From 8e7e7a7c0366b556ea5181c5c594903d08fbe903 Mon Sep 17 00:00:00 2001 From: Nilesh Patra Date: Fri, 15 Oct 2021 01:15:15 +0530 Subject: [PATCH] Rediff patches --- debian/patches/clean_less | 10 +++++----- debian/patches/series | 2 +- debian/patches/skip_test_remote.patch | 8 ++++---- 3 files changed, 10 insertions(+), 10 deletions(-) diff --git a/debian/patches/clean_less b/debian/patches/clean_less index 393b90a..b1ad6c7 100644 --- a/debian/patches/clean_less +++ b/debian/patches/clean_less @@ -4,12 +4,12 @@ Description: Do not clean *.bam files --- a/tests/pysam_data/Makefile +++ b/tests/pysam_data/Makefile -@@ -89,7 +89,7 @@ explicit_index.cram: ex1.cram +@@ -100,7 +100,7 @@ cp ex1.cram $@ clean: -- rm -fr *.bam *.bai *.fai *.pileup* *.cram \ -+ rm -fr *.bai *.fai *.pileup* *.cram \ - *~ calDepth *.dSYM pysam_*.sam \ - ex2.sam ex2.sam.gz ex1.sam \ +- rm -fr [a-z]*.bam *.bai *.csi *.fai *.gzi *.pileup* [a-z]*.cram *.crai \ ++ rm -fr *.bai *.csi *.fai *.gzi *.pileup* [a-z]*.cram *.crai \ + all.stamp *~ calDepth *.dSYM pysam_*.sam \ + ex2.sam ex2.sam.gz ex1.sam ex1.fa.gz \ with_md.sam.gz \ diff --git a/debian/patches/series b/debian/patches/series index f6eec3b..520a149 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -1,5 +1,5 @@ skip_test_remote.patch -spelling +#spelling #hts1.10 #samtools_v1.10_full # samtools_v1.10 diff --git a/debian/patches/skip_test_remote.patch b/debian/patches/skip_test_remote.patch index e2dfeb8..7148f8e 100644 --- a/debian/patches/skip_test_remote.patch +++ b/debian/patches/skip_test_remote.patch @@ -4,7 +4,7 @@ Description: Skip tests trying to access remote site --- a/tests/AlignmentFile_test.py +++ b/tests/AlignmentFile_test.py -@@ -499,17 +499,6 @@ class TestIO(unittest.TestCase): +@@ -503,17 +503,6 @@ "tmp_ex2.sam", "rb", "wh") @@ -22,7 +22,7 @@ Description: Skip tests trying to access remote site def testCRAM2BAM(self): # ignore header (md5 sum) self.checkEcho("ex2.cram", -@@ -1616,6 +1605,7 @@ class TestDoubleFetchCRAMWithReference(T +@@ -1638,6 +1627,7 @@ reference_filename = os.path.join(BAM_DATADIR, 'ex1.fa') @@ -32,7 +32,7 @@ Description: Skip tests trying to access remote site '''test remote access. --- a/tests/tabix_test.py +++ b/tests/tabix_test.py -@@ -1014,6 +1014,7 @@ for vcf_file in vcf_files: +@@ -1017,6 +1017,7 @@ globals()[n] = type(n, (TestVCFFromVariantFile,), dict(filename=vcf_file,)) @@ -40,7 +40,7 @@ Description: Skip tests trying to access remote site class TestRemoteFileHTTP(unittest.TestCase): url = "http://genserv.anat.ox.ac.uk/downloads/pysam/test/example.gtf.gz" -@@ -1053,25 +1054,28 @@ class TestRemoteFileHTTP(unittest.TestCa +@@ -1056,25 +1057,28 @@ self.assertEqual(list(self.local_file.header), []) -- 2.30.2