[med-svn] [mira] 04/04: new upstream release
Michael Crusoe
misterc-guest at moszumanska.debian.org
Wed May 4 22:23:07 UTC 2016
This is an automated email from the git hooks/post-receive script.
misterc-guest pushed a commit to branch master
in repository mira.
commit 02778bc4bcc408a0e90b81b75a980ca381bdfbcf
Author: Michael R. Crusoe <crusoe at ucdavis.edu>
Date: Mon May 2 22:52:33 2016 -0700
new upstream release
---
debian/changelog | 19 ++
debian/control | 62 +++--
debian/mans/convert_project.1 | 302 ---------------------
debian/mans/fasta2frag.1 | 95 -------
debian/mans/fastaselect.1 | 47 ----
debian/mans/fastatool.1 | 49 ----
debian/mans/fastqselect.1 | 47 ----
debian/mans/fixACE4consed.1 | 32 ---
debian/mans/mira.1 | 53 ----
debian/mans/miraSearchESTSNPs.1 | 43 ---
debian/mans/mirabait.1 | 131 ----------
debian/mans/miraconvert.1 | 327 -----------------------
debian/mans/miradiff.1 | 36 ---
debian/mans/miramem.1 | 33 ---
debian/mans/miramer.1 | 36 ---
debian/mans/scftool.1 | 50 ----
debian/mira-examples.examples | 2 +-
debian/mira-examples.lintian-overrides | 2 +-
debian/mira-rfam-12s-rrna.install | 3 +
debian/mira-rfam-12s-rrna.lintian-overrides | 2 +
debian/mira-rfam-12s-rrna.postinst | 10 +
debian/mira-rfam-12s-rrna.postrm | 7 +
debian/patches/fix_strange_link_issue.patch | 16 --
debian/patches/gcc-6.patch | 16 --
debian/patches/make-reproducible | 19 --
debian/patches/man-directory | 9 +
debian/patches/series | 5 +-
debian/patches/sls-rrna-fix | 19 ++
debian/patches/spelling.patch | 390 +---------------------------
debian/rules | 78 ++----
30 files changed, 130 insertions(+), 1810 deletions(-)
diff --git a/debian/changelog b/debian/changelog
index dccb5f6..24f9afd 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,22 @@
+mira (4.9.6-1) unstable; urgency=medium
+
+ * New upstream release.
+ * dropped all patches except for one spelling fix, as they were incorporated
+ upstream
+ * dropped the -examples package for now, as the minidemo is missing from
+ upstream in this release.
+ * our manpages have been adopted and adapted upstream, so they have been
+ removed
+ * added architecture independent package for rfam 12s rRNA database
+ * enable building docs & rfam packages separately
+ * Standards-Version bump to 3.9.8
+ * Updated package descriptions to remove tools that upstream no longer
+ provides
+ * minidemo is missing from 4.9.6, commented out -examples package for now
+ * cleaned out unnecessary stanzas from debian/rules
+
+ -- Michael R. Crusoe <michael.crusoe at gmail.com> Wed, 04 May 2016 11:18:26 -0700
+
mira (4.9.5-6) unstable; urgency=medium
* Fix build issue with gcc-6
diff --git a/debian/control b/debian/control
index 7f57ee3..0c72d87 100644
--- a/debian/control
+++ b/debian/control
@@ -5,14 +5,12 @@ Uploaders: Charles Plessy <plessy at debian.org>,
Tim Booth <tbooth at ceh.ac.uk>,
Andreas Tille <tille at debian.org>,
Thorsten Alteholz <debian at alteholz.de>,
- Michael R. Crusoe <crusoe at ucdavis.edu>
+ Michael R. Crusoe <michael.crusoe at gmail.com>
Section: science
Priority: optional
Build-Depends: debhelper (>= 9),
- dblatex,
dh-autoreconf,
autoconf-archive,
- docbook-xsl,
libbz2-dev,
libexpat1-dev,
libgoogle-perftools-dev [i386 amd64],
@@ -25,7 +23,9 @@ Build-Depends: debhelper (>= 9),
libboost-filesystem-dev,
libboost-system-dev,
libboost-iostreams-dev
-Standards-Version: 3.9.6
+Build-Depends-Indep: docbook-xsl,
+ dblatex
+Standards-Version: 3.9.8
Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/mira.git
Vcs-Git: https://anonscm.debian.org/git/debian-med/mira.git
Homepage: http://chevreux.org/projects_mira.html
@@ -34,8 +34,9 @@ Package: mira-assembler
Architecture: any
Depends: ${shlibs:Depends},
${misc:Depends}
-Suggests: mira-examples,
- mira-doc
+Recommends: mira-rfam-12s-rrna
+Suggests: mira-doc,
+# mira-examples,
Description: Whole Genome Shotgun and EST Sequence Assembler
The mira genome fragment assembler is a specialised assembler for
sequencing projects classified as 'hard' due to high number of similar
@@ -52,39 +53,36 @@ Description: Whole Genome Shotgun and EST Sequence Assembler
The package provides the following executables:
Binaries provided:
* mira: for assembly of genome sequences
- * miramem: estimating memory needed to assemble projects. Realised through
- link to mira.
- * convert_project: for converting project file types into other types
- * caf2fasta, caf2gbf, caf2text, caf2html, gbf2caf and gbf2fasta are some
- frequently used file converters (realised through links to convert_project)
- * scftool: set of tools useful when working with SCF trace files
- * fastatool: set of tools useful when working with FASTA trace files
- .
- Scripts provided:
- * fasta2frag: fragmenting sequences into smaller, overlapping
- subsequences. Useful for simulating shotgun sequences. Can create
- subsequences in both directions (/default) and also paired-end sequences.
- * fastaselect: given a FASTA file (and possibly a FASTA quality file) and
- a file with names of reads, select the sequences from the input FASTA (and
- quality file) and writes them to an output FASTA
- * fastqselect: like fastaselect, only for FASTQ
- * fixACE4consed: Consed has a bug which incapacitates it from reading
- consensus tags in ACE files written by the MIRA assembler (and possibly
- other programs). This script massages an ACE file so that consed can read
- the consensus tags.
+ * miramem: estimating memory needed to assemble projects.
+ * mirabait: a "grep" like tool to select reads with kmers up to 256 bases.
+ * miraconvert: is a tool to convert, extract and sometimes recalculate all
+ kinds of data related to sequence assembly files.
+
+#Package: mira-examples
+#Architecture: all
+#Depends: ${misc:Depends}
+#Suggests: mira-assembler,
+# mira-doc
+#Description: files to experiment with the mira assembler
+# The mira genome fragment assembler is a specialised assembler for
+# sequencing projects classified as 'hard' due to high number of similar
+# repeats.
+# .
+# This package contains a series of files to exploit the functionality
+# of mira.
-Package: mira-examples
+Package: mira-rfam-12s-rrna
Architecture: all
Depends: ${misc:Depends}
-Suggests: mira-assembler,
- mira-doc
-Description: files to experiment with the mira assembler
+Pre-Depends: mira-assembler
+Suggests: mira-doc
+Description: extract of RFAM 12 rRNA database
The mira genome fragment assembler is a specialised assembler for
sequencing projects classified as 'hard' due to high number of similar
repeats.
.
- This package contains a series of files to exploit the functionality
- of mira.
+ This package contains data to enable MIRA and MIRABAIT to search for rRNA and
+ rDNA. This data set contains an excerpt of the RFAM database.
Package: mira-doc
Architecture: all
diff --git a/debian/mans/convert_project.1 b/debian/mans/convert_project.1
deleted file mode 100644
index 028746c..0000000
--- a/debian/mans/convert_project.1
+++ /dev/null
@@ -1,302 +0,0 @@
-.TH CONVERT_PROJECT "1" "June 2013" "3.9.17" "User Commands"
-.SH NAME
-convert_project \- convert assembly and sequencing file types
-.SH DESCRIPTION
-This program is part of the MIRA assembler package. It is used to convert
-project file types into other types. Please check out the
-documentation below for more detailed information about convert_project.
-.SH SYNOPSIS
-.IP convert_project
-[\-f <fromtype>] [\-t <totype> [\-t <totype> ...]]
-[\-aChimMsuZ]
-[\-AcflnNoqrtvxXyz {...}]
-{infile} {outfile} [<totype> <totype> ...]
-.SH OPTIONS
-.TP
-\fB\-f\fR <fromtype>
-load this type of project files, where fromtype is:
-.TP
-caf
-a complete assembly or single sequences from CAF
-.TP
-maf
-a complete assembly or single sequences from CAF
-.TP
-fasta
-sequences from a FASTA file
-.TP
-fastq
-sequences from a FASTQ file
-.TP
-gbf
-sequences from a GBF file
-.TP
-phd
-sequences from a PHD file
-.TP
-fofnexp
-sequences in EXP files from file of filenames
-.TP
-\fB\-t\fR <totype>
-write the sequences/assembly to this type (multiple
-mentions of \fB\-t\fR are allowed):
-.TP
-ace
-sequences or complete assembly to ACE
-.TP
-caf
-sequences or complete assembly to CAF
-.TP
-maf
-sequences or complete assembly to MAF
-.TP
-sam
-complete assembly to SAM
-.TP
-samnbb
-like above, but leaving out reference (backbones) in mapping assemblies
-.TP
-gbf
-sequences or consensus to GBF
-.TP
-gff3
-consensus to GFF3
-.TP
-wig
-assembly coverage info to wiggle file
-.TP
-gcwig
-assembly gc content info to wiggle file
-.TP
-fasta
-sequences or consensus to FASTA file (qualities to
-.IP
-\&.qual)
-.TP
-fastq
-sequences or consensus to FASTQ file
-.TP
-exp
-sequences or complete assembly to EXP files in
-.IP
-directories. Complete assemblies are suited for gap4
-import as directed assembly.
-Note: using caf2gap to import into gap4 is recommended though
-.TP
-text
-complete assembly to text alignment (only when \fB\-f\fR is
-.IP
-caf, maf or gbf)
-.TP
-html
-complete assembly to HTML (only when \fB\-f\fR is caf, maf or
-.IP
-gbf)
-.TP
-tcs
-complete assembly to tcs
-.TP
-hsnp
-surrounding of SNP tags (SROc, SAOc, SIOc) to HTML
-(only when \fB\-f\fR is caf, maf or gbf)
-.TP
-asnp
-analysis of SNP tags
-(only when \fB\-f\fR is caf, maf or gbf)
-.TP
-cstats
-contig statistics file like from MIRA
-(only when source contains contigs)
-.TP
-crlist
-contig read list file like from MIRA
-(only when source contains contigs)
-.TP
-maskedfasta
-reads where sequencing vector is masked out
-(with X) to FASTA file (qualities to .qual)
-.TP
-scaf
-sequences or complete assembly to single sequences CAF
-.TP
-\fB\-a\fR
-Append to target files instead of rewriting
-.TP
-\fB\-A\fR <string>
-String with MIRA parameters to be parsed
-Useful when setting parameters affecting consensus
-calling like \fB\-CO\fR:mrpg etc.
-E.g.: \fB\-a\fR "454_SETTINGS \fB\-CO\fR:mrpg=3"
-.TP
-\fB\-b\fR
-Blind data
-Replaces all bases in reads/contigs with a 'c'
-.TP
-\fB\-C\fR
-Perform hard clip to reads
-When reading formats which define clipping points, will
-.IP
-save only the unclipped part into the result file.
-.IP
-Applies only to files/formats which do not contain
-.IP
-contigs.
-.TP
-\fB\-d\fR
-Delete gap only columns
-When output is contigs: delete columns that are
-.IP
-entirely gaps (like after having deleted reads during
-editing in gap4 or similar)
-.IP
-When output is reads: delete gaps in reads
-.TP
-\fB\-F\fR
-Filter to read groups
-Special use case, do not use yet.
-.TP
-\fB\-m\fR
-Make contigs (only for \fB\-t\fR = caf or maf)
-Encase single reads as contig singlets into the CAF/MAF
-file.
-.TP
-\fB\-n\fR <filename>
-when given, selects only reads or contigs given by
-name in that file.
-.TP
-\fB\-i\fR
-when \fB\-n\fR is used, inverts the selection
-.TP
-\fB\-o\fR
-fastq quality Offset (only for \fB\-f\fR = 'fastq')
-Offset of quality values in FASTQ file. Default of 0
-tries to automatically recognise.
-.TP
-\fB\-Q\fR <quality>
-Set default quality for bases in file types without quality values
-Furthermore, do not stop if expected quality files are missing (e.g. '.fasta')
-.TP
-\fB\-R\fR <name>
-Rename contigs/singlets/reads with given name string
-to which a counter is appended.
-Known bug: will create duplicate names if input
-.IP
-contains contigs/singlets as well as free reads, i.e.
-reads not in contigs nor singlets.
-.TP
-\fB\-S\fR <name>
-(name)Scheme for renaming reads, important for paired\-ends
-Only 'solexa' is currently supported.
-.SS The following switches work only when input (CAF or MAF) contains contigs.
-Beware: CAF and MAf can also contain just reads.
-.TP
-\fB\-M\fR
-Do not extract contigs (or their consensus), but the
-sequence of the reads they are composed of.
-.TP
-\fB\-N\fR <filename>
-like \fB\-n\fR, but sorts output according to order given
-in file.
-.TP
-\fB\-r\fR [cCqf]
-Recalculate consensus and / or consensus quality values
-and / or SNP feature tags.
-\&'c' recalc cons & cons qualities (with IUPAC)
-\&'C' recalc cons & cons qualities (forcing non\-IUPAC)
-\&'q' recalc consensus qualities only
-\&'f' recalc SNP features
-Note: only the last of cCq is relevant, f works as a
-.IP
-switch and can be combined with cQq (e.g. "\-r C \fB\-r\fR f")
-.IP
-Note: if the CAF/MAF contains multiple strains,
-recalculation of cons & cons qualities is forced, you
-.IP
-can just influence whether IUPACs are used or not.
-.TP
-\fB\-s\fR
-split output into multiple files instead of creating a
-single file
-.TP
-\fB\-u\fR
-\&'fillUp strain genomes'
-Fill holes in the genome of one strain (N or @)
-with sequence from a consensus of other strains
-Takes effect only with \fB\-r\fR and \fB\-t\fR gbf or fasta/q
-in FASTA/Q: bases filled up are in lower case
-in GBF: bases filled up are in upper case
-.TP
-\fB\-q\fR <integer>
-Defines minimum quality a consensus base of a strain
-must have, consensus bases below this will be 'N'
-Default: 0
-Only used with \fB\-r\fR, and \fB\-f\fR is caf/maf and \fB\-t\fR is (fasta
-.IP
-or gbf)
-.TP
-\fB\-v\fR
-Print version number and exit
-.TP
-\fB\-x\fR <integer>
-Minimum contig or read length
-When loading, discard all contigs / reads with a
-length less than this value. Default: 0 (=switched off)
-Note: not applied to reads in contigs!
-.TP
-\fB\-X\fR <integer>
-Similar to \fB\-x\fR but applies only to reads and
-then to the clipped length.
-.TP
-\fB\-y\fR <integer>
-Minimum average contig coverage
-When loading, discard all contigs with an
-average coverage less than this value.
-Default: 1
-.TP
-\fB\-z\fR <integer>
-Minimum number of reads in contig
-When loading, discard all contigs with a
-number of reads less than this value.
-Default: 0 (=switched off)
-.TP
-\fB\-l\fR <integer>
-when output as text or HTML: number of bases shown in
-one alignment line. Default: 60.
-.TP
-\fB\-c\fR <character>
-when output as text or HTML: character used to pad
-endgaps. Default: ' ' (blank)
-.PP
-Aliases:
-caf2html, exp2fasta, ... etc. Any combination of "<validfromtype>2<validtotype>"
-can be used as program name (also using links) so as that convert_project
-automatically sets \fB\-f\fR and \fB\-t\fR accordingly.
-.SH EXAMPLES
-.IP
-convert_project source.maf dest.sam
-.IP
-convert_project source.caf dest.fasta wig ace
-.IP
-convert_project \-x 2000 \-y 10 source.caf dest.caf
-.IP
-caf2html \-l 100 \-c . source.caf dest
-.SH "SEE ALSO"
-A more extensive documentation is provided in the mira-doc package and can be found at
-/usr/share/doc/mira-assembler/DefinitiveGuideToMIRA.html.
-.PP
-You can also subscribe one of the MIRA mailing lists at
-.IP
-http://www.chevreux.org/mira_mailinglists.html
-.PP
-After subscribing, mail general questions to the MIRA talk mailing list:
-.IP
-mira_talk at freelists.org
-.SH BUGS
-To report bugs or ask for features, please use the new ticketing system at:
-.IP
-http://sourceforge.net/apps/trac/mira\-assembler/
-.SH AUTHOR
-The author of the mira code is Bastien Chevreux <bach at chevreux.org>
-.PP
-This manual page was written by Andreas Tille <tille at debian.org> but can be freely used for any other
-distribution.
diff --git a/debian/mans/fasta2frag.1 b/debian/mans/fasta2frag.1
deleted file mode 100644
index cb978c7..0000000
--- a/debian/mans/fasta2frag.1
+++ /dev/null
@@ -1,95 +0,0 @@
-.TH FASTA2FRAG "1" "June 2013" "3.9.17" "User Commands"
-.SH NAME
-.B fasta2frag \- splits a single fasta sequence into several overlapping fragments.
-.SH DESCRIPTION
-This program is part of the MIRA assembler package. The purpose of fasta2frag
-is to fragment sequences into smaller, overlapping
-subsequences. It can be used for simulating shotgun sequences. It can create
-subsequences in both directions (/default) and also paired-end sequences.
-Please check out the
-documentation below for more detailed information about fasta2frag.
-.SH SYNOPSIS
-fasta2frag
-\fI<options> infile outfile\fR
-.SH OPTIONS
-\fB\-l\fR
-int Length of fragments (default=3000)
-.TP
-\fB\-i\fR
-int Increment of fragment start site (default=2500)
-.TP
-\fB\-p\fR
-int Paired end (default=0 is off, 1 is on)
-.TP
-\fB\-P\fR
-int In paired\-end mode, reverse one of the reads
-(0 is off, default=1 is on)
-.TP
-\fB\-s\fR
-int Strobe sequencing (default=0 is off, 1 is on)
-.TP
-\fB\-q\fR
-int Default quality when no quality data present (default=30)
-.TP
-\fB\-r\fR
-int Reverse every nth fragment (default=2)
-.TP
-\fB\-c\fR
-int Circularise fragments so that they form a ring
-.IP
-(default=0 is is off, 1 would be on)
-.TP
-\fB\-qualdivisor\fR
-int Divide quality values by this (default=1)
-.TP
-\fB\-minqual\fR
-int But give it at least this qual (default=0)
-.TP
-\fB\-insert_size\fR
-int paired\-end: insert size (default=3000)
-.TP
-\fB\-insert_stdev\fR int
-paired\-end: standard dev (default=900)
-this is not working at the moment
-.TP
-\fB\-pairednaming\fR string
-naming scheme for paired\-end:
-sanger, 454 (default) or solexa
-.TP
-\fB\-minmut\fR
-int min. number of mutations/seq. errors (def=0)
-.TP
-\fB\-maxmut\fR
-int max. number of mutations/seq. errors (def=0)
-.TP
-\fB\-strobeon\fR
-int number of bases read during strobe on
-.TP
-\fB\-strobeoff\fR
-int number of bases during strobe off
-.TP
-\fB\-startoffset\fR
-int start at offset position
-.TP
-\fB\-namesuffix\fR
-string suffix name with string
-.SH "SEE ALSO"
-A more extensive documentation is provided in the mira-doc package and can be found at
-/usr/share/doc/mira-assembler/DefinitiveGuideToMIRA.html.
-.PP
-You can also subscribe one of the MIRA mailing lists at
-.IP
-http://www.chevreux.org/mira_mailinglists.html
-.PP
-After subscribing, mail general questions to the MIRA talk mailing list:
-.IP
-mira_talk at freelists.org
-.SH BUGS
-To report bugs or ask for features, please use the new ticketing system at:
-.IP
-http://sourceforge.net/apps/trac/mira\-assembler/
-.SH AUTHOR
-The author of the mira code is Bastien Chevreux <bach at chevreux.org>
-.PP
-This manual page was written by Andreas Tille <tille at debian.org> but can be freely used for any other
-distribution.
diff --git a/debian/mans/fastaselect.1 b/debian/mans/fastaselect.1
deleted file mode 100644
index 1a133a8..0000000
--- a/debian/mans/fastaselect.1
+++ /dev/null
@@ -1,47 +0,0 @@
-.TH FASTASELECT "1" "June 2013" "3.9.17" "User Commands"
-.SH NAME
-.B fastaselect \- select fasta sequences in a file
-.SH DESCRIPTION
-This script selects fasta sequences in a file according to names given
-in a name file. Given a FASTA file (and possibly a FASTA quality file) and
-a file with names of reads, select the sequences from the input FASTA (and
-quality file) and writes them to an output FASTA.
-.PP
-If fasta quality file is present (same basename, but with .qual appended),
-then also selects sequences from there.
-.PP
-Please check out the documentation below for more detailed information.
-.SH SYNOPSIS
-fastaselect \fI<options>\fR
-.SH OPTIONS
-.TP
-\fB\-infile\fR
-name filename containing all fasta sequences
-.TP
-\fB\-name\fR
-name filename containing all names of sequences to select
-.TP
-\fB\-outfile\fR name
-filename where to write selcted sequences to
-.SH "SEE ALSO"
-fastqselect(1)
-.PP
-A more extensive documentation is provided in the mira-doc package and can be found at
-/usr/share/doc/mira-assembler/DefinitiveGuideToMIRA.html.
-.PP
-You can also subscribe one of the MIRA mailing lists at
-.IP
-http://www.chevreux.org/mira_mailinglists.html
-.PP
-After subscribing, mail general questions to the MIRA talk mailing list:
-.IP
-mira_talk at freelists.org
-.SH BUGS
-To report bugs or ask for features, please use the new ticketing system at:
-.IP
-http://sourceforge.net/apps/trac/mira\-assembler/
-.SH AUTHOR
-The author of the mira code is Bastien Chevreux <bach at chevreux.org>
-.PP
-This manual page was written by Andreas Tille <tille at debian.org> but can be freely used for any other
-distribution.
diff --git a/debian/mans/fastatool.1 b/debian/mans/fastatool.1
deleted file mode 100644
index cd3a917..0000000
--- a/debian/mans/fastatool.1
+++ /dev/null
@@ -1,49 +0,0 @@
-.TH FASTATOOL "1" "June 2013" "3.9.17" "User Commands"
-.SH NAME
-.B fastatool \- Provides a set of tools useful when working with FASTA files.
-.SH DESCRIPTION
-This program is part of the MIRA assembler package.
-Fastatool provides a set of tools useful when working with FASTA trace files.
-.PP
-Please check out the documentation below for more detailed information.
-.SH SYNOPSIS"
-fastatool \fI<toolname>\fR \fI<tool parameters>\fR
-.SH OPTIONS
-.TP
-clip
-Clips bases on the left and right of a FASTA sequence, writes result to STDOUT.
-.IP
-Usage:
-.TP
- clipFASTA \-l leftclip \-r rightclip fastainfile
-.TP
-sanitize
-Deletes sequences with non-IUPAC bases or empty sequences from a FASTA file,
-writes the 'surviving' sequences to a new file.
-If a quality file is given, a cleaned version of that is also written.
-The sequences in the quality files (if given) MUST be in the same order than
-in the fasta file.
-.IP
-Usage:
-.TP
- sanitizeFASTA fastainfile fastaoutfile [fastaqualin fastaqualoutfile]
-.SH "SEE ALSO"
-A more extensive documentation is provided in the mira-doc package and can be found at
-/usr/share/doc/mira-assembler/DefinitiveGuideToMIRA.html.
-.PP
-You can also subscribe one of the MIRA mailing lists at
-.IP
-http://www.chevreux.org/mira_mailinglists.html
-.PP
-After subscribing, mail general questions to the MIRA talk mailing list:
-.IP
-mira_talk at freelists.org
-.SH BUGS
-To report bugs or ask for features, please use the new ticketing system at:
-.IP
-http://sourceforge.net/apps/trac/mira\-assembler/
-.SH AUTHOR
-The author of the mira code is Bastien Chevreux <bach at chevreux.org>
-.PP
-This manual page was written by Andreas Tille <tille at debian.org> but can be freely used for any other
-distribution.
diff --git a/debian/mans/fastqselect.1 b/debian/mans/fastqselect.1
deleted file mode 100644
index dea7157..0000000
--- a/debian/mans/fastqselect.1
+++ /dev/null
@@ -1,47 +0,0 @@
-.TH FASTQSELECT "1" "June 2013" "3.9.17" "User Commands"
-.SH NAME
-.B fastqselect \- select fastq sequences in a file
-.SH DESCRIPTION
-This script selects fastq sequences in a file according to names given
-in a name file. Given a FASTQ file (and possibly a FASTQ quality file) and
-a file with names of reads, select the sequences from the input FASTQ (and
-quality file) and writes them to an output FASTQ.
-.PP
-If fastq quality file is present (same basename, but with .qual appended),
-then also selects sequences from there.
-.PP
-Please check out the documentation below for more detailed information.
-.SH SYNOPSIS
-fastqselect \fI<options>\fR
-.SH OPTIONS
-.TP
-\fB\-infile\fR
-name filename containing all fastq sequences
-.TP
-\fB\-name\fR
-name filename containing all names of sequences to select
-.TP
-\fB\-outfile\fR name
-filename where to write selcted sequences to
-.SH "SEE ALSO"
-fastaselect(1)
-.PP
-A more extensive documentation is provided in the mira-doc package and can be found at
-/usr/share/doc/mira-assembler/DefinitiveGuideToMIRA.html.
-.PP
-You can also subscribe one of the MIRA mailing lists at
-.IP
-http://www.chevreux.org/mira_mailinglists.html
-.PP
-After subscribing, mail general questions to the MIRA talk mailing list:
-.IP
-mira_talk at freelists.org
-.SH BUGS
-To report bugs or ask for features, please use the new ticketing system at:
-.IP
-http://sourceforge.net/apps/trac/mira\-assembler/
-.SH AUTHOR
-The author of the mira code is Bastien Chevreux <bach at chevreux.org>
-.PP
-This manual page was written by Andreas Tille <tille at debian.org> but can be freely used for any other
-distribution.
diff --git a/debian/mans/fixACE4consed.1 b/debian/mans/fixACE4consed.1
deleted file mode 100644
index b81fa43..0000000
--- a/debian/mans/fixACE4consed.1
+++ /dev/null
@@ -1,32 +0,0 @@
-.TH fixACE4consed "1" "June 2013" "3.9.17" "User Commands"
-.SH NAME
-fixACE4consed \- workaround to allow consed loading the ACE generated by MIRA
-.SH DESCRIPTION
-The ACE output of MIRA is conforming to the file specification given in the
-consed documentation. However, due to a bug in consed, consed cannot correctly
-load tags set by MIRA.
-.PP
-The script fixACE4consed implements a workaround to allow consed loading the
-ACE generated by MIRA.
-.SH SYNOPSIS
-fixACE4consed infile.ace >outfile.ace
-.SH "SEE ALSO"
-A more extensive documentation is provided in the mira-doc package and can be found at
-/usr/share/doc/mira-assembler/DefinitiveGuideToMIRA.html.
-.PP
-You can also subscribe one of the MIRA mailing lists at
-.IP
-http://www.chevreux.org/mira_mailinglists.html
-.PP
-After subscribing, mail general questions to the MIRA talk mailing list:
-.IP
-mira_talk at freelists.org
-.SH BUGS
-To report bugs or ask for features, please use the new ticketing system at:
-.IP
-http://sourceforge.net/apps/trac/mira\-assembler/
-.SH AUTHOR
-The author of the mira code is Bastien Chevreux <bach at chevreux.org>
-.PP
-This manual page was written by Andreas Tille <tille at debian.org> but can be freely used for any other
-distribution.
diff --git a/debian/mans/mira.1 b/debian/mans/mira.1
deleted file mode 100644
index 2fa7874..0000000
--- a/debian/mans/mira.1
+++ /dev/null
@@ -1,53 +0,0 @@
-.TH 3.9.17 "1" "June 2013" "User Commands"
-.SH NAME
-mira \- The Genome and EST Sequence Assembly System
-.SH DESCRIPTION
-The mira genome fragment assembler is a specialised assembler for
-sequencing projects classified as 'hard' due to high number of similar
-repeats. For expressed sequence tags (ESTs) transcripts, miraEST is
-specialised on reconstructing pristine mRNA transcripts while
-detecting and classifying single nucleotide polymorphisms (SNP)
-occurring in different variations thereof.
-.PP
-The assembler is routinely used for such various tasks as mutation
-detection in different cell types, similarity analysis of transcripts
-between organisms, and pristine assembly of sequences from various
-sources for oligo design in clinical microarray experiments.
-.PP
-The purpose of the \fBmira\fR executable is to assemble sequencing data.
-.SH SYNOPSIS
-mira
-[\fIOPTION\fR] manifest_file [\fImanifest_file\fR] ...
-.SH OPTIONS
-.TP
-\fB\-c\fR / \fB\-\-cwd=\fRdirectory
-Change working directory
-.TP
-\fB\-r\fR / \fB\-\-resume\fR
-Resume an interrupted assembly
-.TP
-\fB\-h\fR / \fB\-\-help\fR
-Print short help and exit
-.TP
-\fB\-v\fR / \fB\-\-version\fR
-Print version and exit
-.SH "SEE ALSO"
-A more extensive documentation is provided in the mira-doc package and can be found at
-/usr/share/doc/mira-assembler/DefinitiveGuideToMIRA.html.
-.PP
-You can also subscribe one of the MIRA mailing lists at
-.IP
-http://www.chevreux.org/mira_mailinglists.html
-.PP
-After subscribing, mail general questions to the MIRA talk mailing list:
-.IP
-mira_talk at freelists.org
-.SH BUGS
-To report bugs or ask for features, please use the new ticketing system at:
-.IP
-http://sourceforge.net/apps/trac/mira\-assembler/
-.SH AUTHOR
-The author of the mira code is Bastien Chevreux <bach at chevreux.org>
-.PP
-This manual page was written by Andreas Tille <tille at debian.org> but can be freely used for any other
-distribution.
diff --git a/debian/mans/miraSearchESTSNPs.1 b/debian/mans/miraSearchESTSNPs.1
deleted file mode 100644
index 0e7cebd..0000000
--- a/debian/mans/miraSearchESTSNPs.1
+++ /dev/null
@@ -1,43 +0,0 @@
-.TH miraSearchESTSNPs "1" "June 2013" "3.9.17" "User Commands"
-.SH NAME
-miraSearchESTSNPs \- Pipeline to discover SNPs in ESTs from different strains
-.SH DESCRIPTION
-The program miraSearchESTSNPs can be used for assembly of EST data from
-different strains (or organisms) and SNP detection within this assembly.
-This is the former miraEST program which was renamed as many people got
-confused regarding whether to use MIRA in est mode or miraEST.
-.PP
-miraSearchESTSNPs is a pipeline that reconstructs the pristine mRNA
-transcript sequences gathered in EST sequencing projects of more than
-one strain, which can be a reliable basis for subsequent analysis steps
-like clustering or exon analysis. This means that even genes that
-contain only one transcribed SNP on different alleles are first treated
-as different transcripts. The optional last step of the assembly process
-can be configured as a simple clusterer that can assemble transcripts
-containing the same exon sequence -- but only differ in SNP positions --
-into one consensus sequence. Such SNPs can then be analysed, classified
-and reliably assigned to their corresponding mRNA transcriptome
-sequence. However, it is important to note that miraSearchESTSNPs is an
-assembler and not a full blown clustering tool.
-.SH SYNOPSIS
-In version 3.9.17 this functionality is deactivated.
-.SH "SEE ALSO"
-A more extensive documentation is provided in the mira-doc package and can be found at
-/usr/share/doc/mira-assembler/DefinitiveGuideToMIRA.html.
-.PP
-You can also subscribe one of the MIRA mailing lists at
-.IP
-http://www.chevreux.org/mira_mailinglists.html
-.PP
-After subscribing, mail general questions to the MIRA talk mailing list:
-.IP
-mira_talk at freelists.org
-.SH BUGS
-To report bugs or ask for features, please use the new ticketing system at:
-.IP
-http://sourceforge.net/apps/trac/mira\-assembler/
-.SH AUTHOR
-The author of the mira code is Bastien Chevreux <bach at chevreux.org>
-.PP
-This manual page was written by Andreas Tille <tille at debian.org> but can be freely used for any other
-distribution.
diff --git a/debian/mans/mirabait.1 b/debian/mans/mirabait.1
deleted file mode 100644
index 14a66b5..0000000
--- a/debian/mans/mirabait.1
+++ /dev/null
@@ -1,131 +0,0 @@
-.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.43.3.
-.TH MIRABAIT: "1" "August 2013" "MIRALIB version 3.9.18" "User Commands"
-.SH NAME
-mirabait \- select reads from a read collection
-.SH SYNOPSIS
-.B mirabait
-[\fI\-f <fromtype>\fR] [\fI\-t <totype> [\-t <totype> ...]\fR] [\fI\-iklor\fR] baitfile infile <basename_for_outfile(s)>
-.SH DESCRIPTION
-\fBmirabait\fR selects reads from a read collection which
-are partly similar or equal to sequences defined as target
-baits. Similarity is defined by finding a user-adjustable number of
-common k-mers (sequences of k consecutive bases) which are the same in
-the bait sequences and the screened sequences to be selected, either in forward
-or reverse complement direction.
-.SH OPTIONS
-.TP
-\fB\-f\fR <fromtype>
-load this type of project files, where fromtype is:
-.TP
-caf
-sequences from CAF
-.TP
-maf
-sequences from MAF
-.TP
-phd
-sequences from a PHD
-.TP
-gbf
-sequences from a GBF
-.TP
-fasta
-sequences from a FASTA
-.TP
-fastq
-sequences from a FASTQ
-.TP
-\fB\-t\fR <totype>
-write the sequences to this type (multiple mentions
-of \fB\-t\fR are allowed):
-.TP
-fasta
-sequences to FASTA
-.TP
-fastq
-sequences to FASTQ
-.TP
-caf
-sequences to CAF
-.TP
-maf
-sequences to MAF
-.TP
-txt
-sequence names to text file
-.TP
-\fB\-k\fR
-k\-mer, length of bait in bases (<32, default=31)
-.TP
-\fB\-n\fR
-Min. number of k\-mer baits needed (default=1)
-.TP
-\fB\-i\fR
-Inverse hit: writes only sequences that do not hit bait
-.TP
-\fB\-r\fR
-No checking of reverse complement direction
-.TP
-\fB\-o\fR
-fastq quality Offset (only for \fB\-f\fR = 'fastq')
-Offset of quality values in FASTQ file. Default: 33
-A value of 0 tries to automatically recognise.
-.TP
-\fB\-f\fR <fromtype>
-load this type of project files, where fromtype is:
-.TP
-caf
-sequences from CAF
-.TP
-maf
-sequences from MAF
-.TP
-phd
-sequences from a PHD
-.TP
-gbf
-sequences from a GBF
-.TP
-fasta
-sequences from a FASTA
-.TP
-fastq
-sequences from a FASTQ
-.TP
-\fB\-t\fR <totype>
-write the sequences to this type (multiple mentions
-of \fB\-t\fR are allowed):
-.TP
-fasta
-sequences to FASTA
-.TP
-fastq
-sequences to FASTQ
-.TP
-caf
-sequences to CAF
-.TP
-maf
-sequences to MAF
-.TP
-txt
-sequence names to text file
-.TP
-\fB\-k\fR
-k\-mer, length of bait in bases (<32, default=31)
-.TP
-\fB\-n\fR
-Min. number of k\-mer baits needed (default=1)
-.TP
-\fB\-i\fR
-Inverse hit: writes only sequences that do not hit bait
-.TP
-\fB\-r\fR
-No checking of reverse complement direction
-.TP
-\fB\-o\fR
-fastq quality Offset (only for \fB\-f\fR = 'fastq')
-Offset of quality values in FASTQ file. Default: 33
-A value of 0 tries to automatically recognise.
-.SH AUTHOR
-Bastien Chevreux (bach at chevreux.org)
diff --git a/debian/mans/miraconvert.1 b/debian/mans/miraconvert.1
deleted file mode 100644
index 671499b..0000000
--- a/debian/mans/miraconvert.1
+++ /dev/null
@@ -1,327 +0,0 @@
-.TH MIRACONVERT "1" "December 2015" "miraconvert 4.9.5" "User Commands"
-.SH NAME
-miraconvert \- convert assembly and sequencing file types
-.SH SYNOPSIS
-.B miraconvert
-[\-f <fromtype>] [\-t <totype> [\-t <totype> ...]] [\-aAChimMsuZ] [\-cflnNoPqrtvxXyYz {...}] {infile} {outfile} [<totype> <totype> ...]
-.SH OPTIONS
-.TP
-\fB\-f\fR \fI<fromtype>\fR
-load this type of project files, where fromtype is:
-.IP
-\fIcaf\fR
-a complete assembly or single sequences from CAF
-.IP
-\fImaf\fR
-a complete assembly or single sequences from CAF
-.IP
-\fIfasta\fR
-sequences from a FASTA file
-.IP
-\fIfastq\fR
-sequences from a FASTQ file
-.IP
-\fIgb[f|k|ff]\fR
-sequences from a GenBank file
-.IP
-\fIphd\fR
-sequences from a PHD file
-.IP
-\fIfofnexp\fR
-sequences in EXP files from file of filenames
-.TP
-\fB\-t\fR \fI<totype>\fR
-write the sequences/assembly to this type (multiple
-mentions of \fB\-t\fR are allowed):
-.IP
-\fIace\fR
-sequences or complete assembly to ACE
-.IP
-\fIcaf\fR
-sequences or complete assembly to CAF
-.IP
-\fImaf\fR
-sequences or complete assembly to MAF
-.IP
-\fIsam\fR
-complete assembly to SAM
-.IP
-\fIsamnbb\fR
-like above, but leaving out reference (backbones) in mapping assemblies
-.IP
-\fIgb[f|k|ff]\fR
-sequences or consensus to GenBank
-.IP
-\fIgff3\fR
-consensus to GFF3
-.IP
-\fIwig\fR
-assembly coverage info to wiggle file
-.IP
-\fIgcwig\fR
-assembly gc content info to wiggle file
-.IP
-\fIfasta\fR
-sequences or consensus to FASTA file (qualities to \&.qual)
-.IP
-\fIfastq\fR
-sequences or consensus to FASTQ file
-.IP
-\fIexp\fR
-sequences or complete assembly to EXP files in
-directories. Complete assemblies are suited for gap4
-import as directed assembly.
-Note: using caf2gap to import into gap4 is recommended
-though
-.IP
-\fItext\fR
-complete assembly to text alignment (only when \fB\-f\fR is
-\fIcaf\fR, \fImaf\fR or \fIgbf\fR)
-.IP
-\fIhtml\fR
-complete assembly to HTML (only when \fB\-f\fR is \fIcaf\fR, \fImaf\fR or \fIgbf\fR)
-.IP
-\fItcs\fR
-complete assembly to tcs
-.IP
-\fIhsnp\fR
-surrounding of SNP tags (SROc, SAOc, SIOc) to HTML
-(only when \fB\-f\fR is \fIcaf\fR, \fImaf\fR or \fIgbf\fR)
-.IP
-\fIasnp\fR
-analysis of SNP tags
-(only when \fB\-f\fR is \fIcaf\fR, \fImaf\fR or \fIgbf\fR)
-.IP
-\fIcstats\fR
-contig statistics file like from MIRA
-(only when source contains contigs)
-.IP
-\fIcrlist\fR
-contig read list file like from MIRA
-(only when source contains contigs)
-.IP
-\fImaskedfasta\fR
-reads where sequencing vector is masked out
-(with X) to FASTA file (qualities to .qual)
-.IP
-\fIscaf\fR
-sequences or complete assembly to single sequences CAF
-.TP
-\fB\-a\fR
-Append to target files instead of rewriting
-.TP
-\fB\-A\fR
-Do not Adjust sequence case
-.IP
-When reading formats which define clipping points,
-and saving to formats which do not have clipping
-information, miraconvert normally adjusts the case of
-read sequences: lower case for clipped parts, upper
-case for unclipped parts of reads.
-Use \fB\-A\fR if you do not want this. See also \fB\-C\fR.
-.IP
-Applies only to files/formats which do not contain
-contigs.
-.TP
-\fB\-b\fR
-Blind data
-.IP
-Replaces all bases in reads/contigs with a 'c'
-.TP
-\fB\-C\fR
-Perform hard clip to reads
-.IP
-When reading formats which define clipping points, will
-save only the unclipped part into the result file.
-.IP
-Applies only to files/formats which do not contain
-contigs.
-.TP
-\fB\-d\fR
-Delete gap only columns
-.IP
-When output is contigs: delete columns that are
-entirely gaps (like after having deleted reads during
-editing in gap4 or similar)
-.IP
-When output is reads: delete gaps in reads
-.TP
-\fB\-F\fR
-Filter read groups to different files
-.IP
-Works only for input files with readgroups (CAF/MAF)
-3 (or 4) files generated: one or two for paired, one
-for unpaired and one for debris reads.
-.IP
-Reads in paired file are interlaced by default, use \fB\-F\fR
-twice to create separate files.
-.TP
-\fB\-m\fR
-Make contigs (only for \fB\-t\fR = \fIcaf\fR or \fImaf\fR)
-.IP
-Encase single reads as contig singlets into the CAF/MAF
-file.
-.TP
-\fB\-n\fR <filename>
-when given, selects only reads or contigs given by
-name in that file.
-.TP
-\fB\-N\fR <filename>
-like \fB\-n\fR, but sorts output according to order given
-in file.
-.TP
-\fB\-i\fR
-when \fB\-n\fR is used, inverts the selection
-.TP
-\fB\-o\fR <quality>t
-FASTQ quality Offset (only for \fB\-f\fR = 'fastq')
-.IP
-Offset of quality values in FASTQ file. Default of 33
-loads Sanger/Phred style files, using 0 tries to
-automatically recognise.
-.TP
-\fB\-P\fR <string>
-String with MIRA parameters to be parsed
-.IP
-Useful when setting parameters affecting consensus
-calling like \fB\-CO\fR:mrpg etc.
-.IP
-E.g.: \fB\-P\fR "454_SETTINGS \fB\-CO\fR:mrpg=3"
-.TP
-\fB\-q\fR <quality>
-Set default quality for bases in file types without
-quality values. Furthermore, do not stop if expected
-quality files are missing (e.g. '.fasta')
-.TP
-\fB\-R\fR <name>
-Rename contigs/singlets/reads with given name string
-to which a counter is appended.
-.IP
-Known bug: will create duplicate names if input
-contains contigs/singlets as well as free reads, i.e.
-reads not in contigs nor singlets.
-.TP
-\fB\-S\fR <name>
-(name)Scheme for renaming reads, important for
-paired\-ends. Only 'solexa' is currently supported.
-.TP
-\fB\-T\fR
-When converting single reads, trim/clip away stretches
-of N and X and ends of reads. Note: remember to use \fB\-C\fR to
-also perform a hard clip (e.g. with FASTA as output).
-.TP
-\fB\-v\fR
-Print version number and exit
-.TP
-\fB\-Y\fR <integer>
-Yield. Max (clipped/padded) bases to convert.
-.IP
-When used on reads: output will contain first reads of
-file where length of clipped bases totals at least \fB\-Y\fR.
-When used on contigs: output will contain first contigs
-of file where length of padded contigs totals at least
-\fB\-Y\fR.
-.P
-The following switches work only when input (CAF or MAF)
-contains contigs. Beware: CAF and MAf can also contain
-just reads.
-.TP
-\fB\-M\fR
-Do not extract contigs (or their consensus), but the
-sequence of the reads they are composed of.
-.TP
-\fB\-r\fR [\fIcCqf\fR]
-Recalculate consensus and / or consensus quality values
-and / or SNP feature tags.
-.IP
-\&'\fIc\fR' recalc cons & cons qualities (with IUPAC)
-.IP
-\&'\fIC\fR' recalc cons & cons qualities (forcing non\-IUPAC)
-.IP
-\&'\fIq\fR' recalc consensus qualities only
-.IP
-\&'\fIf\fR' recalc SNP features
-.IP
-Note: only the last of \fIcCq\fR is relevant, \fIf\fR works as a
-switch and can be combined with \fIcQq\fR (e.g. "\fB\-r\fR \fIC\fR \fB\-r\fR \fIf\fR")
-.IP
-Note: if the CAF/MAF contains multiple strains,
-recalculation of cons & cons qualities is forced, you
-can just influence whether IUPACs are used or not.
-.TP
-\fB\-s\fR
-split output into multiple files instead of creating a
-single file
-.TP
-\fB\-u\fR
-\&'fillUp strain genomes'
-.IP
-Fill holes in the genome of one strain (N or @)
-with sequence from a consensus of other strains
-.IP
-Takes effect only with \fB\-r\fR and \fB\-t\fR gbf or fasta/q
-in FASTA/Q: bases filled up are in lower case
-in GBF: bases filled up are in upper case
-.TP
-\fB\-Q\fR <integer>
-Defines minimum quality a consensus base of a strain
-must have, consensus bases below this will be 'N'
-Default: 0
-.IP
-Only used with \fB\-r\fR, and \fB\-f\fR is caf/maf and \fB\-t\fR is (fasta
-or gbf)
-.TP
-\fB\-V\fR <integer>
-Defines minimum coverage a consensus base of a strain
-must have, bases with coverage below this will be 'N'
-Default: 0
-.IP
-Only used with \fB\-r\fR, and \fB\-t\fR is (fasta
-or gbf)
-.TP
-\fB\-x\fR <integer>
-Minimum contig or unclipped read length
-.IP
-When loading, discard all contigs / reads with a
-length less than this value. Default: 0 (=switched off)
-.IP
-Note: not applied to reads in contigs!
-.TP
-\fB\-X\fR <integer>
-Similar to \fB\-x\fR but applies only to reads and
-then to the clipped length.
-.TP
-\fB\-y\fR <integer>
-Minimum average contig coverage
-When loading, discard all contigs with an
-average coverage less than this value.
-Default: 1
-.TP
-\fB\-z\fR <integer>
-Minimum number of reads in contig
-When loading, discard all contigs with a
-number of reads less than this value.
-Default: 0 (=switched off)
-.TP
-\fB\-l\fR <integer>
-when output as text or HTML: number of bases shown in
-one alignment line. Default: 60.
-.TP
-\fB\-c\fR <character>
-when output as text or HTML: character used to pad
-endgaps. Default: ' ' (blank)
-.SH EXAMPLES
-.IP
-miraconvert source.maf dest.sam
-.IP
-miraconvert source.caf dest.fasta wig ace
-.IP
-miraconvert \-x 2000 \-y 10 source.caf dest.caf
-.IP
-miraconvert \-x 40 \-C \-F \-F source.maf .fastq
-.IP
-miraconvert: Missing infile and out\-basename as arguments!
-.SH AUTHOR
-The program \fBmiraconvert\fR was written by Bastien Chevreux <bach at chevreux.org>.
-.P
-This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/mans/miradiff.1 b/debian/mans/miradiff.1
deleted file mode 100644
index 7085ede..0000000
--- a/debian/mans/miradiff.1
+++ /dev/null
@@ -1,36 +0,0 @@
-.TH MIRADIFF "1" "June 2013" "3.9.17" "User Commands"
-.SH NAME
-miradiff \- diff two data sets of mira(1)
-.SH DESCRIPTION
-This program is part of the MIRA assembler package. Please check out the
-documentation below for more detailed information about miradiff.
-.SH SYNOPSIS
-miradiff
-[\fIOPTION\fR]
-.SH OPTIONS
-.TP
-\fB\-h\fR / \fB\-\-help\fR
-Print short help and exit
-.TP
-\fB\-v\fR / \fB\-\-version\fR
-Print version and exit
-.SH "SEE ALSO"
-A more extensive documentation is provided in the mira-doc package and can be found at
-/usr/share/doc/mira-assembler/DefinitiveGuideToMIRA.html.
-.PP
-You can also subscribe one of the MIRA mailing lists at
-.IP
-http://www.chevreux.org/mira_mailinglists.html
-.PP
-After subscribing, mail general questions to the MIRA talk mailing list:
-.IP
-mira_talk at freelists.org
-.SH BUGS
-To report bugs or ask for features, please use the new ticketing system at:
-.IP
-http://sourceforge.net/apps/trac/mira\-assembler/
-.SH AUTHOR
-The author of the mira code is Bastien Chevreux <bach at chevreux.org>
-.PP
-This manual page was written by Andreas Tille <tille at debian.org> but can be freely used for any other
-distribution.
diff --git a/debian/mans/miramem.1 b/debian/mans/miramem.1
deleted file mode 100644
index edf907d..0000000
--- a/debian/mans/miramem.1
+++ /dev/null
@@ -1,33 +0,0 @@
-.TH MIRAMEM "1" "June 2013" "3.9.17" "User Commands"
-.SH NAME
-miramem \- estimating needed memory for a MIRA assembly project
-.SH DESCRIPTION
-When called from the command line, it will ask a number of questions and
-then print out an estimate of the amount of RAM needed to assemble the
-project. Take this estimate with a grain of salt, depending on the
-sequences properties, variations in the estimate can be +/- 30% for
-bacteria and 'simple' eukaryotes. The higher the number of repeats is,
-the more likely you will need to restrict memory usage in some way or
-another.
-.SH SYNOPSIS
-miramem
-.SH "SEE ALSO"
-A more extensive documentation is provided in the mira-doc package and can be found at
-/usr/share/doc/mira-assembler/DefinitiveGuideToMIRA.html.
-.PP
-You can also subscribe one of the MIRA mailing lists at
-.IP
-http://www.chevreux.org/mira_mailinglists.html
-.PP
-After subscribing, mail general questions to the MIRA talk mailing list:
-.IP
-mira_talk at freelists.org
-.SH BUGS
-To report bugs or ask for features, please use the new ticketing system at:
-.IP
-http://sourceforge.net/apps/trac/mira\-assembler/
-.SH AUTHOR
-The author of the mira code is Bastien Chevreux <bach at chevreux.org>
-.PP
-This manual page was written by Andreas Tille <tille at debian.org> but can be freely used for any other
-distribution.
diff --git a/debian/mans/miramer.1 b/debian/mans/miramer.1
deleted file mode 100644
index bf12ac2..0000000
--- a/debian/mans/miramer.1
+++ /dev/null
@@ -1,36 +0,0 @@
-.TH MIRAMER "1" "June 2013" "3.9.17" "User Commands"
-.SH NAME
-miramer \- handle k-mer statistics of a data set
-.SH DESCRIPTION
-This program is part of the MIRA assembler package. Please check out the
-documentation below for more detailed information about miramer.
-.SH SYNOPSIS
-miramer
-[\fIOPTION\fR]
-.SH OPTIONS
-.TP
-\fB\-h\fR / \fB\-\-help\fR
-Print short help and exit
-.TP
-\fB\-v\fR / \fB\-\-version\fR
-Print version and exit
-.SH "SEE ALSO"
-A more extensive documentation is provided in the mira-doc package and can be found at
-/usr/share/doc/mira-assembler/DefinitiveGuideToMIRA.html.
-.PP
-You can also subscribe one of the MIRA mailing lists at
-.IP
-http://www.chevreux.org/mira_mailinglists.html
-.PP
-After subscribing, mail general questions to the MIRA talk mailing list:
-.IP
-mira_talk at freelists.org
-.SH BUGS
-To report bugs or ask for features, please use the new ticketing system at:
-.IP
-http://sourceforge.net/apps/trac/mira\-assembler/
-.SH AUTHOR
-The author of the mira code is Bastien Chevreux <bach at chevreux.org>
-.PP
-This manual page was written by Andreas Tille <tille at debian.org> but can be freely used for any other
-distribution.
diff --git a/debian/mans/scftool.1 b/debian/mans/scftool.1
deleted file mode 100644
index bb6f431..0000000
--- a/debian/mans/scftool.1
+++ /dev/null
@@ -1,50 +0,0 @@
-.TH SCFTOOL "1" "June 2013" "3.9.17" "User Commands"
-.SH NAME
-scftool \- provides a set of tools useful when working with SCF trace files.
-.SH SYNOPSIS
-.IP
-scftool
-<\fBtoolname\fR> <\fBtool parameters\fR>
-.SH OPTIONS
-Available tools:
-.IP convert
-Cuts the given range out of an SCF file and makes a new SCF out of it.
-.IP
-To get help more specific help please type \fIscftool convert\fR
-.IP cut
-Cuts a given range of a SCF file into a new SCF file.
-.IP remix
-Combines trace information of a SCF file with new bases, qualities and peak
-values (either in FASTA or PHD format) into a new SCF file.
-.SH EXAMPLES
-Example for cut:
-.IP
-scftool cut infile lower_base_bound upper_base_bound outfile
-.PP
-Usage of remix (when using PHD files as input for bases, quals and peaks):
-.IP
-scftool remix scf_infile phd_infile scf_outfile
-.PP
-Usage of remix (when using FASTA files as input for bases, quals and peaks):
-.IP
-scftool remix scf_infile bases_infile quals_infile peaks_infile scf_outfile
-.SH "SEE ALSO"
-A more extensive documentation is provided in the mira-doc package and can be found at
-/usr/share/doc/mira-assembler/DefinitiveGuideToMIRA.html.
-.PP
-You can also subscribe one of the MIRA mailing lists at
-.IP
-http://www.chevreux.org/mira_mailinglists.html
-.PP
-After subscribing, mail general questions to the MIRA talk mailing list:
-.IP
-mira_talk at freelists.org
-.SH BUGS
-To report bugs or ask for features, please use the new ticketing system at:
-.IP
-http://sourceforge.net/apps/trac/mira\-assembler/
-.SH AUTHOR
-The author of the mira code is Bastien Chevreux <bach at chevreux.org>
-.PP
-This manual page was written by Andreas Tille <tille at debian.org> but can be freely used for any other
-distribution.
diff --git a/debian/mira-examples.examples b/debian/mira-examples.examples
index 85d39e6..4a32932 100644
--- a/debian/mira-examples.examples
+++ b/debian/mira-examples.examples
@@ -1 +1 @@
-minidemo
+#minidemo
diff --git a/debian/mira-examples.lintian-overrides b/debian/mira-examples.lintian-overrides
index 98bc551..e9bde92 100644
--- a/debian/mira-examples.lintian-overrides
+++ b/debian/mira-examples.lintian-overrides
@@ -1,3 +1,3 @@
# Exclude false positives that are verbose copies from upstream tarball
-mira-examples: package-contains-timestamped-gzip usr/share/doc/mira-examples/examples/minidemo/data/scf/*.scf.gz
+#mira-examples: package-contains-timestamped-gzip usr/share/doc/mira-examples/examples/minidemo/data/scf/*.scf.gz
diff --git a/debian/mira-rfam-12s-rrna.install b/debian/mira-rfam-12s-rrna.install
new file mode 100644
index 0000000..e542a95
--- /dev/null
+++ b/debian/mira-rfam-12s-rrna.install
@@ -0,0 +1,3 @@
+src/other/sls/rfam_rrna-21-12.sls.gz usr/share/mira/
+src/other/sls/mira-install-sls-rrna.sh usr/share/mira/
+
diff --git a/debian/mira-rfam-12s-rrna.lintian-overrides b/debian/mira-rfam-12s-rrna.lintian-overrides
new file mode 100644
index 0000000..a13e808
--- /dev/null
+++ b/debian/mira-rfam-12s-rrna.lintian-overrides
@@ -0,0 +1,2 @@
+# tarball is from upstream
+mira-rfam-12s-rrna: package-contains-timestamped-gzip usr/share/mira/rfam_rrna-21-12.sls.gz
diff --git a/debian/mira-rfam-12s-rrna.postinst b/debian/mira-rfam-12s-rrna.postinst
new file mode 100755
index 0000000..8534dc9
--- /dev/null
+++ b/debian/mira-rfam-12s-rrna.postinst
@@ -0,0 +1,10 @@
+#!/bin/bash
+
+set -e
+
+mkdir -p /usr/share/mira/mhs
+/usr/share/mira/mira-install-sls-rrna.sh /usr/share/mira/rfam_rrna-21-12.sls.gz
+cd /usr/share/mira/mhs
+ln -s -f rfam_rrna-21-12.mhs.gz filter_default_rrna.mhs.gz
+
+#DEBHELPER#
diff --git a/debian/mira-rfam-12s-rrna.postrm b/debian/mira-rfam-12s-rrna.postrm
new file mode 100755
index 0000000..0f5df46
--- /dev/null
+++ b/debian/mira-rfam-12s-rrna.postrm
@@ -0,0 +1,7 @@
+#!/bin/bash
+
+set -e
+
+#DEBHELPER#
+
+rm -Rf /usr/share/mira/mhs
diff --git a/debian/patches/fix_strange_link_issue.patch b/debian/patches/fix_strange_link_issue.patch
deleted file mode 100644
index 308e6cb..0000000
--- a/debian/patches/fix_strange_link_issue.patch
+++ /dev/null
@@ -1,16 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Wed, 01 Jul 2015 22:00:48 +0200
-Description: The missing '&&' in the statement leads to a strange
- "No such directory miramer" error
-
---- mira.orig/src/progs/Makefile.am
-+++ mira/src/progs/Makefile.am
-@@ -51,7 +51,7 @@
- rm -f mirabait$(EXEEXT) && \
- $(LN_S) mira$(EXEEXT) mirabait$(EXEEXT) &&\
- rm -f miraconvert$(EXEEXT) && \
-- $(LN_S) mira$(EXEEXT) miraconvert$(EXEEXT) \
-+ $(LN_S) mira$(EXEEXT) miraconvert$(EXEEXT) && \
- rm -f miramer$(EXEEXT) && \
- $(LN_S) mira$(EXEEXT) miramer$(EXEEXT)
-
diff --git a/debian/patches/gcc-6.patch b/debian/patches/gcc-6.patch
deleted file mode 100644
index 1580bc9..0000000
--- a/debian/patches/gcc-6.patch
+++ /dev/null
@@ -1,16 +0,0 @@
-Description: Fix build issue with gcc-6
-Bug-Debian: http://bugs.debian.org/822474
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Mon, 25 Apr 2016 23:46:32 +0200
-
---- a/src/mira/contig_consensus.C
-+++ b/src/mira/contig_consensus.C
-@@ -30,7 +30,7 @@
- #include "util/timer.H"
-
- #include <boost/lexical_cast.hpp>
--
-+#include <numeric>
-
- using namespace std;
-
diff --git a/debian/patches/make-reproducible b/debian/patches/make-reproducible
deleted file mode 100644
index 6e05ff1..0000000
--- a/debian/patches/make-reproducible
+++ /dev/null
@@ -1,19 +0,0 @@
-Author: Michael R. Crusoe <crusoe at ucdavis.edu>
-Description: Make reproducible
-Fixes a FTBFS when the locale uses non-ASCII characters when printing the date.
-Also makes the build more reproducible
---- mira.orig/src/progs/Makefile.am
-+++ mira/src/progs/Makefile.am
-@@ -16,10 +16,8 @@
-
- compileinfo.itxt:
- @/bin/echo -n "Compiled by: " >compileinfo.itxt.xxd
-- @whoami >>compileinfo.itxt.xxd
-- @date >>compileinfo.itxt.xxd
-- @/bin/echo -n "On: " >>compileinfo.itxt.xxd
-- @uname -a >>compileinfo.itxt.xxd
-+ @$$DEBIAN_MAINTAINER >>compileinfo.itxt.xxd
-+ @echo $$SOURCE_DATE_EPOCH >>compileinfo.itxt.xxd
- @echo "Making .H out of .xxd" $@
- @$(SHELL) -ec 'grep -v "^#" compileinfo.itxt.xxd | xxd -i >compileinfo.itxt.xxd.H'
- @rm compileinfo.itxt.xxd
diff --git a/debian/patches/man-directory b/debian/patches/man-directory
new file mode 100644
index 0000000..48f1e82
--- /dev/null
+++ b/debian/patches/man-directory
@@ -0,0 +1,9 @@
+Author: Michael R. Crusoe
+Description: Follow the FHS
+--- mira.orig/man/Makefile.am
++++ mira/man/Makefile.am
+@@ -1,3 +1,3 @@
+
+ dist_pkgdata_DATA = mirabait.1 miradiff.1 miramer.1 mira.1 miraconvert.1 miramem.1
+-pkgdatadir=$(prefix)/man/man1
++pkgdatadir=$(prefix)/share/man/man1
diff --git a/debian/patches/series b/debian/patches/series
index 13aa111..6bc6dc6 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,4 +1,3 @@
-make-reproducible
-fix_strange_link_issue.patch
spelling.patch
-gcc-6.patch
+sls-rrna-fix
+man-directory
diff --git a/debian/patches/sls-rrna-fix b/debian/patches/sls-rrna-fix
new file mode 100644
index 0000000..06b1e32
--- /dev/null
+++ b/debian/patches/sls-rrna-fix
@@ -0,0 +1,19 @@
+Author: Michael R. Crusoe <michael.crusoe at gmail.com>
+Description: ship the rfam database, don't run unpacker yet
+
+--- mira.orig/src/other/sls/Makefile.am
++++ mira/src/other/sls/Makefile.am
+@@ -6,13 +6,6 @@
+ mira-createsls
+
+
+-install-exec-hook:
+- cp mira-install-sls-rrna.sh $(DESTDIR)$(bindir) && \
+- mkdir -p $(prefix)/share/mira/mhs && \
+- ./mira-install-sls-rrna.sh rfam_rrna-21-12.sls.gz && \
+- cd $(prefix)/share/mira/mhs && \
+- $(LN_S) -f rfam_rrna-21-12.mhs.gz filter_default_rrna.mhs.gz
+-
+ uninstall-hook:
+ rm $(DESTDIR)$(bindir)/mira-install-sls-rrna.sh && \
+ rm -f $(prefix)/share
diff --git a/debian/patches/spelling.patch b/debian/patches/spelling.patch
index 4163069..309b684 100644
--- a/debian/patches/spelling.patch
+++ b/debian/patches/spelling.patch
@@ -4,393 +4,25 @@ Description: Fix spelling
Remark: Lintian found another issue ressize -> resize but I can not find
this inside the code
---- mira.orig/src/util/fileanddisk.C
-+++ mira/src/util/fileanddisk.C
-@@ -866,7 +866,7 @@
- getCanonicalFileAndZipType(tmptype,dummypathto,dummystem,overridetype,ziptype);
- if(overridetype.empty()){
- tmptype=tmptype.substr(1,999);
-- MIRANOTIFY(Notify::FATAL,"You tried to explicitely define a file type via " << tmptype << "::" << dn << ", however the type '" << tmptype << "' is not known to MIRA.");
-+ MIRANOTIFY(Notify::FATAL,"You tried to explicitly define a file type via " << tmptype << "::" << dn << ", however the type '" << tmptype << "' is not known to MIRA.");
- }
- //cout << "###" << overridetype << "###\n";
- }
---- mira.orig/configure.ac
-+++ mira/configure.ac
-@@ -1751,7 +1751,7 @@
- echo "problems in compilation/linking. Please give it a try and report success"
- echo "or failure."
- echo
-- echo "Type 'make' to make the binaries and if no error occured,"
-+ echo "Type 'make' to make the binaries and if no error occurred,"
- echo "then 'make install' to install them."
- echo
- echo "In case of failure, please help to fix if you can."
---- mira.orig/doc/docbook/chap_bonus_part.xml
-+++ mira/doc/docbook/chap_bonus_part.xml
-@@ -61,7 +61,7 @@
- </para>
- <para>
- Today was a day where I had - the first time ever - ups and downs
-- occuring absolutely simultaneously. Something which is physically
-+ occurring absolutely simultaneously. Something which is physically
- impossible, I know, but don't tell any physicist or astronomist about
- that or else they'll embark you on a lengthy discussion on how
- isochronicity is a myth by telling you stories on lightning, thunder and
-@@ -259,7 +259,7 @@
- <itemizedlist>
- <listitem>
- an artefact was very sporadically observed during MIRA runs where sequences
-- (containing lot's of 'A') suddenly contained at least one '@'. This occured
-+ (containing lot's of 'A') suddenly contained at least one '@'. This occurred
- after several passes, i.e., not on loading.
- </listitem>
- <listitem>
-@@ -276,7 +276,7 @@
- </listitem>
- <listitem>
- MIRA loaded the data twice flawlessly before the artefact in the filesystem
-- occured.
-+ occurred.
- </listitem>
- </itemizedlist>
- <para>
-@@ -339,7 +339,7 @@
- </listitem>
- <listitem>
- the disk controllers and UDMA controller are innocent! Some of the glitches observed in
-- previous weeks occured during runs of MIRA, inside the MIRA address space,
-+ previous weeks occurred during runs of MIRA, inside the MIRA address space,
- long after initial loading, when UDMA had already finished their job.
- </listitem>
- </itemizedlist>
---- mira.orig/minidemo/demo1/runme.sh
-+++ mira/minidemo/demo1/runme.sh
-@@ -29,7 +29,7 @@
- echo
- echo "If all went well, the results are in '*_results' directory."
- echo " also have a look at files in '*_info', e.g. at the contigstats file.."
--echo "Consult log_assmbly.txt and/or stderr if errors occured."
-+echo "Consult log_assmbly.txt and/or stderr if errors occurred."
- echo
- echo "(and please read the comments on top of the 'runme.sh' script)"
-
---- mira.orig/minidemo/demo2/runme.sh
-+++ mira/minidemo/demo2/runme.sh
-@@ -17,7 +17,7 @@
- echo
- echo "If all went well, the results are in 'demo2_results' directory."
- echo " also have a look at files in 'demo2_info', e.g. at the contigstats file.."
--echo "Consult log_assmbly.txt and/or stderr if errors occured."
-+echo "Consult log_assmbly.txt and/or stderr if errors occurred."
- echo
- echo "(and please read the comments on top of the 'runme.sh' script)"
-
---- mira.orig/minidemo/demo3/runme.sh
-+++ mira/minidemo/demo3/runme.sh
-@@ -9,7 +9,7 @@
- mira --params=demo3.par | tee log_assmbly.txt
- echo
- echo "If all went well, the results are in 'demo3_out*' files/directories."
--echo "Consult log_assmbly.txt and/or stderr if errors occured."
-+echo "Consult log_assmbly.txt and/or stderr if errors occurred."
- echo
- echo "(and please read the comments on top of the 'runme.sh' script)"
-
---- mira.orig/minidemo/demo4/runme.sh
-+++ mira/minidemo/demo4/runme.sh
-@@ -16,7 +16,7 @@
- mira -job=denovo,genome,normal,sanger -lowqualitydata --fasta=../data/fasta_set1/U13small_m.fasta -DIRECTORY:scf=../data/scf SANGER_SETTINGS -CLIPPING:qc=yes -LR:mxti=no | tee log_assembly.txt
- echo
- echo "If all went well, the results are in 'mira_out*' files/directories."
--echo "Consult log_assmbly.txt and/or stderr if errors occured."
-+echo "Consult log_assmbly.txt and/or stderr if errors occurred."
- echo
- echo "(and please read the comments on top of the 'runme.sh' script)"
-
---- mira.orig/minidemo/demo5/runme.sh
-+++ mira/minidemo/demo5/runme.sh
-@@ -16,7 +16,7 @@
- mira --project=nmpvc -job=denovo,genome,normal,sanger -lowqualitydata --fasta=../data/fasta_set1/U13small_nm.fasta -DIRECTORY:scf=../data/scf SANGER_SETTINGS -CLIPPING:qc=yes -LR:mxti=no > run_nmpvc.log
- echo
- echo "If all went well, the results are in 'nmpvc_results' directory."
--echo "Consult run_nmpvc.log and/or stderr if errors occured."
-+echo "Consult run_nmpvc.log and/or stderr if errors occurred."
-
- echo
- echo
-@@ -25,7 +25,7 @@
- mira --project=nmqconly --job=denovo,genome,normal,sanger -lowqualitydata --fasta=../data/fasta_set1/U13small_nm.fasta -DIRECTORY:scf=../data/scf SANGER_SETTINGS -CLIPPING:pvlc=no:qc=yes:emlc=no -LR:mxti=no > run_nmqconly.log
- echo
- echo "If all went well, the results are in 'nmqconly_results' directory."
--echo "Consult run_nmqconly.log and/or stderr if errors occured."
-+echo "Consult run_nmqconly.log and/or stderr if errors occurred."
-
- echo
- echo
-@@ -34,6 +34,6 @@
- mira --project=nmnocl --job=denovo,genome,normal,sanger -lowqualitydata --noclipping --fasta=../data/fasta_set1/U13small_nm.fasta -DIRECTORY:scf=../data/scf -LR:mxti=no > run_nmnocl.log
- echo
- echo "If all went well, the results are in 'nmnocl_results' directory."
--echo "Consult run_nmnocl.log and/or stderr if errors occured."
-+echo "Consult run_nmnocl.log and/or stderr if errors occurred."
- echo
- echo "(and please read the comments on top of the 'runme.sh' script)"
---- mira.orig/minidemo/estdemo1/runme.sh
-+++ mira/minidemo/estdemo1/runme.sh
-@@ -18,4 +18,4 @@
- miraSearchESTSNPs --fasta | tee run.log
- echo "Done."
- echo "If all went well, the results are in 'step3_results' directory."
--echo "Consult run.log and/or stderr if errors occured."
-+echo "Consult run.log and/or stderr if errors occurred."
---- mira.orig/src/io/so.obo
-+++ mira/src/io/so.obo
-@@ -7212,7 +7212,7 @@
- [Term]
- id: SO:0000858
- name: orthologous
--def: "An attribute describing a kind of homology where divergence occured after a speciation event." [SO:ke]
-+def: "An attribute describing a kind of homology where divergence occurred after a speciation event." [SO:ke]
- is_a: SO:0000857 ! homologous
-
- [Term]
-@@ -9696,7 +9696,7 @@
- id: SO:0001146
- name: polypeptide_variation_site
- alt_id: BS:00336
--def: "A site of sequence variation (alteration). Alternative sequence due to naturally occuring events such as polymorphisms and altermatve splicing or experimental methods such as site directed mutagenesis." [EBIBS:GAR, SO:ke]
-+def: "A site of sequence variation (alteration). Alternative sequence due to naturally occurring events such as polymorphisms and altermatve splicing or experimental methods such as site directed mutagenesis." [EBIBS:GAR, SO:ke]
- comment: For example, was a substitution natural or mutated as part of an experiment? This term is added to merge the biosapiens term sequence_variations.
- subset: biosapiens
- synonym: "sequence_variations" EXACT []
---- mira.orig/src/memorc/memorc.C
-+++ mira/src/memorc/memorc.C
-@@ -24,7 +24,7 @@
-
- uint32 MemORC::MOC_innewcount=0;
-
--bool MemORC::MOC_mostfatalerroroccured=false;
-+bool MemORC::MOC_mostfatalerroroccurred=false;
- bool MemORC::MOC_allhot=false;
-
- bool MemORC::MOC_fillondelete=false;
-@@ -170,14 +170,14 @@
-
- void * MemORC::internalMAlloc(size_t n)
- {
-- if(MOC_mostfatalerroroccured){
-+ if(MOC_mostfatalerroroccurred){
- abort();
- }
- void * newmem=malloc(n);
- // Most significant bit set? Come on ... not on x86_64! Must be a magic number
- // for invalid mem
- if(reinterpret_cast<uint64>(newmem)&0x8000000000000000ull){
-- MOC_mostfatalerroroccured=true;
-+ MOC_mostfatalerroroccurred=true;
- printf("Houston, we have a malloc pointer problem: %p\n",newmem);
- statistics();
- MemORC::checkAllMemBlocks();
---- mira.orig/src/memorc/memorc.H
-+++ mira/src/memorc/memorc.H
-@@ -18,7 +18,7 @@
-
- static uint32 MOC_innewcount;
-
-- static bool MOC_mostfatalerroroccured;
-+ static bool MOC_mostfatalerroroccurred;
- static bool MOC_newallocsgetthisnocheckflag;
- static bool MOC_allhot;
- static bool MOC_fillondelete; // unused atm
---- mira.orig/src/mira/assembly_io.C
-+++ mira/src/mira/assembly_io.C
-@@ -270,7 +270,7 @@
+--- mira.orig/src/mira/contig_consensus.C
++++ mira/src/mira/contig_consensus.C
+@@ -2578,7 +2578,7 @@
}
-
- if(hassomeerror){
-- MIRANOTIFY(Notify::FATAL,"While looking at or loading ancillary files named in the manifest, some errors occured. Please check the log.");
-+ MIRANOTIFY(Notify::FATAL,"While looking at or loading ancillary files named in the manifest, some errors occurred. Please check the log.");
+ default : {
+ cout << "seqtype: " << seqtype << endl;
+- MIRANOTIFY(Notify::INTERNAL, "Uknown seqtype to rate?");
++ MIRANOTIFY(Notify::INTERNAL, "Unknown seqtype to rate?");
}
-
- // delayed creation of backbone contigs from single reads
-@@ -516,7 +516,7 @@
}
- if(hassomeerror){
-- MIRANOTIFY(Notify::FATAL,"While looking at or loading data files named in the manifest, some errors occured. Please check the log.");
-+ MIRANOTIFY(Notify::FATAL,"While looking at or loading data files named in the manifest, some errors occurred. Please check the log.");
- }
- }
-
---- mira.orig/src/mira/assembly_pbcorrect.C
-+++ mira/src/mira/assembly_pbcorrect.C
-@@ -986,7 +986,7 @@
- if(isupper(oread.getBaseInSequence(posor))
- && (oread.getQualities())[posor]>0){
- // adjustment vector must match!!! {pos-1, pos, pos+1}
-- // if deletion occured next to it, don't take. E.g. {pos-1, pos, pos+2}
-+ // if deletion occurred next to it, don't take. E.g. {pos-1, pos, pos+2}
- //
- // Rationale: e.g. xATAAAAx -> xATAx (RLE: 114) -> xAx (RLE: 1) -> ouch!
- // xAAAAAAx -> xA**x (RLE: 5--) -> xAx (RLE: 5) -> OK
-@@ -1870,7 +1870,7 @@
- BUGIFTHROW(AS_naclipl.size()!=AS_readpool.size(),"AS_naclipl.size() " << AS_naclipl.size() << " != AS_readpool.size() " << AS_readpool.size());
- BUGIFTHROW(AS_naclipr.size()!=AS_readpool.size(),"AS_naclipr.size() " << AS_naclipr.size() << " != AS_readpool.size() " << AS_readpool.size());
-
-- // *sigh* through indels occuring in the generatePBEdits() call prior to the call to this function,
-+ // *sigh* through indels occurring in the generatePBEdits() call prior to the call to this function,
- // things may be slightly out of sync
- // just make sure this is called late in the whole correction proces, ideally (next to) last pass
-
---- mira.orig/src/mira/assembly_swalign.C
-+++ mira/src/mira/assembly_swalign.C
-@@ -663,7 +663,7 @@
-
- void Assembly::makeAlignments(bool (* checkfunction)(Assembly & as,int32,int32), bool takefullskimfilenames, const bool trans100percent, int32 version, const string prefix, const string postfix, const string tmpfname)
- {
-- //pr�fen, ob AS_posfmatch und ...cmatch nach alignments gel�scht werden k�nnen
-+ //pr?fen, ob AS_posfmatch und ...cmatch nach alignments gel?scht werden k?nnen
-
- FUNCSTART("void Assembly::makeAlignments()");
-
-@@ -1600,7 +1600,7 @@
-
- /*************************************************************************
- *
-- * Checks an ADS for mismatches occuring at RepeatMarkerBase positions
-+ * Checks an ADS for mismatches occurring at RepeatMarkerBase positions
- *
- * Function does not care about quality, those tags are set by the contig
- * and are therefore not to be questioned
-@@ -1715,7 +1715,7 @@
- int32 r2newctagfrom=-1;
- int32 r2newctagto=-1;
-
-- bool problemoccured=false;
-+ bool problemoccurred=false;
-
- // keep count in this loop forward, is used further downward!
- for(uint32 count=0; count<ads.getOverlapLen(); ++count, ++cons, r1index+=r1delta, r2index+=r2delta, ++alseq1, ++alseq2){
-@@ -1729,21 +1729,21 @@
-
- if(r1index<0) {
- cout << "Megaproblem: r1index<0" << endl;
-- problemoccured=true;
-+ problemoccurred=true;
- }
- if(r1index >= static_cast<int32>(AS_readpool.getRead(id1).getLenSeq())){
- cout << "Megaproblem: r1index >= AS_readpool.getRead(id1).getLenSeq()" << endl;
-- problemoccured=true;
-+ problemoccurred=true;
- }
- if(r2index<0) {
- cout << "Megaproblem: r2index<0" << endl;
-- problemoccured=true;
-+ problemoccurred=true;
- }
- if(r2index >= static_cast<int32>(AS_readpool.getRead(id2).getLenSeq())){
- cout << "Megaproblem: r2index >= AS_readpool.getRead(id2).getLenSeq()" << endl;
-- problemoccured=true;
-+ problemoccurred=true;
- }
-- if(problemoccured){
-+ if(problemoccurred){
- cout << "ADSfrm: (" << id1 << ") " << AS_readpool.getRead(id1).getName() << " (" << id2 << ") " << AS_readpool.getRead(id2).getName() << endl << endl;
-
- Read::setCoutType(Read::AS_CAF);
---- mira.orig/src/mira/read.C
-+++ mira/src/mira/read.C
-@@ -774,7 +774,7 @@
- * Initial version tried to preserve the adjustments of the original reads,
- * but the PacBio corrector routines depend on continuous adjustment values
- * (0,1,2,3,...) to find out where during correction insertions or deletions
-- * occured.
-+ * occurred.
- * As I am not sure what the original adjustments could be used for and
- * I do not want to keep two vectors, I'm switching to continuous for
- * the moment.
-@@ -2486,7 +2486,7 @@
- /*************************************************************************
- *
- * starting from the actual quality clips, clip more from the ends while
-- * the characters occuring are X, N, *. That is, results will differ
-+ * the characters occurring are X, N, *. That is, results will differ
- * whether or not a previous quality clipping might have happened or not
- *
- * stretches with other bases will be merged while being <= 'gapsize',
--- mira.orig/src/progs/mira.C
+++ mira/src/progs/mira.C
-@@ -239,7 +239,7 @@
+@@ -245,7 +245,7 @@
}
- catch (exception& e)
- {
-- cout << "A 'standard' exception occured (that's NOT normal):\n" << e.what() << "\n\nIf the cause is not immediatly obvious, please contact: bach at chevreux.org\n\n";
+ catch (std::exception& e) {
+ cout.flush(); cerr.flush();
+- cout << "A 'standard' exception occurred (that's NOT normal):\n" << e.what() << "\n\nIf the cause is not immediatly obvious, please contact: bach at chevreux.org\n\n";
+ cout << "A 'standard' exception occurred (that's NOT normal):\n" << e.what() << "\n\nIf the cause is not immediately obvious, please contact: bach at chevreux.org\n\n";
doAbort();
}
catch(...){
---- mira.orig/src/mira/contig_consensus.C
-+++ mira/src/mira/contig_consensus.C
-@@ -2563,7 +2563,7 @@
- }
- default : {
- cout << "seqtype: " << seqtype << endl;
-- MIRANOTIFY(Notify::INTERNAL, "Uknown seqtype to rate?");
-+ MIRANOTIFY(Notify::INTERNAL, "Unknown seqtype to rate?");
- }
- }
-
---- mira.orig/THANKS
-+++ mira/THANKS
-@@ -31,8 +31,8 @@
- sequences and thoroughly testing the 454 assemblies
- Gerrit Schramm from Roche in helping me out to understand some of the less
- well known things regarding the 454 sequencing system
--Hern�ndez Alvarez
-- Alfredo Jos� providing patches to have MIRA compile again on Solaris
-+Hern?ndez Alvarez
-+ Alfredo Jos? providing patches to have MIRA compile again on Solaris
- Lionel Guy implementing bug fixes in sff_extract and making available
- data sets to hunt down some ugly bugs in MIRA
- Sven Klages for insightful feedback and providing a fix for the ACE
-@@ -52,7 +52,7 @@
- Jorge Duarte from BIOGEMMA for making available test sets to track down
- memory corruption bugs
- Dag Ahren making available a test set to track down a rather nasty
-- problem occuring during clipping
-+ problem occurring during clipping
- Jan van Haarst Running benchmarks over NFS to find poorly performing
- input/output routines
- Peter Cock Invaluable feedback for implementing SAM format and
---- mira.orig/doc/docbook/chap_seqtechdesc_part.xml
-+++ mira/doc/docbook/chap_seqtechdesc_part.xml
-@@ -246,7 +246,7 @@
- <para>
- Note that projects using reads ≤ 100 bp assembled fine with MIRA
- 4.9.3 and before as the default algorithms for proposed-end-clip
-- (<arg>-CL:pec</arg>) implicitly caught chimeras occuring near the
-+ (<arg>-CL:pec</arg>) implicitly caught chimeras occurring near the
- read ends and the remaining chimeras were caught by the algorithms
- for low level chimeras.
- </para>
---- mira.orig/src/mira/contig_analysis.C
-+++ mira/src/mira/contig_analysis.C
-@@ -342,7 +342,7 @@
- /*************************************************************************
- *
- * Checks a (newly entered at call time, but might be used for other means)
-- * read whether it has mismatches occuring at SRMB or WRMB position
-+ * read whether it has mismatches occurring at SRMB or WRMB position
- *
- * Gives back 'true' if a certain level of danger is attained
- *
-@@ -4061,7 +4061,7 @@
- CEBUG("readswithgaps: " << readswithgaps << "\treadswithnogaps: " << readswithnogaps << '\n');
- CEBUG("hasgapsforward: " << hasgapsforward << "\thasgapsreverse: " << hasgapsreverse << '\n');
- CEBUG("maxgaprunlen: " << maxgaprunlen << '\n');
-- CEBUG("most frequent gap size: " << mostfrequentgapsize << "\toccuring: " << gapruns[mostfrequentgapsize]<<'\n');
-+ CEBUG("most frequent gap size: " << mostfrequentgapsize << "\toccurring: " << gapruns[mostfrequentgapsize]<<'\n');
-
- if(readswithgaps<mingroupsize) continue;
- if(needbothstrands && !(hasgapsforward && hasgapsreverse)) continue;
diff --git a/debian/rules b/debian/rules
index 5c0cd78..7c29b1f 100755
--- a/debian/rules
+++ b/debian/rules
@@ -2,10 +2,8 @@
# Uncomment this to turn on verbose mode.
export DH_VERBOSE=1
-#Hacky thing to allow building against tcmalloc without installing
-#troublesome libbgoogle-perftools-dev, see README.Debian
-export DEB_CFLAGS_MAINT_APPEND=-L$(CURDIR)/lib
export DEBIAN_MAINTAINER=$(dpkg-parsechangelog -SMaintainer)
+export DEB_BUILD_MAINT_OPTIONS=hardening=+all
pkg=mira-assembler
exampledir=usr/share/doc/mira-examples/examples/minidemo/data/bbdataset1/
@@ -13,88 +11,44 @@ exampledir=usr/share/doc/mira-examples/examples/minidemo/data/bbdataset1/
include /usr/share/dpkg/default.mk
%:
- dh $@ --with autoreconf
+ dh $@ --with autoreconf --parallel
-override_dh_auto_install :
+override_dh_auto_install-arch:
make install DESTDIR=$(CURDIR)/debian/$(pkg)
+
+override_dh_auto_install-indep:
#There is no installation target for the docs
mkdir -p $(CURDIR)/debian/tmp/usr/share/doc/$(pkg)
cp -r -t $(CURDIR)/debian/tmp/usr/share/doc/$(pkg) doc/docbook/bookfigures doc/docbook/images \
doc/docbook/doccss doc/docbook/DefinitiveGuideToMIRA.html || true
-override_dh_installexamples:
- dh_installexamples
- # avoid duplicated files
- if cmp $(CURDIR)/debian/mira-examples/$(exampledir)/cjejuni_demo_in.fasta.qual $(CURDIR)/debian/mira-examples/$(exampledir)/cjejuni_demo_in.sanger.fasta.qual >/dev/null ; then \
- echo "removing copy of $(exampledir)/cjejuni_demo_in.fasta.qual and create symling" ; \
- rm -f $(CURDIR)/debian/mira-examples/$(exampledir)/cjejuni_demo_in.sanger.fasta.qual ; \
- ln -s cjejuni_demo_in.fasta.qual.gz $(CURDIR)/debian/mira-examples/$(exampledir)/cjejuni_demo_in.sanger.fasta.qual.gz ; \
- fi
- if cmp $(CURDIR)/debian/mira-examples/$(exampledir)/cjejuni_demo_in.fasta $(CURDIR)/debian/mira-examples/$(exampledir)/cjejuni_demo_in.sanger.fasta >/dev/null ; then \
- echo "removing copy of $(exampledir)/cjejuni_demo_in.fasta and create symling" ; \
- rm -f $(CURDIR)/debian/mira-examples/$(exampledir)/cjejuni_demo_in.sanger.fasta ; \
- ln -s cjejuni_demo_in.fasta.gz $(CURDIR)/debian/mira-examples/$(exampledir)/cjejuni_demo_in.sanger.fasta.gz ; \
- fi
- if cmp $(CURDIR)/debian/mira-examples/$(exampledir)/cjejuni_NCTC11168_first40kb.gbf $(CURDIR)/debian/mira-examples/$(exampledir)/cjejuni_demo_backbone_in.gbf >/dev/null ; then \
- echo "removing copy of $(exampledir)/cjejuni_NCTC11168_first40kb.gbf and create symling" ; \
- rm -f $(CURDIR)/debian/mira-examples/$(exampledir)/cjejuni_demo_backbone_in.gbf ; \
- ln -s cjejuni_NCTC11168_first40kb.gbf.gz $(CURDIR)/debian/mira-examples/$(exampledir)/cjejuni_demo_backbone_in.gbf.gz ; \
- fi
- if cmp $(CURDIR)/debian/mira-examples/$(exampledir)/cjejuni_demo_traceinfo_in.xml $(CURDIR)/debian/mira-examples/$(exampledir)/cjejuni_demo_traceinfo_in.sanger.xml >/dev/null ; then \
- echo "removing copy of $(exampledir)/cjejuni_demo_traceinfo_in.xml and create symling" ; \
- rm -f $(CURDIR)/debian/mira-examples/$(exampledir)/cjejuni_demo_traceinfo_in.sanger.xml ; \
- ln -s cjejuni_demo_traceinfo_in.xml.gz $(CURDIR)/debian/mira-examples/$(exampledir)/cjejuni_demo_traceinfo_in.sanger.xml.gz ; \
- fi
-
-override_dh_auto_test:
+override_dh_auto_test-arch:
make check
-#Make the docs
-override_dh_auto_build:
+override_dh_auto_test-indep:
+
+override_dh_auto_build-arch:
# some *.cc files are created by old flex version which breaks the build
# see bug #812681
find -name '*.ll' | sed -e 's/[.]ll$$/.cc/' | xargs rm
- dh_auto_build --parallel
-ifneq (,$(findstring mira-doc, $(shell dh_listpackages)))
- dh_auto_build --sourcedir=doc --parallel
-endif
+ dh_auto_build
-#Remove unneeded .tcl extensions from scripts
-override_dh_install:
- dh_install
- if [ -d debian/$(pkg) ] ; then \
- for f in $$(ls debian/$(pkg)/usr/bin/*.tcl) ; do mv "$$f" "$${f%.tcl}"; done \
- fi
- # In version 3.9.17 executing miraSearchESTSNPs just leads to "De-activated atm, sorry."
- # If this is the case, it should not be installed
- for deactivated in miraSearchESTSNPs miraclip ; do \
- if [ -e debian/$(pkg)/usr/bin/$${deactivated} ] ; then \
- if [ "`debian/$(pkg)/usr/bin/$${deactivated} 2>&1 | tee`" = "De-activated atm, sorry." ] ; then rm -f debian/$(pkg)/usr/bin/$${deactivated} ; fi \
- else \
- echo "debian/$(pkg)/usr/bin/$${deactivated} does not exist" ; \
- fi ; \
- done
+override_dh_auto_build-indep:
+ dh_auto_build --sourcedir=doc
+
+override_dh_installchangelogs:
+ dh_installchangelogs src/mira/CHANGES.txt
#Must clean up the docs before cleaning out config.status
#Then scrub some junk not picked up by 'make clean'
override_dh_auto_clean:
( cd doc ; make clean ) || true
- dh_auto_clean
+ dh_auto_clean || true
find * -name Makefile -exec rm '{}' ';'
find * -name '*.xxd.H' -exec rm '{}' ';'
find * -name '*.par.H' -exec rm '{}' ';'
find * -name 'compileinfo.*' -exec rm '{}' ';'
-override_dh_clean:
- dh_clean
- rm -rf lib
-
-override_dh_auto_configure :
- mkdir lib
- ln -s /usr/lib/libtcmalloc_minimal.so.4 lib/libtcmalloc_minimal.so
- #dh_auto_configure
- dh_auto_configure -- --with-boost-libdir=/usr/lib/$(DEB_HOST_MULTIARCH)
-
override_dh_builddeb:
dh_builddeb -- -Z xz
--
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