab = "%features", axis.lty = 1, legend = FALSE,
+ beside = TRUE, col = c(2, 1), las = 2, density = 30,
+ ylim = c(0, 100), border = 2, add = TRUE)
+
+ legend(x = "top", bty = "n", horiz = TRUE,
+ fill = c("grey", 2, 2), density = c(NA,30,NA),
+ border = c("grey", 2, 2),
+ legend = c("% in genome", "detected", "% in sample"))
+
+
+ # Datos2
+ barplot(biotable2[c(1,3),],
+ main = paste("Detection per group:", nom2),
+ xlab = "", ylab = "%features", axis.lty = 1, legend = FALSE,
+ beside = TRUE, col = c("grey", 4), las = 2,
+ ylim = c(0, 100), border = c("grey", 4))
+
+ rect(par("usr")[1], par("usr")[3], par("usr")[2], par("usr")[4],
+ col = "white")
+
+ barplot(biotable2[c(1,3),],
+ main = paste("Detection per group:", nom2),
+ xlab = "", ylab = "%features", axis.lty = 1, legend = FALSE,
+ beside = TRUE, col = c("grey", 4), las = 2, add = TRUE,
+ ylim = c(0, 100), border = c("grey", 4))
+
+ barplot(biotable2[c(2,4),],
+ main = paste("Detection per group:", nom2),
+ xlab = "", ylab = "%features", axis.lty = 1, legend = FALSE,
+ beside = TRUE, col = c(4, 1), las = 2, density = 30,
+ ylim = c(0, 100), border = 4, add = TRUE)
+
+ legend(x = "top", bty = "n", horiz = TRUE,
+ fill = c("grey", 4, 4), density = c(NA,30,NA),
+ border = c("grey", 4, 4),
+ legend = c("% in genome", "detected", "% in sample"))
+
+ garbage <- dev.off()
+ }
+
+
+}
+
+
+###########################################################################
+###########################################################################
+
+
+#### SATURATION GLOBAL PLOT
+
+png(filename = paste(opt$dirOut, "GlobalSaturation.png", sep=""),
+ width = 3*480, height = 3*480, units = "px", pointsize = 3*12)
+# pdf(file = file.path(opt$dirOut, "GlobalSaturation.pdf"),
+# width = 7, height = 7)
+
+
+par(mar = c(5,6,4,6), bg = "#e6e6e6")
+
+satur.plot2(datos1 = misdatos1, datos2 = misdatos2, k = k,
+ tit = "Global Saturation Plot",
+ #yleftlim = NULL, yrightlim = NULL,
+ cex.main = cm, cex.lab = cl, cex.axis = ca, cex = cc,
+ legend = c(nom1, nom2))
+
+garbage <- dev.off()
+
+
+
+
+
+
+
+
+############################################################################
+
+
+
+#### SATURATION PLOTS per BIOTYPE
+
+if (!is.null(opt$info)) {
+
+
+
+satbio.mine <- saturbio.dat(datos1 = misdatos1, datos2 = misdatos2, k = k,
+ infobio = myinfo, biotypes = biotipus)
+
+
+for (i in 1:length(biotipus)) {
+
+ png(paste(opt$dirOut, names(biotipus)[i],".png", sep = ""),
+ width = 3*480, height = 3*480, pointsize = 3*12)
+
+# pdf(paste(opt$dirOut, names(biotipus)[i],".pdf", sep = ""),
+# width = 7, height = 7)
+
+
+
+ par(mar = c(5,6,4,6), bg = "#e6e6e6")
+
+ titulo <- paste("Number of features with reads >", k)
+
+ saturbio.plot(depth1 = satbio.mine$depth1, depth2 = satbio.mine$depth2,
+ sat1 = satbio.mine$cond1[[i]], sat2 = satbio.mine$cond2[[i]],
+ newdet1 = satbio.mine$newdet1[[i]],
+ newdet2 = satbio.mine$newdet2[[i]],
+ bionum = satbio.mine$bionum[i],
+ main = paste(names(biotipus)[i],
+ " (", satbio.mine$bionum[i], ")", sep = ""),
+ legend = c(nom1, nom2),
+ yleftlim = c(0, satbio.mine$bionum[i]),
+ ylabL = titulo,
+ ylabR = "New detections per million reads",
+ cex = cc, cex.main = cm, cex.lab = cl)
+
+ garbage <- dev.off()
+}
+
+
+
+
+############################################################################
+############################################################################
+
+
+
+#### COUNTS DISTRIBUTION -- per BIOTYPE
+
+countdist.mine <- countsbio.dat(misdatos1, misdatos2, k = k, nbox = 1,
+ infobio = myinfo, biotypes = biotipus)
+
+countlist <- countdist.mine$cond1[[1]]
+
+for (i in 2:length(countdist.mine$cond1)) {
+ countlist <- c(countlist, countdist.mine$cond1[[i]])
+}
+names(countlist) <- names(countdist.mine$cond1)
+
+ysup <- max(sapply(countlist, quantile, probs = 0.75, na.rm = TRUE),
+ na.rm = TRUE)*1.3
+
+if (is.null(misdatos2)) {
+
+ png(paste(opt$dirOut, "counts_boxplot.png", sep=""),
+ width = 3*480, height = 3*480, pointsize = 3*12)
+# pdf(paste(opt$dirOut, "counts_boxplot.pdf", sep=""),
+# width = 7, height = 7)
+
+ par(mar = c(11,4,6,2), bg = "#e6e6e6")
+
+} else {
+
+ countlist2 <- countdist.mine$cond2[[1]]
+
+ for (i in 2:length(countdist.mine$cond2)) {
+ countlist2 <- c(countlist2, countdist.mine$cond2[[i]])
+ }
+ names(countlist2) <- names(countdist.mine$cond2)
+
+ ysup2 <- max(sapply(countlist2, quantile, probs = 0.75, na.rm = TRUE),
+ na.rm = TRUE)*1.3
+
+ ysup <- max(ysup, ysup2, na.rm = TRUE)
+
+ png(paste(opt$dirOut, "counts_boxplot.png", sep=""),
+ width = 3*480*2, height = 3*480, pointsize = 3*12)
+# pdf(paste(opt$dirOut, "counts_boxplot.pdf", sep=""), width = 7*2, height = 7)
+
+
+ par(mar = c(11,4,6,2), mfrow = c(1,2), bg = "#e6e6e6")
+
+}
+
+
+boxplot(countlist[ordre], las = 2,
+ main = paste("Counts distribution per group:", nom1),
+ ylim = c(k, ysup), col = 2)
+
+rect(par("usr")[1], par("usr")[3], par("usr")[2], par("usr")[4], col = "white")
+
+boxplot(countlist[ordre], las = 2,
+ main = paste("Counts distribution per group:", nom1),
+ ylim = c(k, ysup), col = 2, add = TRUE,
+ ylab = "Read counts of detected features")
+
+cuantos <- sapply(countlist, length)
+cuantos1 <- which(cuantos == 1)
+sumant <- sapply(countlist, sum, na.rm = TRUE)
+sumant0 <- which(sumant == 0)
+cuantosNA <- intersect(cuantos1, sumant0)
+cuantos[cuantosNA] <- 0
+mtext(cuantos[ordre], 3, at = 1:length(countlist), cex = 1, las = 2)
+
+
+if (!is.null(misdatos2)) {
+
+ boxplot(countlist2[ordre], las = 2,
+ main = paste("Counts distribution per group:", nom2),
+ ylim = c(k, ysup), col = 4)
+
+ rect(par("usr")[1], par("usr")[3], par("usr")[2], par("usr")[4],
+ col = "white")
+
+ boxplot(countlist2[ordre], las = 2,
+ main = paste("Counts distribution per group:", nom2),
+ ylim = c(k, ysup), col = 4, add = TRUE,
+ ylab = "Read counts of detected features")
+
+ cuantos <- sapply(countlist2, length)
+ cuantos1 <- which(cuantos == 1)
+ sumant <- sapply(countlist2, sum, na.rm = TRUE)
+ sumant0 <- which(sumant == 0)
+ cuantosNA <- intersect(cuantos1, sumant0)
+ cuantos[cuantosNA] <- 0
+ mtext(cuantos[ordre], 3, at = 1:length(countlist2), cex = 1, las = 2)
+
+}
+
+garbage <- dev.off()
+
+
+
+
+############################################################################
+
+
+#### COUNTS DISTRIBUTION -- per BIOTYPE + sequencing depth
+
+countbio.mine <- countsbio.dat(misdatos1, misdatos2, k = k,
+ infobio = myinfo, biotypes = biotipus)
+
+
+for (i in 1:length(biotipus)) {
+
+ png(paste(opt$dirOut, names(biotipus)[i],"_boxplot.png", sep = ""),
+ width = 3*480, height = 3*480, pointsize = 3*12)
+# pdf(paste(opt$dirOut, names(biotipus)[i],"_boxplot.pdf", sep = ""),
+# width = 7, height = 7)
+
+
+ countbio.plot(depth1 = countbio.mine$depth1,
+ depth2 = countbio.mine$depth2,
+ sat1 = countbio.mine$cond1[[i]],
+ sat2 = countbio.mine$cond2[[i]],
+ bionum = countbio.mine$bionum[[i]], las = 1, cex = 1.2,
+ legend = c(nom1, nom2),
+ main = names(biotipus)[i],
+ ylab = "Read counts of detected features",
+ xlab = "Sequencing Depth (million reads)")
+
+ garbage <- dev.off()
+}
+
+
+
+}
+
+
+
diff --git a/src/main/resources/org/bioinfo/ngs/qc/qualimap/species/human.61.genes.biotypes.txt b/src/main/resources/org/bioinfo/ngs/qc/qualimap/species/human.61.genes.biotypes.txt
new file mode 100644
index 0000000..feb98c7
--- /dev/null
+++ b/src/main/resources/org/bioinfo/ngs/qc/qualimap/species/human.61.genes.biotypes.txt
@@ -0,0 +1,53515 @@
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diff --git a/src/main/resources/org/bioinfo/ngs/qc/qualimap/species/human.biotypes.groups.txt b/src/main/resources/org/bioinfo/ngs/qc/qualimap/species/human.biotypes.groups.txt
new file mode 100644
index 0000000..256ef88
--- /dev/null
+++ b/src/main/resources/org/bioinfo/ngs/qc/qualimap/species/human.biotypes.groups.txt
@@ -0,0 +1,31 @@
+IG_C_gene IG
+IG_C_pseudogene IG
+IG_D_gene IG
+IG_J_gene IG
+IG_J_pseudogene IG
+IG_V_gene IG
+IG_V_pseudogene IG
+lincRNA lincRNA
+miRNA miRNA
+miRNA_pseudogene miRNA
+misc_RNA misc_RNA
+misc_RNA_pseudogene misc_RNA
+Mt_rRNA mitocondrial
+Mt_tRNA mitocondrial
+Mt_tRNA_pseudogene mitocondrial
+polymorphic_pseudogene pseudogene
+processed_transcript processed_transcript
+protein_coding protein_coding
+pseudogene pseudogene
+rRNA rRNA
+rRNA_pseudogene rRNA
+scRNA_pseudogene scRNA_pseudogene
+snoRNA snoRNA
+snoRNA_pseudogene snoRNA
+snRNA snRNA
+snRNA_pseudogene snRNA
+TR_C_gene TR
+TR_J_gene TR
+tRNA_pseudogene tRNA_pseudogene
+TR_V_gene TR
+TR_V_pseudogene TR
diff --git a/src/main/resources/org/bioinfo/ngs/qc/qualimap/species/human.hg19.gc_histogram.txt b/src/main/resources/org/bioinfo/ngs/qc/qualimap/species/human.hg19.gc_histogram.txt
new file mode 100644
index 0000000..ff54b06
--- /dev/null
+++ b/src/main/resources/org/bioinfo/ngs/qc/qualimap/species/human.hg19.gc_histogram.txt
@@ -0,0 +1,1002 @@
+#HISTOGRAM WINDOW_SIZE=1000, SHOT_COUNT=2864484, INPUT_CONFIG=hg19.list
+0 : 0.000000
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diff --git a/src/main/resources/org/bioinfo/ngs/qc/qualimap/species/mouse.61.genes.biotypes.txt b/src/main/resources/org/bioinfo/ngs/qc/qualimap/species/mouse.61.genes.biotypes.txt
new file mode 100644
index 0000000..7e1bad9
--- /dev/null
+++ b/src/main/resources/org/bioinfo/ngs/qc/qualimap/species/mouse.61.genes.biotypes.txt
@@ -0,0 +1,36817 @@
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diff --git a/src/main/resources/org/bioinfo/ngs/qc/qualimap/species/mouse.biotypes.groups.txt b/src/main/resources/org/bioinfo/ngs/qc/qualimap/species/mouse.biotypes.groups.txt
new file mode 100644
index 0000000..256ef88
--- /dev/null
+++ b/src/main/resources/org/bioinfo/ngs/qc/qualimap/species/mouse.biotypes.groups.txt
@@ -0,0 +1,31 @@
+IG_C_gene IG
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+IG_V_pseudogene IG
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diff --git a/src/main/resources/org/bioinfo/ngs/qc/qualimap/species/mouse.mm10.gc_histogram.txt b/src/main/resources/org/bioinfo/ngs/qc/qualimap/species/mouse.mm10.gc_histogram.txt
new file mode 100644
index 0000000..60940f6
--- /dev/null
+++ b/src/main/resources/org/bioinfo/ngs/qc/qualimap/species/mouse.mm10.gc_histogram.txt
@@ -0,0 +1,1002 @@
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diff --git a/src/main/resources/org/bioinfo/ngs/qc/qualimap/species/mouse.mm9.gc_histogram.txt b/src/main/resources/org/bioinfo/ngs/qc/qualimap/species/mouse.mm9.gc_histogram.txt
new file mode 100644
index 0000000..1714007
--- /dev/null
+++ b/src/main/resources/org/bioinfo/ngs/qc/qualimap/species/mouse.mm9.gc_histogram.txt
@@ -0,0 +1,1002 @@
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+413 : 0.006745
+414 : 0.006832
+415 : 0.006833
+416 : 0.006986
+417 : 0.006885
+418 : 0.006976
+419 : 0.006997
+420 : 0.007019
+421 : 0.006961
+422 : 0.006891
+423 : 0.006823
+424 : 0.006860
+425 : 0.006757
+426 : 0.006754
+427 : 0.006847
+428 : 0.006703
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+430 : 0.006666
+431 : 0.006625
+432 : 0.006609
+433 : 0.006576
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+437 : 0.006409
+438 : 0.006488
+439 : 0.006304
+440 : 0.006367
+441 : 0.006308
+442 : 0.006261
+443 : 0.006245
+444 : 0.006103
+445 : 0.006096
+446 : 0.006014
+447 : 0.005899
+448 : 0.005826
+449 : 0.005796
+450 : 0.005771
+451 : 0.005716
+452 : 0.005586
+453 : 0.005494
+454 : 0.005417
+455 : 0.005251
+456 : 0.005274
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+458 : 0.005043
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+460 : 0.004920
+461 : 0.004952
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+463 : 0.004705
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+466 : 0.004504
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+468 : 0.004376
+469 : 0.004227
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+472 : 0.004038
+473 : 0.003996
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+475 : 0.003866
+476 : 0.003756
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+479 : 0.003615
+480 : 0.003512
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+482 : 0.003346
+483 : 0.003250
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+485 : 0.003147
+486 : 0.003062
+487 : 0.002977
+488 : 0.002927
+489 : 0.002788
+490 : 0.002764
+491 : 0.002684
+492 : 0.002685
+493 : 0.002574
+494 : 0.002539
+495 : 0.002469
+496 : 0.002416
+497 : 0.002354
+498 : 0.002234
+499 : 0.002252
+500 : 0.002267
+501 : 0.002134
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+503 : 0.002064
+504 : 0.001957
+505 : 0.001945
+506 : 0.001909
+507 : 0.001879
+508 : 0.001798
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+593 : 0.000131
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+629 : 0.000058
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+665 : 0.000027
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+667 : 0.000024
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+670 : 0.000022
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+680 : 0.000021
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+714 : 0.000010
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+718 : 0.000011
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+723 : 0.000008
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+728 : 0.000006
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+738 : 0.000005
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+744 : 0.000004
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+753 : 0.000002
+754 : 0.000003
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+756 : 0.000003
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+760 : 0.000005
+761 : 0.000002
+762 : 0.000001
+763 : 0.000005
+764 : 0.000004
+765 : 0.000002
+766 : 0.000001
+767 : 0.000003
+768 : 0.000003
+769 : 0.000002
+770 : 0.000002
+771 : 0.000002
+772 : 0.000002
+773 : 0.000003
+774 : 0.000001
+775 : 0.000002
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+791 : 0.000001
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diff --git a/src/test/java/org/bioinfo/ngs/qc/qualimap/test/BamQCTest.java b/src/test/java/org/bioinfo/ngs/qc/qualimap/test/BamQCTest.java
new file mode 100644
index 0000000..c068283
--- /dev/null
+++ b/src/test/java/org/bioinfo/ngs/qc/qualimap/test/BamQCTest.java
@@ -0,0 +1,145 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.test;
+
+import org.bioinfo.ngs.qc.qualimap.beans.BamQCRegionReporter;
+import org.bioinfo.ngs.qc.qualimap.process.BamStatsAnalysis;
+import org.junit.Test;
+
+import java.io.*;
+import java.util.*;
+
+import static org.junit.Assert.assertTrue;
+
+public class BamQCTest {
+
+
+ List<TestConfig> tests;
+
+
+ public BamQCTest() throws IOException {
+
+ Environment testEnv = new Environment();
+
+ tests = new ArrayList<TestConfig>();
+
+ tests.add( new TestConfig("bamqc/test001.txt", testEnv) );
+ tests.add( new TestConfig("bamqc/test002.txt", testEnv) );
+ tests.add( new TestConfig("bamqc/test003.txt", testEnv) );
+ tests.add( new TestConfig("bamqc/test004.txt", testEnv) );
+ tests.add( new TestConfig("bamqc/test005.txt", testEnv) );
+ //tests.add( new TestConfig("bamqc/test006.txt", testEnv) );
+ //tests.add( new TestConfig("bamqc/test007.txt", testEnv) );
+ }
+
+ @Test
+ public void testStats() {
+
+
+ for (TestConfig test : tests) {
+
+ System.err.println("\nRunning test " + test.getPath() + "\n");
+
+
+ BamStatsAnalysis bamQc = new BamStatsAnalysis(test.getPathToBamFile()) ;
+
+ String pathToRegionFile = test.getPathToRegionFile();
+ if (pathToRegionFile != null && !pathToRegionFile.isEmpty()) {
+ bamQc.setSelectedRegions(pathToRegionFile);
+ bamQc.setComputeOutsideStats(test.getComputeOutsideStats());
+ }
+
+ BamQCRegionReporter bamQcReporter = new BamQCRegionReporter(false, true);
+
+
+ try {
+ bamQc.run();
+ bamQcReporter.loadReportData(bamQc.getBamStats());
+ bamQcReporter.computeChartsBuffers(bamQc.getBamStats(), bamQc.getLocator(), bamQc.isPairedData());
+ } catch (Exception e) {
+ assertTrue("Error calculating stats. " + e.getMessage(), false);
+ e.printStackTrace();
+ return;
+ }
+
+ Properties calculatedProps = bamQcReporter.generateBamQcProperties();
+
+ // For generating correct tests
+ try {
+ calculatedProps.store(new FileOutputStream(test.getResultsPath() + ".new"), null);
+ } catch (IOException e) {
+ e.printStackTrace();
+ }
+
+ compareProperties(calculatedProps, test.getResultsPath());
+
+ if (test.getComputeOutsideStats() && test.getOutsideResultsPath() != null) {
+ BamQCRegionReporter outsideReporter = new BamQCRegionReporter(true, false);
+ outsideReporter.loadReportData(bamQc.getOutsideBamStats());
+ /*outsideReporter.computeChartsBuffers(bamQc.getOutsideBamStats(),
+ bamQc.getLocator(), bamQc.isPairedData());*/
+ Properties outsideProps = outsideReporter.generateBamQcProperties();
+
+ /*try {
+ outsideProps.store(new FileOutputStream(test.getOutsideResultsPath()), null);
+ } catch (IOException e) {
+ e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates.
+ }*/
+
+ compareProperties(outsideProps, test.getOutsideResultsPath());
+ }
+
+ }
+ }
+
+
+ void compareProperties(Properties calculatedProps, String pathToValidProperties){
+ Properties validProps = new Properties();
+ try {
+ validProps.load(new BufferedInputStream(new FileInputStream(pathToValidProperties)));
+ } catch (IOException e) {
+ assertTrue("Error loading valid stats.", false);
+ e.printStackTrace();
+ return;
+ }
+
+ final List<String> keysToSkip = Arrays.asList("meanMappingQualityX", "numWindowsX", "aPercentX");
+
+ for (String key : calculatedProps.stringPropertyNames()) {
+ if (keysToSkip.contains(key)) {
+ continue;
+ }
+ if (validProps.containsKey(key)) {
+ //System.out.println("Property: " + key);
+ String expectedValue = validProps.getProperty(key);
+ String calculatedValue = calculatedProps.getProperty(key);
+ String errorMessage = "Stats are not equal. Key: " + key +
+ "\nExpected: " + expectedValue + "\nCalculated: " + calculatedValue;
+ assertTrue(errorMessage, expectedValue.equals(calculatedValue));
+ } else {
+ assertTrue("Item \"" + key + "\" is not found in result properties.", false);
+ }
+ }
+ }
+
+
+
+}
diff --git a/src/test/java/org/bioinfo/ngs/qc/qualimap/test/Environment.java b/src/test/java/org/bioinfo/ngs/qc/qualimap/test/Environment.java
new file mode 100644
index 0000000..86738aa
--- /dev/null
+++ b/src/test/java/org/bioinfo/ngs/qc/qualimap/test/Environment.java
@@ -0,0 +1,79 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.test;
+
+import java.io.File;
+
+/**
+ * Created by kokonech
+ * Date: 6/6/12
+ * Time: 11:50 AM
+ */
+
+/**
+ * This class provides common environment for running Qualimap tests.
+ * It can be used to access Qualimap test directory and also
+ * process special variables (such as $COMMON_DATA_DIR for example) in test
+ * configuration files.
+ */
+public class Environment {
+
+ String qualimapTestDir;
+ String qualimapDataDir;
+
+ final static String TEST_ROOT_DIR = "$TEST_ROOT_DIR";
+ final static String COMMON_DATA_DIR = "$COMMON_DATA_DIR";
+
+ void initQualimapTestDir() {
+
+ qualimapTestDir = System.getenv("QUALIMAP_TEST_DIR");
+
+ if (qualimapTestDir == null) {
+ System.out.println("QUALIMAP_TEST_DIR environment variable is not set. Setting current dir..");
+ qualimapTestDir = new File("").getAbsolutePath() + File.separator + "test";
+ }
+ }
+
+
+ public Environment() {
+ initQualimapTestDir();
+
+ qualimapTestDir += File.separator;
+ //check that directory is valid
+ File testDir = new File(qualimapTestDir);
+ if (! (testDir.exists() && testDir.isDirectory()) ) {
+ throw new RuntimeException("Failed to init test QualiMap test directory: " + qualimapTestDir );
+ }
+
+ qualimapDataDir = qualimapTestDir + File.separator + "common_data";
+ }
+
+
+ public String getQualimapTestDir() {
+ return qualimapTestDir;
+ }
+
+
+ public String processAttrValue(String attrVal) {
+ return attrVal.replace(TEST_ROOT_DIR, qualimapTestDir)
+ .replace(COMMON_DATA_DIR, qualimapDataDir);
+}
+}
diff --git a/src/test/java/org/bioinfo/ngs/qc/qualimap/test/HistogramTest.java b/src/test/java/org/bioinfo/ngs/qc/qualimap/test/HistogramTest.java
new file mode 100644
index 0000000..faae4c8
--- /dev/null
+++ b/src/test/java/org/bioinfo/ngs/qc/qualimap/test/HistogramTest.java
@@ -0,0 +1,59 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.test;
+
+import org.bioinfo.ngs.qc.qualimap.beans.GenericHistogram;
+import org.junit.Test;
+
+import static org.junit.Assert.assertTrue;
+
+/**
+ * Created by kokonech
+ * Date: 10/5/12
+ * Time: 11:33 AM
+ */
+public class HistogramTest {
+
+
+
+ @Test
+ public void testHistogram(){
+
+ GenericHistogram hist = new GenericHistogram(2,true);
+
+ int[] d1 = {1,1,1,1,1};
+ int[] d2 = {1,1,1,1};
+
+ hist.updateHistogram(d1);
+ hist.updateHistogram(d2);
+
+ double[] histData = hist.getHist();
+
+ assertTrue(histData[0] == 1.1);
+ assertTrue(histData[1] == 0.9);
+
+
+
+
+ }
+
+
+}
\ No newline at end of file
diff --git a/src/test/java/org/bioinfo/ngs/qc/qualimap/test/JunctionLocationMapTest.java b/src/test/java/org/bioinfo/ngs/qc/qualimap/test/JunctionLocationMapTest.java
new file mode 100644
index 0000000..e9b7afe
--- /dev/null
+++ b/src/test/java/org/bioinfo/ngs/qc/qualimap/test/JunctionLocationMapTest.java
@@ -0,0 +1,62 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.test;
+
+import org.bioinfo.ngs.qc.qualimap.common.JunctionLocationMap;
+import org.junit.Test;
+
+import static junit.framework.Assert.assertFalse;
+import static org.junit.Assert.assertTrue;
+
+/**
+ * Created by kokonech
+ * Date: 8/19/14
+ * Time: 10:31 AM
+ */
+public class JunctionLocationMapTest {
+
+ @Test
+ public void simpleTests() {
+
+ JunctionLocationMap locationMap = new JunctionLocationMap();
+
+ locationMap.put("chr1", 25, 30);
+ locationMap.put("chr1", 25, 80);
+ locationMap.put("chr1", 100, 200);
+ assert(locationMap.size("chr1") == 4);
+
+
+ locationMap.setupIntervalTreeMap();
+
+ assertTrue(locationMap.hasOverlap("chr1", 26));
+ assertTrue(locationMap.hasOverlap("chr1", 79));
+ assertFalse(locationMap.hasOverlap("chr1", 780));
+
+
+
+
+
+
+ }
+
+
+
+}
diff --git a/src/test/java/org/bioinfo/ngs/qc/qualimap/test/ReadCountsTest.java b/src/test/java/org/bioinfo/ngs/qc/qualimap/test/ReadCountsTest.java
new file mode 100644
index 0000000..985d94f
--- /dev/null
+++ b/src/test/java/org/bioinfo/ngs/qc/qualimap/test/ReadCountsTest.java
@@ -0,0 +1,234 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.test;
+
+import org.bioinfo.ngs.qc.qualimap.common.LibraryProtocol;
+import org.bioinfo.ngs.qc.qualimap.process.ComputeCountsTask;
+import org.junit.Test;
+import static org.junit.Assert.assertTrue;
+
+import java.io.BufferedReader;
+import java.io.FileReader;
+import java.io.IOException;
+import java.util.*;
+
+/**
+ * Created by kokonech
+ * Date: 12/12/11
+ * Time: 4:11 PM
+ */
+public class ReadCountsTest {
+
+ ArrayList<TestConfig> externalTests = new ArrayList<TestConfig>();
+ ArrayList<TestConfig> internalTests = new ArrayList<TestConfig>();
+
+ Map<String,Long> expectedCounts;
+ long noFeatureExpected, ambigExpected, lowQualExpected, notAlignedExpected, notUniqueExpected;
+
+
+
+ public ReadCountsTest() throws IOException {
+
+ Environment testEnv = new Environment();
+
+ internalTests.add(new TestConfig("count-reads/test001.txt", testEnv) );
+ internalTests.add(new TestConfig("count-reads/test002.txt", testEnv) );
+ internalTests.add(new TestConfig("count-reads/test003.txt", testEnv) );
+ internalTests.add(new TestConfig("count-reads/test004.txt", testEnv) );
+ internalTests.add(new TestConfig("count-reads/test005.txt", testEnv) );
+
+
+ /* External tests use external data */
+ externalTests.add(new TestConfig("count-reads/external/test001.txt", testEnv) );
+ externalTests.add(new TestConfig("count-reads/external/test002.txt", testEnv) );
+ externalTests.add(new TestConfig("count-reads/external/test003.txt", testEnv) );
+ externalTests.add(new TestConfig("count-reads/external/test004.txt", testEnv) );
+ externalTests.add(new TestConfig("count-reads/external/test005.txt", testEnv) );
+ externalTests.add(new TestConfig("count-reads/external/test006.txt", testEnv) );
+
+
+ }
+
+ /*public static
+ <T extends Comparable<? super T>> List<T> asSortedList(Collection<T> c) {
+ List<T> list = new ArrayList<T>(c);
+ java.util.Collections.sort(list);
+ return list;
+ } */
+
+
+ @Test
+ public void externalTests() {
+ runTests(externalTests);
+ }
+
+ @Test
+ public void internalTests() {
+ runTests(internalTests);
+ }
+
+
+ public void runTests(ArrayList<TestConfig> tests) {
+
+
+ for (TestConfig test : tests) {
+
+ System.err.println("Running test " + test.getPath());
+
+ String pathToBamFile = test.getPathToBamFile();
+ if (pathToBamFile.isEmpty()) {
+ assertTrue("Path to region file is empty", false);
+ return;
+ }
+
+ String pathToRegionFile = test.getPathToRegionFile();
+ if (pathToRegionFile.isEmpty()) {
+ assertTrue("Path to region file is empty",false);
+ return;
+
+ }
+
+ String pathToExpectedResults = test.getResultsPath();
+ if (pathToExpectedResults.isEmpty()) {
+ assertTrue("Path to result is empty",false);
+ return;
+
+ }
+
+ ComputeCountsTask computeCountsTask = new ComputeCountsTask(pathToBamFile, pathToRegionFile);
+
+ String libraryType = test.getSpecificAttribute("strand");
+ if (libraryType != null) {
+ assertTrue(ComputeCountsTask.supportedLibraryProtocol(libraryType));
+ computeCountsTask.setProtocol(LibraryProtocol.getProtocolByName(libraryType));
+ }
+
+ String pairedAnalysis = test.getSpecificAttribute("paired");
+ if (pairedAnalysis != null) {
+ if (pairedAnalysis.equalsIgnoreCase("yes")) {
+ computeCountsTask.setPairedEndAnalysis();
+ }
+ }
+
+ String sortingReauried = test.getSpecificAttribute("sorting");
+ if (sortingReauried != null) {
+ if (sortingReauried.equalsIgnoreCase("yes")) {
+ computeCountsTask.setSortingRequired();
+ }
+ }
+
+
+ try {
+ computeCountsTask.run();
+ Map<String,Double> readCounts = computeCountsTask.getReadCounts();
+
+ /*List<String> geneNames = asSortedList(readCounts.keySet());
+
+ for (String key : geneNames) {
+ System.out.println(key + ":" + readCounts.get(key));
+ }*/
+
+ System.out.println("No feature: " + computeCountsTask.getNoFeatureNumber());
+ System.out.println("Not unique alignment: " + computeCountsTask.getAlignmentNotUniqueNumber());
+ System.out.println("Not aligned: " + computeCountsTask.getNotAlignedNumber());
+ System.out.println("Ambiguous: " + computeCountsTask.getAmbiguousNumber());
+
+
+ loadExpectedResults(pathToExpectedResults) ;
+
+ assertTrue("Number of \"ambiguous\" reads is wrong!",
+ ambigExpected == computeCountsTask.getAmbiguousNumber());
+
+ assertTrue("Number of \"no feature\" reads is wrong!",
+ noFeatureExpected == computeCountsTask.getNoFeatureNumber());
+
+
+
+ for (Map.Entry<String,Double> entry: readCounts.entrySet()) {
+
+ String geneName = entry.getKey();
+ if (!expectedCounts.containsKey(geneName)) {
+ assertTrue("Gene is not presented in expected results: " + geneName, false);
+ return;
+ }
+
+ long expected = expectedCounts.get(geneName);
+ long calculated = entry.getValue().longValue();
+
+ if (expected != calculated ) {
+ String report = " Expected value (" + expected + ") " +
+ "doesn't match the calculated (" + calculated + ") " +
+ "for gene " + geneName;
+ assertTrue(report, false);
+ //System.err.println(report);
+ }
+ }
+
+
+ } catch (Exception e) {
+ assertTrue("Error calculating stats. " + e.getMessage(), false);
+ e.printStackTrace();
+ return;
+ }
+
+
+ }
+ }
+
+ private void loadExpectedResults(String pathToResults) throws IOException {
+ BufferedReader reader = new BufferedReader(new FileReader(pathToResults));
+ expectedCounts = new HashMap<String, Long>();
+
+ String line;
+ while ( (line = reader.readLine()) != null ) {
+ if (line.isEmpty()) {
+ continue;
+ }
+
+ if (line.startsWith("no_feature")) {
+ noFeatureExpected = Long.parseLong(line.split("\t")[1]);
+ }
+
+ if (line.startsWith("ambiguous")) {
+ ambigExpected = Long.parseLong(line.split("\t")[1]);
+ }
+
+ if (line.startsWith("not_unique")) {
+ notUniqueExpected = Long.parseLong(line.split("\t")[1]);
+ }
+
+ if (line.startsWith("not_aligned")) {
+ notAlignedExpected = Long.parseLong(line.split("\t")[1]);
+ }
+
+ if (line.startsWith("too_low_aQual")) {
+ lowQualExpected = Long.parseLong(line.split("\t")[1]);
+ }
+
+ String[] values = line.split("\t");
+ expectedCounts.put( values[0].trim(), Long.parseLong(values[1]));
+
+ }
+
+ }
+
+
+}
diff --git a/src/test/java/org/bioinfo/ngs/qc/qualimap/test/RnaSeqTest.java b/src/test/java/org/bioinfo/ngs/qc/qualimap/test/RnaSeqTest.java
new file mode 100644
index 0000000..1bb1934
--- /dev/null
+++ b/src/test/java/org/bioinfo/ngs/qc/qualimap/test/RnaSeqTest.java
@@ -0,0 +1,60 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.test;
+
+import org.bioinfo.commons.utils.StringUtils;
+import org.bioinfo.ngs.qc.qualimap.main.NgsSmartMain;
+import org.junit.Test;
+
+import java.text.DecimalFormat;
+import java.text.NumberFormat;
+import java.util.Locale;
+
+
+public class RnaSeqTest {
+
+ static NumberFormat formatter = DecimalFormat.getInstance(Locale.US);
+
+ @Test
+ public void testBamQC(){
+
+ String []args = {
+ "counts"
+ };
+ try {
+ //NgsSmartMain.main(args);
+ System.out.println("Boo!");
+
+ formatter.setMaximumFractionDigits(2);
+ System.out.println(formatter.format(1000000000));
+ System.out.println(formatter.format(25.15546756745));
+
+
+
+ //formatter.
+
+
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ }
+ }
+}
diff --git a/src/test/java/org/bioinfo/ngs/qc/qualimap/test/TestConfig.java b/src/test/java/org/bioinfo/ngs/qc/qualimap/test/TestConfig.java
new file mode 100644
index 0000000..32e11eb
--- /dev/null
+++ b/src/test/java/org/bioinfo/ngs/qc/qualimap/test/TestConfig.java
@@ -0,0 +1,87 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.test;
+
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileReader;
+import java.io.IOException;
+import java.util.HashMap;
+
+/**
+ * Created by kokonech
+ * Date: 12/12/11
+ * Time: 4:19 PM
+ */
+public class TestConfig {
+
+
+ HashMap<String,String> attributes;
+ String path;
+
+ private final String BAM_FILE_ATTR = "bamfile";
+ private final String RESULTS_FILE_ATTR = "result";
+ private final String OUTSIDE_RESULTS_ATTR = "outside_result";
+ private final String REGIONS_FILE_ATTR = "regions";
+ private final String OUTSIDE_STATS_ATTR = "compute_outside_stats";
+
+ private HashMap<String,String> parseConfigFile(BufferedReader fileReader, Environment testEnv) throws IOException {
+ HashMap<String,String> attrMap = new HashMap<String, String>();
+ String s;
+ while ((s = fileReader.readLine()) != null) {
+ if (s.isEmpty() || s.startsWith("#")) {
+ continue;
+ }
+ String[] attrs = s.split("=");
+ String attrName = attrs[0].trim();
+ String attrValue = testEnv.processAttrValue(attrs[1].trim());
+ attrMap.put( attrName , attrValue);
+ }
+
+ attrMap.put(null,"");
+
+ return attrMap;
+ }
+
+ public TestConfig(String pathToConfig, Environment testEnv ) throws IOException {
+ String qualimapTestDir = testEnv.getQualimapTestDir();
+ path = qualimapTestDir + File.separator + pathToConfig;
+ BufferedReader fileReader = new BufferedReader( new FileReader(path));
+ attributes = parseConfigFile(fileReader,testEnv);
+ }
+
+ public String getPath() {
+ return path;
+ }
+
+ public String getSpecificAttribute(String attrName) { return attributes.get(attrName); }
+
+ public String getOutsideResultsPath() { return attributes.get(OUTSIDE_RESULTS_ATTR); }
+ public String getPathToBamFile() { return attributes.get(BAM_FILE_ATTR); }
+ public String getResultsPath() { return attributes.get(RESULTS_FILE_ATTR); }
+ public String getPathToRegionFile() { return attributes.get(REGIONS_FILE_ATTR); }
+ public boolean getComputeOutsideStats()
+ {
+ return attributes.get(OUTSIDE_STATS_ATTR) != null;
+ }
+
+
+}
diff --git a/src/test/java/org/bioinfo/ngs/qc/qualimap/test/TestEjml.java b/src/test/java/org/bioinfo/ngs/qc/qualimap/test/TestEjml.java
new file mode 100644
index 0000000..6f35c28
--- /dev/null
+++ b/src/test/java/org/bioinfo/ngs/qc/qualimap/test/TestEjml.java
@@ -0,0 +1,84 @@
+/**
+ * QualiMap: evaluation of next generation sequencing alignment data
+ * Copyright (C) 2015 Garcia-Alcalde et al.
+ * http://qualimap.org
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ */
+package org.bioinfo.ngs.qc.qualimap.test;
+
+import org.bioinfo.ngs.qc.qualimap.beans.PrincipleComponentAnalysis;
+import org.ejml.simple.SimpleMatrix;
+import org.junit.Test;
+
+import static org.junit.Assert.assertTrue;
+
+/**
+ * Created by kokonech
+ * Date: 6/12/14
+ * Time: 10:44 AM
+ */
+public class TestEjml {
+
+ @Test
+ public void simpleTest() {
+ double [] data = {1,2.2,3.3,4};
+ SimpleMatrix m = new SimpleMatrix(2,2,true, data);
+ assertTrue(m.get(1,1) == 4);
+
+ }
+
+ @Test
+ public void testPCA() {
+
+ double[] x = {0.69, -1.31, 0.39, 0.09, 1.29, 0.49, 0.19, -0.81, -0.31, -0.71 };
+ double[] y = {0.49, -1.21, 0.99, 0.29, 1.09, 0.79, -0.31, -0.81, -0.31, -1.01 };
+
+ PrincipleComponentAnalysis pca = new PrincipleComponentAnalysis();
+ pca.setup(10, 2);
+
+ for (int i = 0; i < 10; ++i) {
+ double[] sample = {x[i],y[i]};
+ pca.addSample( sample );
+ }
+
+ pca.computeBasis(2);
+ double[] pc1 = pca.getBasisVector(0);
+ assertTrue(pc1.length == 2);
+ System.out.println(pc1[0]);
+ System.out.println(pc1[1]);
+
+
+ /*for (int i = 0; i < 10; ++i) {
+ double[] sample = {x[i],y[i]};
+ double[] cS = pca.sampleToEigenSpace(sample);
+ System.out.println("(" + cS[0] + " " + cS[1] + ")");
+ } */
+
+ double[] s1 = {x[0],y[0]};
+ double[] c1 = pca.sampleToEigenSpace(s1);
+
+ // Expecting (-0.8279702, 0.1751153)
+ double c1Len = c1[0]*c1[0] + c1[1]*c1[1];
+ assertTrue( c1Len - 0.7162 < 0.00001);
+
+
+
+
+
+ }
+
+}
diff --git a/test/bamqc/results/pl.props b/test/bamqc/results/pl.props
new file mode 100644
index 0000000..2a17d79
--- /dev/null
+++ b/test/bamqc/results/pl.props
@@ -0,0 +1,44 @@
+#Mon Apr 08 12:11:51 CEST 2013
+ACGT_CONTENT_GC_Percentage=26.36%
+GLOBALS_Mapped_reads,_only_first_in_pair=2,887,408/34.43%
+GLOBALS_Mapped_reads,_both_in_pair=5,245,862/62.55%
+MAL14=[3291871, 39673830, 12.05]
+MAL13=[2895605, 29094085, 10.05]
+ACGT_CONTENT_Number/percentage_of_G's=36,819,016/13.23%
+MAL12=[2271477, 24170959, 10.64]
+MAL11=[2038337, 27378864, 13.43]
+MAL10=[1687655, 19024621, 11.27]
+COVERAGE_Mean=11.95
+GLOBALS_Read_min/max/mean_length=12/54/49.65
+INSERT_SIZE_Mean=216.77
+GLOBALS_Mapped_reads,_only_second_in_pair=2,942,991/35.09%
+Pf_mito=[5967, 301519, 50.53]
+INDELS_Insertions=75,092
+INDELS_Deletions=72,021
+ACGT_CONTENT_Number/percentage_of_N's=0/0%
+GLOBALS_Reference_size=23,299,734
+GLOBALS_Unmapped_reads=2,555,905/30.48%
+GLOBALS_Duplication_rate=37.42%
+PF_apicoplast_genome_1=[29430, 296964, 10.09]
+MAL9=[1541723, 20508931, 13.3]
+MAL8=[1419563, 17210722, 12.12]
+INDELS_Total_reads_with_indels=147,113
+COVERAGE_Standard_Deviation=118.33
+MAL7=[1501717, 24460910, 16.29]
+MAL6=[1418244, 14824281, 10.45]
+MAL5=[1343552, 18793257, 13.99]
+MAL4=[1204112, 8133661, 6.75]
+MAL3=[1060087, 9092270, 8.58]
+ACGT_CONTENT_Number/percentage_of_C's=36,518,697/13.13%
+MAL2=[947102, 12060361, 12.73]
+MAL1=[643292, 13337149, 20.73]
+ACGT_CONTENT_Number/percentage_of_T's=101,913,784/36.63%
+GLOBALS_Number_of_reads=8,386,304
+MAPPING_QUALITY_Mean_Mapping_Quality=42.37
+GLOBALS_Clipped_reads=2,956,177/35.25%
+GLOBALS_Mapped_reads,_singletons=584,537/6.97%
+GLOBALS_Mapped_reads=5,830,399/69.52%
+INSERT_SIZE_Median=181
+GLOBALS_Paired_reads=5,830,399/69.52%
+INDELS_Homopolymer_indels=49.85%
+ACGT_CONTENT_Number/percentage_of_A's=102,959,340/37.01%
diff --git a/test/bamqc/results/pl_1_and_2.props b/test/bamqc/results/pl_1_and_2.props
new file mode 100644
index 0000000..7fe1724
--- /dev/null
+++ b/test/bamqc/results/pl_1_and_2.props
@@ -0,0 +1,44 @@
+#Mon Apr 08 12:08:31 CEST 2013
+ACGT_CONTENT_GC_Percentage=29.64%
+GLOBALS_Mapped_reads,_only_first_in_pair=257,870/49.55%
+GLOBALS_Mapped_reads,_both_in_pair=476,974/91.66%
+MAL14=[3291871, 0, 0]
+MAL13=[2895605, 0, 0]
+ACGT_CONTENT_Number/percentage_of_G's=4,000,000/15.76%
+MAL12=[2271477, 0, 0]
+MAL11=[2038337, 0, 0]
+MAL10=[1687655, 0, 0]
+COVERAGE_Mean=1.09
+GLOBALS_Read_min/max/mean_length=12/54/48.8
+INSERT_SIZE_Mean=15.34
+GLOBALS_Mapped_reads,_only_second_in_pair=262,526/50.45%
+Pf_mito=[5967, 0, 0]
+INDELS_Insertions=6,754
+INDELS_Deletions=6,808
+ACGT_CONTENT_Number/percentage_of_N's=0/0%
+GLOBALS_Reference_size=23,299,734
+GLOBALS_Unmapped_reads=0/0%
+GLOBALS_Duplication_rate=39.5%
+PF_apicoplast_genome_1=[29430, 0, 0]
+MAL9=[1541723, 0, 0]
+MAL8=[1419563, 0, 0]
+INDELS_Total_reads_with_indels=13,562
+COVERAGE_Standard_Deviation=42.54
+MAL7=[1501717, 0, 0]
+MAL6=[1418244, 0, 0]
+MAL5=[1343552, 0, 0]
+MAL4=[1204112, 0, 0]
+MAL3=[1060087, 0, 0]
+ACGT_CONTENT_Number/percentage_of_C's=3,522,578/13.88%
+MAL2=[947102, 12060361, 12.73]
+MAL1=[643292, 13337149, 20.73]
+ACGT_CONTENT_Number/percentage_of_T's=8,338,650/32.85%
+GLOBALS_Number_of_reads=520,396
+MAPPING_QUALITY_Mean_Mapping_Quality=2.76
+GLOBALS_Clipped_reads=247,464/47.55%
+GLOBALS_Mapped_reads,_singletons=43,422/8.34%
+GLOBALS_Mapped_reads=520,396/100%
+INSERT_SIZE_Median=179
+GLOBALS_Paired_reads=520,396/100%
+INDELS_Homopolymer_indels=48.94%
+ACGT_CONTENT_Number/percentage_of_A's=9,520,962/37.51%
diff --git a/test/bamqc/results/pl_1_and_2_inside.props b/test/bamqc/results/pl_1_and_2_inside.props
new file mode 100644
index 0000000..c3c3dbf
--- /dev/null
+++ b/test/bamqc/results/pl_1_and_2_inside.props
@@ -0,0 +1,46 @@
+#Mon Apr 08 12:10:23 CEST 2013
+ACGT_CONTENT_GC_Percentage=30.85%
+GLOBALS_Mapped_reads,_only_first_in_pair=133,258/25.61%
+GLOBALS_Mapped_reads,_both_in_pair=248,872/47.82%
+MAL14=[0, 0, 0]
+MAL13=[0, 0, 0]
+ACGT_CONTENT_Number/percentage_of_G's=2,252,050/16.9%
+MAL12=[0, 0, 0]
+MAL11=[0, 0, 0]
+MAL10=[0, 0, 0]
+COVERAGE_Mean=20.73
+GLOBALS_Read_min/max/mean_length=12/54/48.8
+GLOBALS_Regions_size/percentage_of_reference=643,292/2.76%
+INSERT_SIZE_Mean=6.41
+GLOBALS_Mapped_reads,_only_second_in_pair=135,977/26.13%
+GLOBALS_Correct_strand_reads=0/0%
+Pf_mito=[0, 0, 0]
+INDELS_Insertions=3,343
+INDELS_Deletions=4,175
+ACGT_CONTENT_Number/percentage_of_N's=0/0%
+GLOBALS_Reference_size=23,299,734
+GLOBALS_Unmapped_reads=0/0%
+GLOBALS_Duplication_rate=39.34%
+PF_apicoplast_genome_1=[0, 0, 0]
+MAL9=[0, 0, 0]
+MAL8=[0, 0, 0]
+INDELS_Total_reads_with_indels=7,518
+COVERAGE_Standard_Deviation=234.87
+MAL7=[0, 0, 0]
+MAL6=[0, 0, 0]
+MAL5=[0, 0, 0]
+MAL4=[0, 0, 0]
+MAL3=[0, 0, 0]
+ACGT_CONTENT_Number/percentage_of_C's=1,859,454/13.95%
+MAL2=[0, 0, 0]
+MAL1=[643292, 13337149, 20.73]
+ACGT_CONTENT_Number/percentage_of_T's=3,635,969/27.28%
+GLOBALS_Number_of_reads=520,396
+MAPPING_QUALITY_Mean_Mapping_Quality=1.06
+GLOBALS_Clipped_reads=117,445/22.57%
+GLOBALS_Mapped_reads,_singletons=20,363/3.91%
+GLOBALS_Mapped_reads=269,235/51.74%
+INSERT_SIZE_Median=179
+GLOBALS_Paired_reads=520,396/100%
+INDELS_Homopolymer_indels=44.2%
+ACGT_CONTENT_Number/percentage_of_A's=5,580,176/41.87%
diff --git a/test/bamqc/results/test001.bam.props b/test/bamqc/results/test001.bam.props
new file mode 100644
index 0000000..00519a1
--- /dev/null
+++ b/test/bamqc/results/test001.bam.props
@@ -0,0 +1,19 @@
+#Sat Apr 06 15:55:03 CEST 2013
+chr1=[250, 2500, 10]
+ACGT_CONTENT_Number/percentage_of_A's=541/21.64%
+GLOBALS_Reference_size=250
+ACGT_CONTENT_Number/percentage_of_C's=775/31%
+GLOBALS_Number_of_reads=125
+ACGT_CONTENT_Number/percentage_of_N's=0/0%
+GLOBALS_Mapped_reads=125/100%
+GLOBALS_Unmapped_reads=0/0%
+GLOBALS_Paired_reads=0/0%
+GLOBALS_Duplication_rate=27.78%
+ACGT_CONTENT_Number/percentage_of_G's=761/30.44%
+GLOBALS_Read_min/max/mean_length=20/20/20
+COVERAGE_Standard_Deviation=5.51
+ACGT_CONTENT_Number/percentage_of_T's=423/16.92%
+MAPPING_QUALITY_Mean_Mapping_Quality=36.55
+COVERAGE_Mean=10
+GLOBALS_Clipped_reads=0/0%
+ACGT_CONTENT_GC_Percentage=61.44%
diff --git a/test/bamqc/test001.txt b/test/bamqc/test001.txt
new file mode 100644
index 0000000..cdb8ea1
--- /dev/null
+++ b/test/bamqc/test001.txt
@@ -0,0 +1,4 @@
+# Testing bam file with small reference size
+bamfile=$COMMON_DATA_DIR/gambusino_reads.sorted.bam
+result=$TEST_ROOT_DIR/bamqc/results/test001.bam.props
+
diff --git a/test/bamqc/test002.txt b/test/bamqc/test002.txt
new file mode 100644
index 0000000..5dfceee
--- /dev/null
+++ b/test/bamqc/test002.txt
@@ -0,0 +1,4 @@
+#Basic test
+bamfile=$COMMON_DATA_DIR/pl_1_and_2.bam
+result=$TEST_ROOT_DIR/bamqc/results/pl_1_and_2.props
+
diff --git a/test/bamqc/test003.txt b/test/bamqc/test003.txt
new file mode 100644
index 0000000..b3528e0
--- /dev/null
+++ b/test/bamqc/test003.txt
@@ -0,0 +1,6 @@
+# Test in regions
+
+bamfile=$COMMON_DATA_DIR/pl_1_and_2.bam
+result=$TEST_ROOT_DIR/bamqc/results/pl_1_and_2_inside.props
+regions=$COMMON_DATA_DIR/test_region_01.gff
+
diff --git a/test/bamqc/test004.txt b/test/bamqc/test004.txt
new file mode 100644
index 0000000..641f674
--- /dev/null
+++ b/test/bamqc/test004.txt
@@ -0,0 +1,6 @@
+#testing guessRegionFormat and bed region parsing
+
+bamfile=$COMMON_DATA_DIR/pl_1_and_2.bam
+result=$TEST_ROOT_DIR/bamqc/results/pl_1_and_2_inside.props
+regions=$COMMON_DATA_DIR/test_region_01_bed
+
diff --git a/test/bamqc/test005.txt b/test/bamqc/test005.txt
new file mode 100644
index 0000000..49b1868
--- /dev/null
+++ b/test/bamqc/test005.txt
@@ -0,0 +1,5 @@
+# some big test
+
+bamfile=/data/qualimap_release_data/alignments/Plasmodium-falciparum-3D7_RNASeq.bam
+result=$TEST_ROOT_DIR/bamqc/results/pl.props
+
diff --git a/test/bamqc/test006.txt b/test/bamqc/test006.txt
new file mode 100644
index 0000000..0d86f69
--- /dev/null
+++ b/test/bamqc/test006.txt
@@ -0,0 +1,6 @@
+# some big test
+
+bamfile=/data/qualimap_release_data/alignments/Plasmodium-falciparum-3D7_RNASeq.bam
+result=$TEST_ROOT_DIR/bamqc/results/pl_inside.props
+regions=/data/qualimap_release_data/annotations/Plasmodium-falciparum-3D7.gff
+
diff --git a/test/bamqc/test007.txt b/test/bamqc/test007.txt
new file mode 100644
index 0000000..44e5f1d
--- /dev/null
+++ b/test/bamqc/test007.txt
@@ -0,0 +1,8 @@
+# the region contains all reads of the file
+
+bamfile=/home/kokonech/sample_data/pl_1_and_2.bam
+result=/home/kokonech/sample_data/pl_1_and_2_inside.properties
+compute_outside_stats=true
+outside_result=/home/kokonech/sample_data/pl_1_and_2_outside.properties
+regions=/home/kokonech/sample_data/pl_big.gff
+
diff --git a/test/common_data/gambusino_chr1.gff b/test/common_data/gambusino_chr1.gff
new file mode 100644
index 0000000..54e5b8f
--- /dev/null
+++ b/test/common_data/gambusino_chr1.gff
@@ -0,0 +1,2 @@
+chr1 region1 region 1 150 500 + . touch
+
diff --git a/test/common_data/gambusino_reads.sorted.bam b/test/common_data/gambusino_reads.sorted.bam
new file mode 100644
index 0000000..9248dc7
Binary files /dev/null and b/test/common_data/gambusino_reads.sorted.bam differ
diff --git a/test/common_data/pl_1_and_2.bam b/test/common_data/pl_1_and_2.bam
new file mode 100644
index 0000000..745b405
Binary files /dev/null and b/test/common_data/pl_1_and_2.bam differ
diff --git a/test/common_data/test_region_01.gff b/test/common_data/test_region_01.gff
new file mode 100644
index 0000000..3ad83b5
--- /dev/null
+++ b/test/common_data/test_region_01.gff
@@ -0,0 +1 @@
+MAL1 qualimap region 1 643292 gene 500 +
diff --git a/test/common_data/test_region_01_bed b/test/common_data/test_region_01_bed
new file mode 100644
index 0000000..8d438c4
--- /dev/null
+++ b/test/common_data/test_region_01_bed
@@ -0,0 +1 @@
+MAL1 0 643292 gene 500 +
diff --git a/test/common_data/transcripts.gtf b/test/common_data/transcripts.gtf
new file mode 100644
index 0000000..b15f5c3
--- /dev/null
+++ b/test/common_data/transcripts.gtf
@@ -0,0 +1,8 @@
+ref1 protein_coding exon 100 200 . + . gene_id "geneA"; transcript_id "tA1"; exon_number "1"; gene_name "A"; transcript_name "A1"; gene_biotype "protein_coding";
+ref1 protein_coding exon 400 500 . + . gene_id "geneA"; transcript_id "tA1"; exon_number "2"; gene_name "A"; transcript_name "A1"; gene_biotype "protein_coding";
+ref1 protein_coding exon 600 700 . + . gene_id "geneA"; transcript_id "tA1"; exon_number "2"; gene_name "A"; transcript_name "A1"; gene_biotype "protein_coding";
+ref1 protein_coding exon 600 750 . + . gene_id "geneB"; transcript_id "tB1"; exon_number "1"; gene_name "B"; transcript_name "B1"; gene_biotype "protein_coding";
+ref1 protein_coding exon 800 1000 . + . gene_id "geneB"; transcript_id "tB1"; exon_number "2"; gene_name "B"; transcript_name "B1"; gene_biotype "protein_coding";
+ref2 protein_coding exon 1201 1400 . - . gene_id "geneC"; transcript_id "tC2"; exon_number "1"; gene_name "C"; transcript_name "C2"; gene_biotype "protein_coding";
+ref2 protein_coding exon 1051 1100 . - . gene_id "geneC"; transcript_id "tC2"; exon_number "2"; gene_name "C"; transcript_name "C2"; gene_biotype "protein_coding";
+ref2 protein_coding exon 1021 1030 . - . gene_id "geneC"; transcript_id "tC2"; exon_number "3"; gene_name "C"; transcript_name "C2"; gene_biotype "protein_coding";
\ No newline at end of file
diff --git a/test/count-reads/external/test001.txt b/test/count-reads/external/test001.txt
new file mode 100644
index 0000000..41eb772
--- /dev/null
+++ b/test/count-reads/external/test001.txt
@@ -0,0 +1,5 @@
+#testing read counts in region. should be only one read
+
+bamfile=/home/kokonech/playgrnd/rna-seq/accepted_hits.20.bam
+regions=/home/kokonech/playgrnd/rna-seq/test001.gtf
+result=/home/kokonech/playgrnd/rna-seq/test001.result
diff --git a/test/count-reads/external/test002.txt b/test/count-reads/external/test002.txt
new file mode 100644
index 0000000..b1ef43c
--- /dev/null
+++ b/test/count-reads/external/test002.txt
@@ -0,0 +1,6 @@
+#testing read counts in region. should be only one read
+
+bamfile=/home/kokonech/playgrnd/rna-seq/accepted_hits.20.bam
+regions=/home/kokonech/playgrnd/rna-seq/bad_gene.gtf
+result=/home/kokonech/playgrnd/rna-seq/bad_gene.result
+
diff --git a/test/count-reads/external/test003.txt b/test/count-reads/external/test003.txt
new file mode 100644
index 0000000..1fbad24
--- /dev/null
+++ b/test/count-reads/external/test003.txt
@@ -0,0 +1,7 @@
+#testing read counts in region. should be only one read
+
+bamfile=/home/kokonech/playgrnd/rna-seq/accepted_hits.20.bam
+regions=/home/kokonech/playgrnd/rna-seq/Homo_sapiens.GRCh37.64.chr20.gtf.filtered
+result=/home/kokonech/playgrnd/rna-seq/test003.result
+
+
diff --git a/test/count-reads/external/test004.txt b/test/count-reads/external/test004.txt
new file mode 100644
index 0000000..bf4808a
--- /dev/null
+++ b/test/count-reads/external/test004.txt
@@ -0,0 +1,6 @@
+#testing read counts in region. should be only one read
+
+bamfile=/home/kokonech/playgrnd/rna-seq/accepted_hits.20.bam
+regions=/home/kokonech/playgrnd/rna-seq/Homo_sapiens.GRCh37.64.chr20.gtf
+result=/home/kokonech/playgrnd/rna-seq/test004.result
+
diff --git a/test/count-reads/external/test005.txt b/test/count-reads/external/test005.txt
new file mode 100644
index 0000000..fe479e5
--- /dev/null
+++ b/test/count-reads/external/test005.txt
@@ -0,0 +1,6 @@
+#testing read counts in region. should be only one read
+
+bamfile=/home/kokonech/playgrnd/rna-seq/accepted_hits.20.bam
+regions=/home/kokonech/playgrnd/rna-seq/Homo_sapiens.GRCh37.64.chr20.gtf.ENSG00000215440
+result=/home/kokonech/playgrnd/rna-seq/test005.result
+
diff --git a/test/count-reads/external/test006.txt b/test/count-reads/external/test006.txt
new file mode 100644
index 0000000..10086d0
--- /dev/null
+++ b/test/count-reads/external/test006.txt
@@ -0,0 +1,7 @@
+#testing read counts in region with strand specific option
+
+bamfile=/home/kokonech/sample_data/accepted_hits.bam
+regions=/home/kokonech/sample_data/mus_musculus.gtf
+result=/home/kokonech/sample_data/test006.result
+strand=strand-specific-forward
+
diff --git a/test/count-reads/reads_001.coord_sort.bam b/test/count-reads/reads_001.coord_sort.bam
new file mode 100644
index 0000000..89b7b58
Binary files /dev/null and b/test/count-reads/reads_001.coord_sort.bam differ
diff --git a/test/count-reads/reads_001.sam b/test/count-reads/reads_001.sam
new file mode 100644
index 0000000..f6b3bed
--- /dev/null
+++ b/test/count-reads/reads_001.sam
@@ -0,0 +1,10 @@
+ at HD VN:1.0 SO:coordinate
+ at SQ SN:ref1 LN:10000
+ at SQ SN:ref2 LN:5000
+R.001 163 ref1 110 50 50M = 410 135 CTTCAAGTACGGAAGAAAGACGACTCCACTATGGAGAAAATGATGTGCAG D<FBFCFF0<A.A>A################################### XA:i:1 MD:Z:42G7 NM:i:1 NH:i:1
+R.001 83 ref1 410 50 50M = 110 -135 TGAAATGCTAGTAGCAGGCAAGTCTCAAATCCGGGCACCAAATCCTAAGC ################################################## XA:i:2 MD:Z:5A26A17 NM:i:2 NH:i:1
+R.002 163 ref1 610 50 50M = 810 135 CTTCAAGTACGGAAGAAAGACGACTCCACTATGGAGAAAATGATGTGCAG D<FBFCFF0<A.A>A################################### XA:i:1 MD:Z:42G7 NM:i:1 NH:i:1
+R.002 83 ref1 810 50 50M = 610 -135 TGAAATGCTAGTAGCAGGCAAGTCTCAAATCCGGGCACCAAATCCTAAGC ################################################## XA:i:2 MD:Z:5A26A17 NM:i:2 NH:i:1
+R.003 147 ref1 100 50 50M = 400 135 CTTCAAGTACGGAAGAAAGACGACTCCACTATGGAGAAAATGATGTGCAG D<FBFCFF0<A.A>A################################### XA:i:1 MD:Z:42G7 NM:i:1 NH:i:1
+R.003 99 ref1 400 50 50M = 100 -135 TGAAATGCTAGTAGCAGGCAAGTCTCAAATCCGGGCACCAAATCCTAAGC ################################################## XA:i:2 MD:Z:5A26A17 NM:i:2 NH:i:1
+R.004 73 ref2 1250 50 50M * 0 0 TGAAATGCTAGTAGCAGGCAAGTCTCAAATCCGGGCACCAAATCCTAAGC ################################################## XA:i:2 MD:Z:5A26A17 NM:i:2 NH:i:1
\ No newline at end of file
diff --git a/test/count-reads/results/test001.result b/test/count-reads/results/test001.result
new file mode 100644
index 0000000..a8dd94b
--- /dev/null
+++ b/test/count-reads/results/test001.result
@@ -0,0 +1,8 @@
+geneA 4
+geneB 1
+geneC 1
+no_feature 0
+ambiguous 1
+too_low_aQual 0
+not_aligned 0
+alignment_not_unique 0
diff --git a/test/count-reads/results/test002.result b/test/count-reads/results/test002.result
new file mode 100644
index 0000000..90f439e
--- /dev/null
+++ b/test/count-reads/results/test002.result
@@ -0,0 +1,8 @@
+geneA 2
+geneB 1
+geneC 1
+no_feature 0
+ambiguous 0
+too_low_aQual 0
+not_aligned 0
+alignment_not_unique 0
diff --git a/test/count-reads/results/test003.result b/test/count-reads/results/test003.result
new file mode 100644
index 0000000..1763f3c
--- /dev/null
+++ b/test/count-reads/results/test003.result
@@ -0,0 +1,8 @@
+geneA 1
+geneB 0
+geneC 0
+no_feature 3
+ambiguous 0
+too_low_aQual 0
+not_aligned 0
+alignment_not_unique 0
diff --git a/test/count-reads/results/test004.result b/test/count-reads/results/test004.result
new file mode 100644
index 0000000..691e329
--- /dev/null
+++ b/test/count-reads/results/test004.result
@@ -0,0 +1,8 @@
+geneA 1
+geneB 1
+geneC 1
+no_feature 1
+ambiguous 0
+too_low_aQual 0
+not_aligned 0
+alignment_not_unique 0
diff --git a/test/count-reads/test001.txt b/test/count-reads/test001.txt
new file mode 100644
index 0000000..b66e5db
--- /dev/null
+++ b/test/count-reads/test001.txt
@@ -0,0 +1,7 @@
+#testing read counts in region
+
+bamfile=$TEST_ROOT_DIR/count-reads/reads_001.sam
+regions=$COMMON_DATA_DIR/transcripts.gtf
+result=$TEST_ROOT_DIR/count-reads/results/test001.result
+strand=non-strand-specific
+paired=no
diff --git a/test/count-reads/test002.txt b/test/count-reads/test002.txt
new file mode 100644
index 0000000..6e8102d
--- /dev/null
+++ b/test/count-reads/test002.txt
@@ -0,0 +1,9 @@
+#testing read counts in region, paired, non-strand-specific
+# checked with htseq v0.5.3:
+# htseq-count -m intersection-strict -s no -o ~/tmp/test.sam reads_001.sam ../common_data/transcripts.gtf
+
+bamfile=$TEST_ROOT_DIR/count-reads/reads_001.sam
+regions=$COMMON_DATA_DIR/transcripts.gtf
+result=$TEST_ROOT_DIR/count-reads/results/test002.result
+strand=non-strand-specific
+paired=yes
diff --git a/test/count-reads/test003.txt b/test/count-reads/test003.txt
new file mode 100644
index 0000000..4ae2c9f
--- /dev/null
+++ b/test/count-reads/test003.txt
@@ -0,0 +1,10 @@
+#testing read counts in region, paired, forward-stranded
+# checked with htseq v0.5.3:
+# htseq-count -m intersection-strict -s forward -o ~/tmp/test.sam reads_001.sam ../common_data/transcripts.gtf
+
+
+bamfile=$TEST_ROOT_DIR/count-reads/reads_001.sam
+regions=$COMMON_DATA_DIR/transcripts.gtf
+result=$TEST_ROOT_DIR/count-reads/results/test003.result
+strand=strand-specific-forward
+paired=yes
diff --git a/test/count-reads/test004.txt b/test/count-reads/test004.txt
new file mode 100644
index 0000000..bae6ce1
--- /dev/null
+++ b/test/count-reads/test004.txt
@@ -0,0 +1,10 @@
+#testing read counts in region, paired, reverse-stranded
+# checked with htseq v0.5.3:
+# htseq-count -m intersection-strict -s reverse -o ~/tmp/test.sam reads_001.sam ../common_data/transcripts.gtf
+
+
+bamfile=$TEST_ROOT_DIR/count-reads/reads_001.sam
+regions=$COMMON_DATA_DIR/transcripts.gtf
+result=$TEST_ROOT_DIR/count-reads/results/test004.result
+strand=strand-specific-reverse
+paired=yes
diff --git a/test/count-reads/test005.txt b/test/count-reads/test005.txt
new file mode 100644
index 0000000..ece0512
--- /dev/null
+++ b/test/count-reads/test005.txt
@@ -0,0 +1,10 @@
+# This test is the same as test004, but requires sorting
+# Use the following command to create file sored by coord:
+# samtools view -Sb reads_001.sam | samtools sort - reads_001.coord_sort
+
+bamfile=$TEST_ROOT_DIR/count-reads/reads_001.coord_sort.bam
+regions=$COMMON_DATA_DIR/transcripts.gtf
+result=$TEST_ROOT_DIR/count-reads/results/test004.result
+strand=strand-specific-reverse
+paired=yes
+sorting=yes
diff --git a/update_version_howto.txt b/update_version_howto.txt
new file mode 100644
index 0000000..3d714c4
--- /dev/null
+++ b/update_version_howto.txt
@@ -0,0 +1,31 @@
+The following files have to updated (new version should be set):
+
+cli/HISTORY
+pom.xml
+
+Make sure all source files have GPL header.
+
+How to add:
+mvn license:format -Dyear=2012
+
+Git tag has to be created.
+
+
+The following pages must be updated:
+
+index.html
+archive.html
+Documentation
+Example reports
+
+Use script to build the version:
+./prepare_new_version.sh
+to create all required elements.
+
+To update qualimap results examples use the github:
+http://github.com/kokonech/kokonech.github.io
+
+
+Currently qualimap is hosted at ssh.cipf.es (subserver wikis)
+
+
diff --git a/util/createPreCalculatedGCContentHistogram.py b/util/createPreCalculatedGCContentHistogram.py
new file mode 100644
index 0000000..f25fb52
--- /dev/null
+++ b/util/createPreCalculatedGCContentHistogram.py
@@ -0,0 +1,96 @@
+import sys
+import argparse
+from Bio import SeqIO
+from Bio.Seq import Seq
+import Bio.SeqUtils as SeqUtils
+import HTSeq
+import numpy as np
+
+
+def idsContainGiven(givenId, transcriptIds):
+ for tId in transcriptIds:
+ if givenId.find(tId) != -1:
+ return True
+
+ return False
+
+if __name__ == "__main__":
+
+ descriptionText = "The script creates a pre-calculated GC-content histogram from FASTA reference dataset. The pre-calucated GC-content histogram is applied in a BAM QC plot \"GC content distribution\" when comparison with a known GC-distribution is activated."
+
+ parser = argparse.ArgumentParser(description = descriptionText,formatter_class=argparse.RawDescriptionHelpFormatter)
+
+ parser.add_argument("-i", action="store", required="true", dest="fastaFile",
+ help="Input genome sequence. ")
+ parser.add_argument("-o", action="store", dest="outFile", default="GC_content.txt",
+ help="Output file. Default is annotations.txt")
+
+ #parser.add_argument("--ignore-strange-chrom", action="store_true", default=False,
+ # dest="ignoreStrangeChromosomes", help="All chromosomes except numbered and X,Y,MT are ignored ")
+
+ args = parser.parse_args()
+
+ print args
+
+ fastaFileName = args.fastaFile
+ outFileName = args.outFile
+ windowSize = 1001
+
+ seqData = SeqIO.parse(fastaFileName, "fasta")
+
+
+
+ numSegments = 0
+ window = []
+
+ for i in range(windowSize):
+ window.append(0)
+
+ for chromosome in seqData:
+
+ k = 0
+ gcSize = 0
+ seq = ""
+ for c in chromosome.seq.upper():
+ if c == "N":
+ continue
+ if c == "G" or c == "C":
+ gcSize +=1
+ k += 1
+
+ if k == windowSize - 1:
+ #print SeqUtils.GC(seq)
+ #print (gcSize)
+ window[gcSize] += 1
+ seq = ""
+ k = 0
+ gcSize = 0
+ numSegments += 1
+ #break
+
+ #seq += c
+
+ print "Chromosome %s is analyzed" % chromosome.name
+
+ print "Analysis is finished, normalizing and reporting resutls..."
+ #print window
+
+ normalizedWindow = []
+
+ for item in window:
+ normalizedWindow.append( float(item)/numSegments )
+
+ outFile = open(outFileName, "w")
+
+ header = "#GC_CONTENT_HISTOGRAM WINDOW_SIZE=%d NUM_SEGMENTS=%d\n" % (windowSize, numSegments)
+ outFile.write(header)
+
+ for i in range(len(normalizedWindow)):
+ outFile.write("%d : %.6f\n" % (i, normalizedWindow[i]) )
+
+
+ outFile.close()
+
+ print "Done."
+
+
diff --git a/util/createQualimapInfoFile.py b/util/createQualimapInfoFile.py
new file mode 100644
index 0000000..a12197e
--- /dev/null
+++ b/util/createQualimapInfoFile.py
@@ -0,0 +1,130 @@
+import sys
+import argparse
+from Bio import SeqIO
+from Bio.Seq import Seq
+import Bio.SeqUtils as SeqUtils
+import HTSeq
+import numpy as np
+
+
+def idsContainGiven(givenId, transcriptIds):
+ for tId in transcriptIds:
+ if givenId.find(tId) != -1:
+ return True
+
+ return False
+
+if __name__ == "__main__":
+
+ descriptionText = "The script extracts features from a GTF file and a FASTA file into Qualimap annotation format. Note: exons have to be sorted according to exon number! This important for correct reverse transcribed cDNA sequences extraction."
+
+ parser = argparse.ArgumentParser(description = descriptionText,formatter_class=argparse.RawDescriptionHelpFormatter)
+
+ parser.add_argument("-g", action="store", required="true", dest="gtfFile",
+ help="Input file with list of genes in GTF format")
+ parser.add_argument("-f", action="store", required="true", dest="fastaFile",
+ help="Input genome sequence. ")
+ parser.add_argument("-o", action="store", dest="outFile", default="annotations.txt",
+ help="Output file. Default is annotations.txt")
+
+ parser.add_argument("--filter", action="store", dest="filterStr", default="",
+ help="Comma-separted list of entries to filter from GTF file \
+ based on given attribute id")
+
+ parser.add_argument("--ignore-strange-chrom", action="store_true", default=False,
+ dest="ignoreStrangeChromosomes", help="All chromosomes except numbered and X,Y,MT are ignored ")
+
+ args = parser.parse_args()
+
+ print args
+
+ gtfFileName = args.gtfFile
+ fastaFileName = args.fastaFile
+ outFileName = args.outFile
+ attr_id = "gene_id"
+
+ # parse GTF file
+
+ gtf_file = HTSeq.GFF_Reader( gtfFileName )
+
+ features = {}
+
+ filtered_transcripts = args.filterStr.split(",")
+ if filtered_transcripts:
+ print "Filtering for: ", filtered_transcripts
+
+ for feature in gtf_file:
+ if feature.type == 'exon':
+ geneName = feature.attr[ attr_id ]
+ #print transcriptName
+ if geneName in features:
+ features[geneName].append(feature)
+ else:
+ features[geneName] = [feature]
+
+ # load & save sequences
+
+ seqData = SeqIO.to_dict(SeqIO.parse(fastaFileName, "fasta"))
+
+ outFile = open(outFileName, "w")
+
+ header = "\"%s\"\t\"%s\"\t\"%s\"\n" % ("biotypes","length","gc")
+ outFile.write(header)
+
+
+ for geneId in features:
+
+ exons = features[geneId]
+
+ print "Processing %s" % geneId
+
+ if len(exons) == 0:
+ continue
+
+ biotype = exons[0].attr["gene_biotype"]
+ length = 0
+ transcripts = {}
+
+ for exon in exons:
+ transcriptId = exon.attr["transcript_id"]
+
+ tSeq = transcripts.get(transcriptId, Seq(""))
+
+ iv = exon.iv
+ seqName = iv.chrom
+ if seqName in seqData:
+ #print "Exon (%s,%d,%d) " % (iv.chrom,iv.start,iv.end)
+ buf = seqData[ iv.chrom ].seq[ iv.start : iv.end ]
+ if iv.strand == '-':
+ buf = buf.reverse_complement()
+ tSeq += buf
+ else:
+ print "Can not locate sequence %s in %s, skipping region..." % (seqName, fastaFileName)
+ transcripts[transcriptId] = tSeq
+
+ gc_array = []
+ lengths = []
+
+ for tSeq in transcripts.values():
+ lengths.append( len(tSeq) )
+ gc_array.append ( SeqUtils.GC(tSeq) )
+
+ #gene_length = len(seq_rec) / len(transcripts)
+ #gc = SeqUtils.GC(seq_rec)
+
+ #print gc_array, lengths
+ gene_length = np.mean(lengths)
+ gene_gc = np.mean(gc_array)
+
+ #print len(seq_rec), len(transcripts),gc
+
+ line = "\"%s\"\t\"%s\"\t%d\t%.2f\n" % (geneId, biotype, gene_length, gene_gc)
+
+ outFile.write ( line )
+
+ #outFile.flush()
+ #sys.stdin.readline()
+
+ outFile.close()
+
+
--
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