[med-svn] [Git][med-team/trimmomatic][master] 10 commits: New upstream version 0.39+dfsg
Andreas Tille
gitlab at salsa.debian.org
Wed Jul 3 08:21:49 BST 2019
Andreas Tille pushed to branch master at Debian Med / trimmomatic
Commits:
38d18d35 by Andreas Tille at 2019-07-03T06:48:35Z
New upstream version 0.39+dfsg
- - - - -
de81129f by Andreas Tille at 2019-07-03T06:48:35Z
Update upstream source from tag 'upstream/0.39+dfsg'
Update to upstream version '0.39+dfsg'
with Debian dir aec57ce63647fecbfbd07e5abf3931b65b80b5df
- - - - -
2ea67e93 by Andreas Tille at 2019-07-03T06:48:35Z
New upstream version
- - - - -
f7da6ac1 by Andreas Tille at 2019-07-03T06:48:35Z
debhelper 12
- - - - -
ae84d20f by Andreas Tille at 2019-07-03T06:48:40Z
Standards-Version: 4.3.0
- - - - -
d6a63aaa by Andreas Tille at 2019-07-03T06:55:56Z
Adapt patches
- - - - -
8563f766 by Andreas Tille at 2019-07-03T06:56:09Z
Secure URI in copyright format
- - - - -
8d52aff1 by Andreas Tille at 2019-07-03T06:56:09Z
Remove trailing whitespace in debian/changelog
- - - - -
a14fe8f6 by Andreas Tille at 2019-07-03T06:56:09Z
Remove trailing whitespace in debian/copyright
- - - - -
4b586edc by Andreas Tille at 2019-07-03T07:09:08Z
Upload to unstable
- - - - -
8 changed files:
- build.xml
- debian/changelog
- debian/compat
- debian/control
- debian/copyright
- debian/patches/buildxmlJbzip2.patch
- src/org/usadellab/trimmomatic/trim/HeadCropTrimmer.java
- src/org/usadellab/trimmomatic/trim/TailCropTrimmer.java
Changes:
=====================================
build.xml
=====================================
@@ -1,5 +1,5 @@
<project name="Trimmomatic" default="dist" basedir=".">
- <property name="version" value="0.38"/>
+ <property name="version" value="0.39"/>
<property name="src" location="src" />
<property name="lib" location="lib" />
=====================================
debian/changelog
=====================================
@@ -1,3 +1,14 @@
+trimmomatic (0.39+dfsg-1) unstable; urgency=medium
+
+ * New upstream version
+ * debhelper 12
+ * Standards-Version: 4.3.0
+ * Secure URI in copyright format
+ * Remove trailing whitespace in debian/changelog
+ * Remove trailing whitespace in debian/copyright
+
+ -- Andreas Tille <tille at debian.org> Wed, 03 Jul 2019 08:56:09 +0200
+
trimmomatic (0.38+dfsg-1) unstable; urgency=medium
* New upstream version
@@ -10,9 +21,9 @@ trimmomatic (0.38+dfsg-1) unstable; urgency=medium
trimmomatic (0.36+dfsg-3) unstable; urgency=medium
* Team upload.
-
+
[ Nadiya Sitdykova ]
- * add autopkgtest test-suite
+ * add autopkgtest test-suite
* add info about debian/tests/test_data
[ Steffen Moeller ]
@@ -24,7 +35,7 @@ trimmomatic (0.36+dfsg-3) unstable; urgency=medium
trimmomatic (0.36+dfsg-2) unstable; urgency=medium
* Team upload.
-
+
[ Fabian Klötzl ]
* allow filenames to contain spaces (Closes: #867535)
@@ -38,7 +49,7 @@ trimmomatic (0.36+dfsg-2) unstable; urgency=medium
trimmomatic (0.36+dfsg-1) unstable; urgency=medium
[ Steffen Moeller ]
- * Introduced EDAM ontology information to
+ * Introduced EDAM ontology information to
debian/upstream/edam
* Added patch to find adapters in /usr/share/trimmomatic
=====================================
debian/compat
=====================================
@@ -1 +1 @@
-11
+12
=====================================
debian/control
=====================================
@@ -4,12 +4,12 @@ Uploaders: Andreas Tille <tille at debian.org>,
Steffen Moeller <moeller at debian.org>
Section: science
Priority: optional
-Build-Depends: debhelper (>= 11~),
+Build-Depends: debhelper (>= 12~),
default-jdk | openjdk-7-jdk,
javahelper,
ant,
libjbzip2-java
-Standards-Version: 4.1.4
+Standards-Version: 4.3.0
Vcs-Browser: https://salsa.debian.org/med-team/trimmomatic
Vcs-Git: https://salsa.debian.org/med-team/trimmomatic.git
Homepage: http://www.usadellab.org/cms/index.php?page=trimmomatic
=====================================
debian/copyright
=====================================
@@ -1,9 +1,9 @@
-Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: Trimmomatic
Upstream-Contact: Federico Giorgi <federico.giorgi at gmail.com>,
Anthony Bolger <bolger at mpimp-golm.mpg.de>
Source: http://www.usadellab.org/cms/index.php?page=trimmomatic
-Files-Excluded:
+Files-Excluded:
lib/*.jar
old
@@ -43,10 +43,10 @@ License: GPL-3+
License: INSDC
INSDC License - as described in ENA site - August 7, 2017
.
- The INSDC will not attach statements to records that restrict access to the
+ The INSDC will not attach statements to records that restrict access to the
data, limit the use of the information in these records, or prohibit certain
- types of publications based on these records. Specifically, no use
- restrictions or licensing requirements will be included in any sequence data
+ types of publications based on these records. Specifically, no use
+ restrictions or licensing requirements will be included in any sequence data
records, and no restrictions or licensing fees will be placed on the
redistribution or use of the database by any party.
.
=====================================
debian/patches/buildxmlJbzip2.patch
=====================================
@@ -4,7 +4,7 @@ Description: Use Debian packaged bzip2 library
--- a/build.xml
+++ b/build.xml
@@ -2,7 +2,7 @@
- <property name="version" value="0.38"/>
+ <property name="version" value="0.39"/>
<property name="src" location="src" />
- <property name="lib" location="lib" />
=====================================
src/org/usadellab/trimmomatic/trim/HeadCropTrimmer.java
=====================================
@@ -2,24 +2,86 @@ package org.usadellab.trimmomatic.trim;
import org.usadellab.trimmomatic.fastq.FastqRecord;
-public class HeadCropTrimmer extends AbstractSingleRecordTrimmer
+public class HeadCropTrimmer implements Trimmer
{
- private int bases;
- private int maxLength=Integer.MAX_VALUE/2;
+ private int firstBases;
+ private int midBases;
+ private int lastBases;
+
+ private int firstMaxLength=Integer.MAX_VALUE/2;
+ private int midMaxLength=Integer.MAX_VALUE/2;
+ private int lastMaxLength=Integer.MAX_VALUE/2;
public HeadCropTrimmer(String args)
{
String arg[]=args.split(":");
- bases=Integer.parseInt(arg[0]);
+ switch(arg.length)
+ {
+ case 1:
+ firstBases=midBases=lastBases=Integer.parseInt(arg[0]);
+ break;
+
+ case 2:
+ firstBases=midBases=lastBases=Integer.parseInt(arg[0]);
+ firstMaxLength=midMaxLength=lastMaxLength=Integer.parseInt(arg[1]);
+ break;
+
+ case 4:
+ firstBases=midBases=Integer.parseInt(arg[0]);
+ firstMaxLength=midMaxLength=Integer.parseInt(arg[1]);
+ lastBases=Integer.parseInt(arg[2]);
+ lastMaxLength=Integer.parseInt(arg[3]);
+ break;
+
+ case 6:
+ firstBases=Integer.parseInt(arg[0]);
+ firstMaxLength=Integer.parseInt(arg[1]);
+ midBases=Integer.parseInt(arg[2]);
+ midMaxLength=Integer.parseInt(arg[3]);
+ lastBases=Integer.parseInt(arg[4]);
+ lastMaxLength=Integer.parseInt(arg[5]);
+ break;
+
+ default:
+
+ }
- if(arg.length>1)
- maxLength=Integer.parseInt(arg[1]);
}
@Override
- public FastqRecord processRecord(FastqRecord in)
+ public FastqRecord[] processRecords(FastqRecord[] in) {
+
+ if(in==null)
+ return null;
+
+ FastqRecord out[]=new FastqRecord[in.length];
+
+ int lastRecord=in.length-1;
+
+ if(in.length>0)
+ {
+ if(in[0]!=null)
+ out[0]=processRecord(in[0], firstBases, firstMaxLength);
+ }
+
+ for(int i=1;i<lastRecord;i++)
+ {
+ if(in[i]!=null)
+ out[i]=processRecord(in[i], midBases, midMaxLength);
+ }
+
+ if(lastRecord>0)
+ {
+ if(in[lastRecord]!=null)
+ out[lastRecord]=processRecord(in[lastRecord], lastBases, lastMaxLength);
+ }
+
+ return out;
+ }
+
+ private FastqRecord processRecord(FastqRecord in, int bases, int maxLength)
{
int len=in.getSequence().length();
=====================================
src/org/usadellab/trimmomatic/trim/TailCropTrimmer.java
=====================================
@@ -2,44 +2,85 @@ package org.usadellab.trimmomatic.trim;
import org.usadellab.trimmomatic.fastq.FastqRecord;
-public class TailCropTrimmer extends AbstractSingleRecordTrimmer
+public class TailCropTrimmer implements Trimmer
{
- private int bases;
- private int maxLength=Integer.MAX_VALUE/2;
-
+ private int firstBases;
+ private int midBases;
+ private int lastBases;
+
+ private int firstMaxLength=Integer.MAX_VALUE/2;
+ private int midMaxLength=Integer.MAX_VALUE/2;
+ private int lastMaxLength=Integer.MAX_VALUE/2;
+
public TailCropTrimmer(String args)
{
String arg[]=args.split(":");
-
- bases=Integer.parseInt(arg[0]);
- if(arg.length>1)
- maxLength=Integer.parseInt(arg[1]);
+ switch(arg.length)
+ {
+ case 1:
+ firstBases=midBases=lastBases=Integer.parseInt(arg[0]);
+ break;
+
+ case 2:
+ firstBases=midBases=lastBases=Integer.parseInt(arg[0]);
+ firstMaxLength=midMaxLength=lastMaxLength=Integer.parseInt(arg[1]);
+ break;
+
+ case 4:
+ firstBases=midBases=Integer.parseInt(arg[0]);
+ firstMaxLength=midMaxLength=Integer.parseInt(arg[1]);
+ lastBases=Integer.parseInt(arg[2]);
+ lastMaxLength=Integer.parseInt(arg[3]);
+ break;
+
+ case 6:
+ firstBases=Integer.parseInt(arg[0]);
+ firstMaxLength=Integer.parseInt(arg[1]);
+ midBases=Integer.parseInt(arg[2]);
+ midMaxLength=Integer.parseInt(arg[3]);
+ lastBases=Integer.parseInt(arg[4]);
+ lastMaxLength=Integer.parseInt(arg[5]);
+ break;
+
+ default:
+
+ }
}
-/*
- @Override
- public FastqRecord[] processRecords(FastqRecord[] in)
- {
+ @Override
+ public FastqRecord[] processRecords(FastqRecord[] in) {
+
if(in==null)
return null;
FastqRecord out[]=new FastqRecord[in.length];
- for(int i=0;i<in.length;i++)
+ int lastRecord=in.length-1;
+
+ if(in.length>0)
+ {
+ if(in[0]!=null)
+ out[0]=processRecord(in[0], firstBases, firstMaxLength);
+ }
+
+ for(int i=1;i<lastRecord;i++)
{
if(in[i]!=null)
- out[i]=processRecord(in[i]);
+ out[i]=processRecord(in[i], midBases, midMaxLength);
}
-
+
+ if(lastRecord>0)
+ {
+ if(in[lastRecord]!=null)
+ out[lastRecord]=processRecord(in[lastRecord], lastBases, lastMaxLength);
+ }
+
return out;
}
- */
-
-
- @Override
- public FastqRecord processRecord(FastqRecord in)
+
+ private FastqRecord processRecord(FastqRecord in, int bases, int maxLength)
{
int len=in.getSequence().length();
View it on GitLab: https://salsa.debian.org/med-team/trimmomatic/compare/4927818f6b784b3d2a9e573cd53413faa5fcaa14...4b586edc6957138d5439c70f5fd2298e08e8d1c3
--
View it on GitLab: https://salsa.debian.org/med-team/trimmomatic/compare/4927818f6b784b3d2a9e573cd53413faa5fcaa14...4b586edc6957138d5439c70f5fd2298e08e8d1c3
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