[med-svn] [Git][med-team/bitseq][master] 5 commits: created gbp.conf

[harish chavre (@Harish1)]

harish chavre pushed to branch master at Debian Med / bitseq


Commits:
8927d2e0 by Harish chavre at 2025-06-17T05:09:08+00:00
created gbp.conf

- - - - -
5b46266b by Harish chavre at 2025-06-17T05:11:02+00:00
New upstream version 0.7.5+dfsg
- - - - -
512f454d by Harish chavre at 2025-06-17T05:11:03+00:00
Update upstream source from tag 'upstream/0.7.5+dfsg'

Update to upstream version '0.7.5+dfsg'
with Debian dir dc18e7a51dd0355b2220579c37426eb418a58e14
- - - - -
e2a66682 by Harish chavre at 2025-06-17T19:57:13+00:00
Add test data and Bowtie alignment outputs for autopkgtest

- - - - -
3167b32e by Harish chavre at 2025-06-18T18:48:43+00:00
Fix autopkgtest

- - - - -


11 changed files:

- debian/tests/Data/Reads.fastq → debian-tests-data/Reads.fastq
- debian/tests/Data/Ref.fasta → debian-tests-data/Ref.fasta
- + debian-tests-data/index.1.ebwt
- + debian-tests-data/index.2.ebwt
- + debian-tests-data/index.3.ebwt
- + debian-tests-data/index.4.ebwt
- + debian-tests-data/index.rev.1.ebwt
- + debian-tests-data/index.rev.2.ebwt
- + debian-tests-data/out.sam
- debian/tests/control
- debian/tests/run-unit-test


Changes:

=====================================
debian/tests/Data/Reads.fastq → debian-tests-data/Reads.fastq
=====================================


=====================================
debian/tests/Data/Ref.fasta → debian-tests-data/Ref.fasta
=====================================


=====================================
debian-tests-data/index.1.ebwt
=====================================
Binary files /dev/null and b/debian-tests-data/index.1.ebwt differ


=====================================
debian-tests-data/index.2.ebwt
=====================================
Binary files /dev/null and b/debian-tests-data/index.2.ebwt differ


=====================================
debian-tests-data/index.3.ebwt
=====================================
Binary files /dev/null and b/debian-tests-data/index.3.ebwt differ


=====================================
debian-tests-data/index.4.ebwt
=====================================
Binary files /dev/null and b/debian-tests-data/index.4.ebwt differ


=====================================
debian-tests-data/index.rev.1.ebwt
=====================================
Binary files /dev/null and b/debian-tests-data/index.rev.1.ebwt differ


=====================================
debian-tests-data/index.rev.2.ebwt
=====================================
Binary files /dev/null and b/debian-tests-data/index.rev.2.ebwt differ


=====================================
debian-tests-data/out.sam
=====================================
@@ -0,0 +1,5 @@
+ at HD	VN:1.0	SO:unsorted
+ at SQ	SN:ref	LN:318
+ at PG	ID:Bowtie	VN:1.3.1	CL:"/usr/bin/bowtie-align-s --wrapper basic-0 -q -v 3 --all -m 100 --sam index Reads.fastq -S out.sam"
+read1	4	*	0	0	*	*	0	0	ACGTACGTACGT	IIIIIIIIIIII	XM:i:0
+read2	4	*	0	0	*	*	0	0	ACGTACGTACGT	JJJJJJJJJJJJ	XM:i:0


=====================================
debian/tests/control
=====================================
@@ -1,3 +1,3 @@
 Tests: run-unit-test
-Depends: @, bowtie, bitseq
+Depends: @, bitseq
 Restrictions: allow-stderr


=====================================
debian/tests/run-unit-test
=====================================
@@ -1,31 +1,30 @@
+#!/bin/sh
 set -e
 
 pkg=bitseq
-
 export LC_ALL=C.UTF-8
+
+CUR_DIR=`pwd`
+
 if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
   AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
   trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
 fi
 
-cp -a "$(dirname "$0")/Data/"* "${AUTOPKGTEST_TMP}/"
+cp ${CUR_DIR}/debian-tests-data/* -a "${AUTOPKGTEST_TMP}"
 
 cd "${AUTOPKGTEST_TMP}"
 
-bowtie-build -f Ref.fasta index
-bowtie -q -v 3 --all -m 100 --sam index Reads.fastq  -S out.sam
+# Check for pre-generated input
+if [ ! -s out.sam ]; then
+    echo "out.sam not found"
+    exit 1
+fi
 
-[ -s out.sam ] && echo "Test passed!" || { echo "Output missing or empty"; exit 1; }
+parseAlignment out.sam   -o result.prob  --trSeqFile Ref.fasta  --trInfoFile Ref.tr  --uniform --verbose
 
-parseAlignment out.sam \
-  -o result.prob \
-  --trSeqFile Ref.fasta \
-  --trInfoFile Ref.tr \
-  --uniform --verbose
-  
 if [ -s result.prob ] && [ -s Ref.tr ]; then
-  echo "parseAlignment test passed"
+    echo " test passed"
 else
-  echo "parseAlignment test failed"
-  exit 1
+    exit 1
 fi



View it on GitLab: https://salsa.debian.org/med-team/bitseq/-/compare/e07930fe2e8adf03d9a08f9299a16b2a09d7ad76...3167b32eff2e733ecd6e8a7f8e99dd8359519107

-- 
View it on GitLab: https://salsa.debian.org/med-team/bitseq/-/compare/e07930fe2e8adf03d9a08f9299a16b2a09d7ad76...3167b32eff2e733ecd6e8a7f8e99dd8359519107
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