[med-svn] [Git][med-team/cufflinks][master] 2 commits: Add autopkgtest
Andreas Tille (@tille)
gitlab at salsa.debian.org
Mon Sep 21 12:47:08 BST 2026
Andreas Tille pushed to branch master at Debian Med / cufflinks
Commits:
11df3a9a by Andreas Tille at 2026-09-21T13:32:49+02:00
Add autopkgtest
- - - - -
c3d1f14a by Andreas Tille at 2026-09-21T13:38:39+02:00
Upload to unstable
- - - - -
9 changed files:
- + debian/README.test
- debian/changelog
- + debian/cufflinks.examples
- debian/docs
- + debian/tests/control
- + debian/tests/data/expected/transcripts.gtf
- + debian/tests/data/reads.sam
- + debian/tests/data/ref.gtf
- + debian/tests/run-unit-test
Changes:
=====================================
debian/README.test
=====================================
@@ -0,0 +1,8 @@
+Notes on how this package can be tested.
+────────────────────────────────────────
+
+This package can be tested by running the provided test:
+
+ sh run-unit-test
+
+in order to confirm its integrity.
=====================================
debian/changelog
=====================================
@@ -1,4 +1,4 @@
-cufflinks (2.2.1+git20190706.dc3b0cb+dfsg-1) UNRELEASED; urgency=medium
+cufflinks (2.2.1+git20190706.dc3b0cb+dfsg-1) unstable; urgency=medium
* New upstream version (latest commit)
* Build with gcc-15
@@ -30,8 +30,9 @@ cufflinks (2.2.1+git20190706.dc3b0cb+dfsg-1) UNRELEASED; urgency=medium
* Reflow Uploaders field (cme)
* Drop 'Rules-Requires-Root: no' from d/control (routine-update)
* debputy lint --auto-fix (routine-update)
+ * Add autopkgtest
- -- Andreas Tille <tille at debian.org> Mon, 21 Sep 2026 10:18:12 +0200
+ -- Andreas Tille <tille at debian.org> Mon, 21 Sep 2026 13:33:58 +0200
cufflinks (2.2.1+dfsg.1-10) unstable; urgency=medium
=====================================
debian/cufflinks.examples
=====================================
@@ -0,0 +1 @@
+debian/tests/data/*
=====================================
debian/docs
=====================================
@@ -1,2 +1,4 @@
README.md
AUTHORS
+debian/README.test
+debian/tests/run-unit-test
=====================================
debian/tests/control
=====================================
@@ -0,0 +1,3 @@
+Tests: run-unit-test
+Depends: @
+Restrictions: allow-stderr
=====================================
debian/tests/data/expected/transcripts.gtf
=====================================
@@ -0,0 +1,3 @@
+chr1 Cufflinks transcript 1001 1600 1000 + . gene_id "CUFF.1"; transcript_id "CUFF.1.1";
+chr1 Cufflinks exon 1001 1200 1000 + . gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "1";
+chr1 Cufflinks exon 1401 1600 1000 + . gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "2";
=====================================
debian/tests/data/reads.sam
=====================================
@@ -0,0 +1,83 @@
+ at HD VN:1.0 SO:coordinate
+ at SQ SN:chr1 LN:100000
+ at RG ID:rg1 SM:sample1
+read1 0 chr1 1001 60 100M * 0 0 AAGCCCAATAAACCACTCTGACTGGCCGAATAGGGATATAGGCAACGACATGTGCGGCGACCCTTGCGACAGTGACGCTTTCGCCGTTGCCTAAACCTAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII RG:Z:rg1
+read2 0 chr1 1001 60 100M * 0 0 TTGAAGGAGTCTAGCAGCCGCAGTAAGGCACAATACCTCGTCCGTGTTACCAGACCAAACAAGACGTCCTCTTCAATGTTTAAATGACCCTCTCGTCATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII RG:Z:rg1
+read3 0 chr1 1001 60 100M * 0 0 AAACCTTTCTACTATGTGTTCCGCAAGAATCAACAACTACAATGGCGCGTCGTGAATAACGCGACGGCTGAGACGAACGGCGCGTGAATGAAGCGCTTAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII RG:Z:rg1
+read4 0 chr1 1001 60 100M * 0 0 ACAGCTCAGGAGCCAGTCCCCTACGTCGCATATCCTGGCCACTGGAGGTGAAGCGAATGGTATCGATACGTAGGAGGTGTGCCTTCGTAGGCTGTTTCTC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII RG:Z:rg1
+read5 0 chr1 1001 60 100M * 0 0 AGGACGCCCAACTATTCTTTCCAATCCTACATCTGTTTCTTGCGTCGTAGCGGGACCCTCCATTGTTACTTATTAGGTTCTCGTTATGTCTCATAATCTC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII RG:Z:rg1
+read6 0 chr1 1001 60 100M * 0 0 AGTGCTGGTGTGATAAGCAAACCACCCTACTGGCACGAAGTTCACAGAAGTGAGATTATGTCTCGTTTGGCAGTCTTGATGCTCGGGGGACACTTCTTTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII RG:Z:rg1
+read7 0 chr1 1026 60 100M * 0 0 AGCTCGGTGTGGTGGGCACGACCCTGGACGCGCGACGAAGCTAAGTTTGCAGTAATTAACCGACATCTTTGTGAACCGACCCACATTTGACGGTACGCTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII RG:Z:rg1
+read8 0 chr1 1026 60 100M * 0 0 CCGCAACGGTATGTGTTAATGGAACAGACTTGCTTATGTGGACGTTGTATAGGGATATTACGTTACGCGTTAACCGATACATACTGGTTTCTCTCCAGTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII RG:Z:rg1
+read9 0 chr1 1026 60 100M * 0 0 GAGGTCTTGGTTGCCTCTAGTTTCTACGATATACTCATGGTAGTGTAACGCATAATCGAAGAGGGTCCTCCCATCTCCTGTGATGCATGGTGTGCTTACT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII RG:Z:rg1
+read10 0 chr1 1026 60 100M * 0 0 GGGATGAATGCGCCGCAAGTAGCAGGTCCCGGCGTGGATACCTGATAGATGGTGACTAGCATGTACAAGTAACCTTGTCTATTGAGCTTCGAGGATGCAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII RG:Z:rg1
+read11 0 chr1 1026 60 100M * 0 0 ACAAGCCCACCCGCAGCCGCAACAGCGACGACTAATTGATCAGTAATTTATTAAGCACGGTGTTAACTTCTGTTTAGTGGGCTAAAATAGCAGATGTAGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII RG:Z:rg1
+read12 0 chr1 1026 60 100M * 0 0 GACCTCAGGAGCTAGACGGGGACCTACAACTTTGCGGGAACCAAGTTTTTGCAGTAGTGACTAACGCCGGGAATTCCTCGATATATAGTTTGATAGCTGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII RG:Z:rg1
+read13 0 chr1 1051 60 100M * 0 0 TACTTATGGCGCAACGGCCACGCCCACTTTGGCTATTGGAGAGTTAAGGAATTATCGTCATAGACACTTCGGGTTGAGAGATGGCGACGGTCAGTGCATG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII RG:Z:rg1
+read14 0 chr1 1051 60 100M * 0 0 AGGCCGTCCCCAGAAGCTCCCCTATGCTGTCCGTCGTTGTTCCCGATGAAGACGTCTACTGATATGCTAGCAGAGCCAGTCTTAAAGCCTAGCGAACTTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII RG:Z:rg1
+read15 0 chr1 1051 60 100M * 0 0 ATACCGTAGCTCAGAATTATGGAGAGCAGCAGGCTTCCATAGCACAGGTTGACGGAGGAGTTTTGCTTGGATATCGGAAGGGTTCTGTAGTGAATGCACT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII RG:Z:rg1
+read16 0 chr1 1051 60 100M * 0 0 ACACGGTACTGGTACGTGGCAACTTAGGTCGTCACATCTAGGAGGCCGCACCCTAGGTCAAGTTTTACGATTGCCCTAACGCCGCGGAGCGCGACCCGAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII RG:Z:rg1
+read17 0 chr1 1051 60 100M * 0 0 AAGCTATGGTCTGTAACTTTTCGCGGGTCGAGCTAGTCCAAGTTCCGGCCTTTGTAATTCCGAAGTTGAATCGGTGATACGGATTGACATGGGCCTAAAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII RG:Z:rg1
+read18 0 chr1 1051 60 100M * 0 0 GTTCCGGCTGGTGTAGGATGATGCATCTCCAACATGTCTCTTACCGTTGCTGGGTCCGGCGGCTGTGGGATTGCGAGAGTGTCCGGCACCACCAATGTAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII RG:Z:rg1
+read19 0 chr1 1076 60 100M * 0 0 ACTTTCGGGAACACTCATTCGAAGAGGTTCTGCAGCTGCAGGCCTTGATACCTGCAGTCTGGGAGGCAATGCTGAGGCCCTCTGTTCCATGAAACCCGTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII RG:Z:rg1
+read20 0 chr1 1076 60 100M * 0 0 CTATATCTTATGATGACAATGAAATAGTCCTGTTTTACGACTCCAAGTTTCCTGCGCAATACCAAATACATTCCACGCGGCGCCTGGACTTAGTGTTCGT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII RG:Z:rg1
+read21 0 chr1 1076 60 100M * 0 0 CTCCGCTATTCTCGCGATGACAGTAACCTCGGACCATCCTCGGTTGGGGTTATGCGGTACCAGTGCCGCTCTGGTTTCGCCTCAAAAATCCACACTGATT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII RG:Z:rg1
+read22 0 chr1 1076 60 100M * 0 0 AATAAGGATCAACCCGGGTAGTTCCGAAATTTTAACATTGAACCTGAAGACGACCTAGCCTGTCAGAATCAGTGAGTTCGTTCTAGCAAGCTCTGGAAAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII RG:Z:rg1
+read23 0 chr1 1076 60 100M * 0 0 TGGACACTTTAAAGAGTAGTTACCTCCGGGTCACTGTGTAGGCTCTACGATGTGTGTCGGCTGCTGGTCGTGTGACCATCTGATTCGCGCTTATTTTAGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII RG:Z:rg1
+read24 0 chr1 1076 60 100M * 0 0 ACGCATGTAAAGCCTGTTCGATAGTAACGGGTCTGTATTGAGAAAGACCCCGTTCTCCTTACTTTACCGAACGGCTAGTGTTAGGTCGACGACGACGCTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII RG:Z:rg1
+read25 0 chr1 1101 60 100M * 0 0 CTTCTCCTGCCGTAGATCCTTTTTTTCAACGAGCGCTTAAGGATCTACGATGGATACCGTCCCCAGGCGGGGACTAGCCCCGCTTCGTTTAATGGTTGAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII RG:Z:rg1
+read26 0 chr1 1101 60 100M * 0 0 TGATCTCTGGGGCTGAAATAACTTATCCGCGAGGAGCATGCTAAACTACCTAAGATCTACTAAAGGGCTCCAACTGCCTTCAACATGTGCCGACGAGCCT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII RG:Z:rg1
+read27 0 chr1 1101 60 100M * 0 0 GACTTACTAAGGCTTGCTAAAAGCAATGTTTACGAGACCGTAGTCACATATAGCAACACTGGCGCGAAGTGAGATTGATCGCGAACAAACATGTCCATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII RG:Z:rg1
+read28 0 chr1 1101 60 100M * 0 0 CTGGAGAACCATATGGGATAGCGGCTGTCCCATACGAGATGACCTTACGAACTGTAACTAATCCGGGTGGTGCACCACACTTGTAGCTGTGAACGACGCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII RG:Z:rg1
+read29 0 chr1 1101 60 100M * 0 0 CGTAGGCATTCATACAAACCCTGAGAAACTCAGAATACTTTATTCGCCGGTCACGTTTAAGTCTCCATGTTGGTGCAGCAGATGCCACCGACTGCCCGGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII RG:Z:rg1
+read30 0 chr1 1101 60 100M * 0 0 GCCTGCTAAACCATAGCCGCGAACCAGAGTAGGGCCTTGCGCCTGGCCATACGCATCGACGGCAGTAGCCAGGAAATTTCTTTGTATCCTAAGAGGAAGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII RG:Z:rg1
+read61 0 chr1 1151 60 50M200N50M * 0 0 TGCGAACCCCGCCCATAAATTACAAATAGAAGAAACCCGAACGGGCCAAACCGCAACTGCTACGTTCCTAGATACTGGAAGTATGTGTCTGTCATGCATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII RG:Z:rg1 XS:A:+
+read62 0 chr1 1151 60 50M200N50M * 0 0 TTAACTTACAGCGCTACTTGGTGTTTGCTAAGTTCCAAAATACTGCGAATTCGTTGGAATATTGTTTAACGCTTCGTTATTTCATGTTGGGAAACGGAGT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII RG:Z:rg1 XS:A:+
+read63 0 chr1 1151 60 50M200N50M * 0 0 ATGGTGACCCGAAGAGCAGATTTGATAGTTGATACGTGCGGTCTACGGAGTCAAGGATTCGAGGTGCTTGTCACTCTGTACGTCCCGTTGACTGGCGCTC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII RG:Z:rg1 XS:A:+
+read64 0 chr1 1151 60 50M200N50M * 0 0 ACCACGTTTTACCGCAGGCATAAAGGATGATCCAAGTACAGGTCTCCACCGTTGATGAGTTCGCGTGGAAACGTGGACTTATGGACGCCTGTAGATTTGT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII RG:Z:rg1 XS:A:+
+read65 0 chr1 1151 60 50M200N50M * 0 0 ACGAGTGTAACTCATCGGAACCCTGTTCGCGGCATGCTTCAACATCGCATTGCAGCAATTTACCCGGTTCTCCGCTCTCAGGCTCGTAATCGTCTTGAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII RG:Z:rg1 XS:A:+
+read66 0 chr1 1151 60 50M200N50M * 0 0 AGCTGAAGTGTGCACGCTGTCAGTCGAGACTGGTGGGGTCGTCTACCACCATGCTTATATGTTTACAGACGCCGCACTACTAGAGATGAGCAATTTGAGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII RG:Z:rg1 XS:A:+
+read67 0 chr1 1151 60 50M200N50M * 0 0 TGCCAGGAATATGCCTAACCTTGCAGTTGCGAGCTTTTGTATGCTTAAGTCCTAGTTATGCCGCTGAAAATTATGGGAAATCCTAATGGTTGGCCCAGAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII RG:Z:rg1 XS:A:+
+read68 0 chr1 1151 60 50M200N50M * 0 0 AATAACTTTTGGTGACCACAACACTCCTCAGTCTTAACCTTTATCCGTAGAATTTGATTTTCAATGAGTTATGTTACGCTGTCCGTCGTTGTCCGATCCC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII RG:Z:rg1 XS:A:+
+read69 0 chr1 1151 60 50M200N50M * 0 0 CTATTGCCAAGGGCCAAGTACACTGGGAGCAATTAAAAACACGCGTTACGGCACTTACTGGCAGGTGCCTCCTTTTGATCAAAGGTCTATACAGTTGGGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII RG:Z:rg1 XS:A:+
+read70 0 chr1 1151 60 50M200N50M * 0 0 GCTTCTGTCGAAGTCGCAGGCAAGCGTAAGGGAAATGATGCCGGGCTCAGCGTACTTAAATCTCTAGTTGTTTTTCCCTTCACTTACGATAAGGACAGGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII RG:Z:rg1 XS:A:+
+read71 0 chr1 1176 60 25M200N75M * 0 0 GGTACCTAGGCCTAAGAATTGTGTTCCTTTCGATTCTGATGACAGAACACTAACAGCCTAGTATAGTCTAGTGAAACGCCGACGTCAGCAAGTAGCTGGT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII RG:Z:rg1 XS:A:+
+read72 0 chr1 1176 60 25M200N75M * 0 0 AACCCTTAGAGTTATATCAGACCGTTACCGCCTTAATGCAATGGTGCGACAGATACGTCGGGTGCGGCTGACATAACTTTAAATAGTGTCAATGCTACAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII RG:Z:rg1 XS:A:+
+read73 0 chr1 1176 60 25M200N75M * 0 0 GCAGCCTGAGTCACTAGTCCCACACGCGCAGTATAGTTGATTGACAGTTGATCGAACTACCCGGAAATTAGGCATCGAGCATATAAAATGACATAGTAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII RG:Z:rg1 XS:A:+
+read74 0 chr1 1176 60 25M200N75M * 0 0 AGTTATCATTTTAGATGCAAAACCGGTTTCCCAACGTGGCCTGGGGACACATGCCCAGCTTGGGTGCATATCACCTCCTGTCTCAGAAGAACGTCGAACC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII RG:Z:rg1 XS:A:+
+read75 0 chr1 1176 60 25M200N75M * 0 0 GCCGCGCCCACGAACTAGCGTCGGCTAACCCCTGGTCACGCGCAGCTCATACTGTTCGGTTTGTACCCTCTCGTTCGGACAGTGCATGTTTTTGTGGTAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII RG:Z:rg1 XS:A:+
+read76 0 chr1 1176 60 25M200N75M * 0 0 TCGAGAGAGCAAAGACGCGGGGCCGAGGGTTATCTCCCTCTTGAGCTTCTTAGCCGATGGCTTTGGAACCGTTCTATCTAGTGACACATACCATGCCGAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII RG:Z:rg1 XS:A:+
+read77 0 chr1 1176 60 25M200N75M * 0 0 AGACGTTCACTTATCCCGTTCGCTGCACTATCGTTTAAGTGGTCTCCTTTCATACCGGACTTAGAAGTTCGCATAATTGTCTAAGACGTTTAACTCTGCC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII RG:Z:rg1 XS:A:+
+read78 0 chr1 1176 60 25M200N75M * 0 0 AACGATCAAGCTGCCACTAATGTAAATCCGCCAATAAGCACACCATAGGCCTTACCAGGCATGATCTCAGGAACTGTACGAGTCGCGTAGATTCACAAGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII RG:Z:rg1 XS:A:+
+read79 0 chr1 1176 60 25M200N75M * 0 0 TCAACGTGCCTCACTGCGGATGACGGCCACCTGCTAATACACCCACCCATTGCCCTCCGGTCGTAGTTCTTTTCTATTAGCCGTTGTGTTAGCTCCCAAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII RG:Z:rg1 XS:A:+
+read80 0 chr1 1176 60 25M200N75M * 0 0 TTTTGTTGATAATCCTGGTGATTCCTAGACGTCGCCAAATTACTCTGGTGTAAGCGCTGACTAAATTGTCCGCCCTCATCCCACCGTTACAGATAGAGAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII RG:Z:rg1 XS:A:+
+read31 0 chr1 1401 60 100M * 0 0 TCAAGTATCTCAAGCCTGGGCAATTCAGATAGTCAACCGATAGTTTGATCGTGCTAGTTGCGACAAGTCATTTCTGATACATCCCCCATATCCGGAATTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII RG:Z:rg1
+read32 0 chr1 1401 60 100M * 0 0 GTATATCCAAAGGTGTTTACGTCTATGCATGGAGGGGTACCGTGGTACTCTTGACAGTCACCCACATAGCGGTTAACGTTCTGGCGAGATACCCCCGTAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII RG:Z:rg1
+read33 0 chr1 1401 60 100M * 0 0 TCCACGGGTTGTGCTGTAAGGGATAGGGGGGCCCATGCATGGTTTACGCTGGCCGATCGCGACGCGTGGGGTATAATCATGTACCCGTTCGCATGCGAAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII RG:Z:rg1
+read34 0 chr1 1401 60 100M * 0 0 GCCCTACTTTTTTAACGAGCAACCGGCATGCAAGGTGTCGTGCCTACCCCACAGATGAAAAAATTTAGTCCAGTAGCTAAGAATCCGCGTGCATCTGCAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII RG:Z:rg1
+read35 0 chr1 1401 60 100M * 0 0 AATCAAAGCTGGTAACAGGGTAAAACCGGTGAGGCATTTGTTTCACACATTTCTGACTTATTAAGGACGATCTGTCAACTTCATGCGGACTTCATTTATT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII RG:Z:rg1
+read36 0 chr1 1401 60 100M * 0 0 GATAATTAAAGCTGGACTGTGTAACAGGGGAACTCTAGCCATCTCGATAATTCTAATTCCCATGTTCGTGGTCCTGGCCCGGCCGAGTTGTAAATCAACG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII RG:Z:rg1
+read37 0 chr1 1426 60 100M * 0 0 CGGCAGCAGTACTCGATTTGAAGCTCGCCGTCACCATATGGCCGAGTCACGAGTGAGCCACTTAGCCGGGGCTAAGTCCAGTATGGAGTTAGCGAACAAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII RG:Z:rg1
+read38 0 chr1 1426 60 100M * 0 0 CTACTACATGAAAACGACGTTTTTGATAAAAAGAGGAGTTTATCCCTGCGGACAAATAGCGCTCCCCGCACATAGAGACTGGCCAGACGTTGGCGGTCAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII RG:Z:rg1
+read39 0 chr1 1426 60 100M * 0 0 CCTGGCGTTTGGTACAGCCGAAAATCAGTCGTCGCTATGACCCTCCCTGACTCAGGCACGTTTAAGAGGCTTGAGTCTGGTTACTCCAGCCCCGACTGAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII RG:Z:rg1
+read40 0 chr1 1426 60 100M * 0 0 TTCCTACACCCACACGCTAGACTTTCCTCCGCGTACTTCAACTCACTAAATCATTGATCTTGATCGTCAGTGCAAAATCGTGACTGGTGGTCTTCGTGGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII RG:Z:rg1
+read41 0 chr1 1426 60 100M * 0 0 TCACTCACTGACTAACTTAAGCGAATTGACTTACGCACCAGCACAGTGTTCAAAGGGGCCTTAGCTAAGGAGGTTTCGTTATAGATCCGTGAGCGATGAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII RG:Z:rg1
+read42 0 chr1 1426 60 100M * 0 0 TGGCGCCTCCCGCCCCGCAAATAATGGTGTCGTCCATTAGTCTATGAACTAGGGCGCGTGGCTTCTGGTGTCCCAGCTTCCCTACTTCGTGGATACACGT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII RG:Z:rg1
+read43 0 chr1 1451 60 100M * 0 0 ATGGGGGGATAGCCGGGTTATGTCCGTTAACGCGGGGTGTGTTCCACCGACCTAAATAATAAGCATGCCGTCCCAAGGTTGTCCTTGGTCATGGTGCGAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII RG:Z:rg1
+read44 0 chr1 1451 60 100M * 0 0 CGGTATTGATGCAGCTTTCCTTCGATCGGGTCACCGATTGTCGACAACAGGCTACACATCGTGTGTAGACAGTATCCGTAACTTCACTACTTGGCAAGTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII RG:Z:rg1
+read45 0 chr1 1451 60 100M * 0 0 CGACACTGACGATCAATCGACCTAGAAGCACTCGGTCATGCGATTGTCCGGTGCACTGGGTATCAGCGATCTCGGTGAAAACCACATCAATTGAGCAACT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII RG:Z:rg1
+read46 0 chr1 1451 60 100M * 0 0 ATAGTGAGAAGACAACTCCCCTAGTTACCTGCTGGGGTTGCCTGGTTTAAGACGAGCCGAGCAATGCCGGCCGGATCAGTCTAGATAAGGTTACATAGAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII RG:Z:rg1
+read47 0 chr1 1451 60 100M * 0 0 CGCCATTACTGTCCGATATGATTCCTCTTCCCAGTGAATTGGCGGAGCGTCTACCGCAAACCGAGAGTTAGCCCGTCATAGCAGCGATAATGGAAGTCTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII RG:Z:rg1
+read48 0 chr1 1451 60 100M * 0 0 GTACCTAACGGTTCAGGGGCGAGTAGCCGTCATCTCCTGGTCCCCCGCTCCGAACGCAGTTGTGCCACCAGCCCAGATCTGCTTTCCCCATAGTCCCACT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII RG:Z:rg1
+read49 0 chr1 1476 60 100M * 0 0 TGTCTTATGTAATTACTATACGTTGGTCTGACTTAACCTTGTACTCTAGGCAAATGATCTTACGCCCCATGGTGCACCAGATTTATCCTTTTAACGCACC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII RG:Z:rg1
+read50 0 chr1 1476 60 100M * 0 0 AGACAGGAAATCCGCTGAAGGGTATAGTCAGGTCCAAATGTGGGCTTTCCGCAAATACTTAGGCACGGAGGGAAGGTACCGGTTACTCTGTTAGGACGGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII RG:Z:rg1
+read51 0 chr1 1476 60 100M * 0 0 CGAGTCTCAGGAGTATCGTGCGCAGACATATCCGTGGCACCATTAAGAAGTAAGAGCGCCGGGTAGCCGAAACGGGCGCCAGGTACATAATAATTCTGGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII RG:Z:rg1
+read52 0 chr1 1476 60 100M * 0 0 CATCATATGTTCCCGGTCGGTTAATAGTTCGGCATAGAGTTTCCCTTAGCTTGCCATATGATCGTAATGTAACCACCTGTTCCGGGTGAATCGAGAAGAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII RG:Z:rg1
+read53 0 chr1 1476 60 100M * 0 0 ACTTGTTTTCCTCCTGTCGCCAAACTTCACTTTCTTTTGCCTATCGTGAATGATACGTAACTAGAGATTTGTGGGCAGGATCAGAGTACAGGCGGGAACC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII RG:Z:rg1
+read54 0 chr1 1476 60 100M * 0 0 TGCGCTCAGACCTTTCTCCGAGAACTTTGTCTTTGCTAGTTGAAGTGGGGAGTTCCGCGAAAATAATGCGGCAAAACAAACTCACGGTATGTGGCAGATT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII RG:Z:rg1
+read55 0 chr1 1501 60 100M * 0 0 GAGGCTATCTCTACTCATGAAAAGTATCAATGCGTATTTTACATTAGGGTAAGGATGCCATCGTAGTATCCACACTTAGTTAAGAGATACTCCAACTATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII RG:Z:rg1
+read56 0 chr1 1501 60 100M * 0 0 CCACAGATCAAATCACTGTGACGCACGAAGCTCGCTCACATCATAAACAGTTCCCGTTCCACTAGGTACCAAGCTCGACACTTCCAAGGCTGGTAAACCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII RG:Z:rg1
+read57 0 chr1 1501 60 100M * 0 0 TAACTGTCGCAGCACTCTCATTATCCTCTGCTCGGCGCAAGCATTTCGCGCCCATTCTTGATCCGTCCATAATATTTATTCAATCCGGCAATGCTATTCT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII RG:Z:rg1
+read58 0 chr1 1501 60 100M * 0 0 CGTAATGAGTGCAGAGAATGTAGGCACCGCATCCGGGTGAAGGTTATGTGACTAATCGAACGACTCCAGTCTGTTAGCAACGTGGTTTGCGCGCTGGACG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII RG:Z:rg1
+read59 0 chr1 1501 60 100M * 0 0 GTCCGCCCCCAAGCTGGCCAGGCGTCGAATTCTGCAGGTGCTGATACAGATCTGAGACCGCAATATCTGAGTCTGTGAGGGGTACTTTGCTTCACCGTGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII RG:Z:rg1
+read60 0 chr1 1501 60 100M * 0 0 TAATGTCTCCCTGTAGGTTCAACGGTAGTCTCAAGTAGTTGTAGAGCACGTCGCAGGTGAGGACCACGGGGGAGCACGGTTGCACCCCATTAACATGGGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII RG:Z:rg1
=====================================
debian/tests/data/ref.gtf
=====================================
@@ -0,0 +1,3 @@
+chr1 test transcript 1001 1600 . + . gene_id "g1"; transcript_id "t1";
+chr1 test exon 1001 1200 . + . gene_id "g1"; transcript_id "t1";
+chr1 test exon 1401 1600 . + . gene_id "g1"; transcript_id "t1";
=====================================
debian/tests/run-unit-test
=====================================
@@ -0,0 +1,75 @@
+#!/bin/bash
+set -e
+
+pkg=cufflinks
+
+export LC_ALL=C.UTF-8
+if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
+ AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
+ # shellcheck disable=SC2064
+ trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
+fi
+
+cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}"
+
+cd "${AUTOPKGTEST_TMP}"
+
+## start with simnple smoke test
+
+# Every binary shipped by the cufflinks package must be installed
+for bin in cufflinks cuffcompare cuffdiff cuffmerge cuffnorm cuffquant \
+ gtf_to_sam compress_gtf; do
+ command -v "$bin" >/dev/null 2>&1 || {
+ echo "ERROR: $bin not found in PATH"
+ exit 1
+ }
+done
+
+# Running cufflinks without arguments prints a version banner to stderr
+# (and exits non-zero). Verify the binary starts and links correctly.
+banner=$(cufflinks 2>&1 >/dev/null || true)
+printf '%s\n' "$banner" | grep -q "cufflinks v" || {
+ echo "ERROR: no version banner from cufflinks"
+ echo "--- output was ---"
+ printf '%s\n' "$banner"
+ exit 1
+}
+
+# Run functional test
+
+# 1) cufflinks: assemble transcripts from the alignments (ab initio)
+cufflinks --no-update-check -o "out" reads.sam
+
+# The GTF contains FPKM/confidence values as floating point numbers, which
+# may differ slightly between platforms. Strip them and compare the
+# (deterministic) transcript structure with the expected result.
+strip_fpkms() {
+ sed -E 's/ (FPKM|frac|conf_lo|conf_hi|cov) "[^"]*";//g; s/[[:space:]]+$//'
+}
+strip_fpkms < "out/transcripts.gtf" > "result.gtf"
+strip_fpkms < expected/transcripts.gtf > "expected.gtf"
+if ! diff -u "expected.gtf" "result.gtf"; then
+ echo "ERROR: assembled transcripts differ from the expected result" >&2
+ exit 1
+fi
+echo "cufflinks assembled the expected transcript"
+
+# 2) cuffcompare: compare the assembly with the reference annotation
+cuffcompare -o "cmp" -r ref.gtf "out/transcripts.gtf"
+# cuffcompare writes the .tmap file next to the query file
+tmap="out/cmp.transcripts.gtf.tmap"
+if ! awk -F '\t' 'NR>1 && $3 == "=" { matched=1 } END { exit !matched }' "$tmap"; then
+ echo "ERROR: cuffcompare did not find an exact match in $tmap" >&2
+ exit 1
+fi
+echo "cuffcompare classified the assembly as an exact match"
+
+# 3) cuffquant: quantitate expression against the reference annotation
+cuffquant --no-update-check -o "quant" -u ref.gtf reads.sam
+if [ ! -f "quant/abundances.cxb" ]; then
+ echo "ERROR: cuffquant did not produce abundances.cxb" >&2
+ exit 1
+fi
+echo "cuffquant produced abundances.cxb"
+
+echo "functional test passed"
View it on GitLab: https://salsa.debian.org/med-team/cufflinks/-/compare/379f4a1a99c85eafd5373a7bc3caa03937a24d31...c3d1f14a24d4a722bab693a6eb2a01fd73eee166
--
View it on GitLab: https://salsa.debian.org/med-team/cufflinks/-/compare/379f4a1a99c85eafd5373a7bc3caa03937a24d31...c3d1f14a24d4a722bab693a6eb2a01fd73eee166
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