Pierre Gruet pushed to branch master at Debian Med / htsjdk
Commits:
c24b7734 by Pierre Gruet at 2024-05-15T21:56:44+02:00
Raising Standards version to 4.7.0 (no change)
- - - - -
ac9f152a by Pierre Gruet at 2024-05-15T22:00:59+02:00
Updating autopkgtest linked to drop-seq after changes in this package
- - - - -
5532e2d6 by Pierre Gruet at 2024-05-15T22:01:10+02:00
Upload to unstable
- - - - -
3 changed files:
- debian/changelog
- debian/control
- debian/tests/drop-seq-run-unit-test
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,10 @@
+htsjdk (4.1.0+dfsg-2) unstable; urgency=medium
+
+ * Raising Standards version to 4.7.0 (no change)
+ * Updating autopkgtest linked to drop-seq after changes in this package
+
+ -- Pierre Gruet <p...@debian.org> Wed, 15 May 2024 22:01:02 +0200
+
htsjdk (4.1.0+dfsg-1) unstable; urgency=medium
* New upstream version 4.1.0+dfsg
=====================================
debian/control
=====================================
@@ -28,7 +28,7 @@ Build-Depends: default-jdk,
libcommons-lang3-java,
libjimfs-java,
scala-library
-Standards-Version: 4.6.2
+Standards-Version: 4.7.0
Vcs-Browser: https://salsa.debian.org/med-team/htsjdk
Vcs-Git: https://salsa.debian.org/med-team/htsjdk.git
Homepage: https://samtools.github.io/htsjdk/
=====================================
debian/tests/drop-seq-run-unit-test
=====================================
@@ -21,25 +21,8 @@ gunzip -r ref/*
gunzip -r org/broadinstitute/dropseq/annotation/*
gunzip -r org/broadinstitute/dropseq/readtrimming/*
mkdir out
-#do_stuff_to_test_package#
echo -e "\e[93m\e[1mTest 1\e[0m"
-drop-seq TagBamWithReadSequenceExtended
INPUT=org/broadinstitute/dropseq/annotation/test.bam \
- OUTPUT=out/TagBamWithReadSequenceExtended-cellular.bam
SUMMARY=TagBamWithReadSequenceExtended-cellular.bam_summary.txt BASE_RANGE=1-12
BASE_QUALITY=10 BARCODED_READ=1 DISCARD_READ=false TAG_NAME=XC
NUM_BASES_BELOW_QUALITY=1
-samtools view out/TagBamWithReadSequenceExtended-cellular.bam >
out/TagBamWithReadSequenceExtended-cellular.sam
-diff out/TagBamWithReadSequenceExtended-cellular.sam
ref/TagBamWithReadSequenceExtended-cellular.sam
-echo -e "\e[92m\e[1mPassed\e[0m"
-echo
-
-echo -e "\e[93m\e[1mTest 2\e[0m"
-drop-seq TagBamWithReadSequenceExtended
INPUT=org/broadinstitute/dropseq/annotation/test.bam \
- OUTPUT=out/TagBamWithReadSequenceExtended-molecular.bam
SUMMARY=TagBamWithReadSequenceExtended-molecular.bam_summary.txt
BASE_RANGE=1-12 BASE_QUALITY=10 BARCODED_READ=1 DISCARD_READ=false TAG_NAME=XM
NUM_BASES_BELOW_QUALITY=1
-samtools view out/TagBamWithReadSequenceExtended-molecular.bam >
out/TagBamWithReadSequenceExtended-molecular.sam
-diff out/TagBamWithReadSequenceExtended-molecular.sam
ref/TagBamWithReadSequenceExtended-molecular.sam
-echo -e "\e[92m\e[1mPassed\e[0m"
-echo
-
-echo -e "\e[93m\e[1mTest 3\e[0m"
drop-seq FilterBam TAG_REJECT=XQ
INPUT=org/broadinstitute/dropseq/readtrimming/N701.subset.tagged_filtered.sam \
OUTPUT=out/FilterBam.bam
samtools view out/FilterBam.bam > out/FilterBam.sam
@@ -47,7 +30,7 @@ diff out/FilterBam.sam ref/FilterBam.sam
echo -e "\e[92m\e[1mPassed\e[0m"
echo
-echo -e "\e[93m\e[1mTest 4\e[0m"
+echo -e "\e[93m\e[1mTest 2\e[0m"
drop-seq TrimStartingSequence INPUT=out/FilterBam.bam
OUTPUT=out/TrimStartingSequence.bam \
OUTPUT_SUMMARY=out/TrimStartingSequence.summary.txt
SEQUENCE=AAGCAGTGGTATCAACGCAGAGTGAATGGG MISMATCHES=0 NUM_BASES=5
samtools view out/TrimStartingSequence.bam > out/TrimStartingSequence.sam
@@ -55,7 +38,7 @@ diff out/TrimStartingSequence.sam ref/TrimStartingSequence.sam
echo -e "\e[92m\e[1mPassed\e[0m"
echo
-echo -e "\e[93m\e[1mTest 5\e[0m"
+echo -e "\e[93m\e[1mTest 3\e[0m"
drop-seq PolyATrimmer INPUT=out/TrimStartingSequence.bam
OUTPUT=out/PolyATrimmer.bam \
OUTPUT_SUMMARY=out/PolyATrimmer.summary.bam MISMATCHES=0 NUM_BASES=6
USE_NEW_TRIMMER=true
samtools view out/PolyATrimmer.bam > out/PolyATrimmer.sam
View it on GitLab:
https://salsa.debian.org/med-team/htsjdk/-/compare/80d13b32682bcff805d8acbf5b86add4677c9491...5532e2d62b6fed55df6d713bf1d753624bc8344c
--
View it on GitLab:
https://salsa.debian.org/med-team/htsjdk/-/compare/80d13b32682bcff805d8acbf5b86add4677c9491...5532e2d62b6fed55df6d713bf1d753624bc8344c
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