Rediff patches

diff --git a/debian/patches/clean_less b/debian/patches/clean_less
index 393b90a152be2228ae9b191887ed5e28497b5bee..b1ad6c7b0edd847f054c078a460c530ddc9e1056 100644 (file)
--- 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 f6eec3ba057c9ea876c974d50431a8887d2ed284..520a149441455f217d4ccae9ae88ef910166787a 100644 (file)
--- 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 e2dfeb8bf75e750563fbbb8b2c1499d1a2be1882..7148f8e1811575546c606b2eb8a367e79707bb73 100644 (file)
--- 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), [])