[med-svn] samtools 12/26: On behalf of Peter Chines, test that filter mask replaces (not just adds to) default mask

[Charles Plessy]

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plessy pushed a commit to branch debian/unstable
in repository samtools.

commit c1e1fa1ac5d8d2333d21a9be93f1f1103ab6174c
Author: Petr Danecek <pd3 at sanger.ac.uk>
Date:   Thu Nov 28 12:39:37 2013 +0000

    On behalf of Peter Chines, test that filter mask replaces (not just adds to) default mask
---
 test/dat/mpileup.out.3 | 11 +++++++++++
 test/test.pl           |  2 ++
 2 files changed, 13 insertions(+)

diff --git a/test/dat/mpileup.out.3 b/test/dat/mpileup.out.3
new file mode 100644
index 0000000..2884f63
--- /dev/null
+++ b/test/dat/mpileup.out.3
@@ -0,0 +1,11 @@
+17	1050	A	6	.$.....	DGIKIF
+17	1051	A	5	.....	HFJHD
+17	1052	A	5	.....	BIKJB
+17	1053	A	5	.....	GFJGB
+17	1054	C	5	.....	I at JHB
+17	1055	C	7	.....^].^].	HKNK9 at A
+17	1056	C	7	.......	HKMK7A@
+17	1057	T	7	.......	JDKJDGF
+17	1058	G	7	.......	HHLKHIH
+17	1059	T	7	.......	EHII?EE
+17	1060	C	7	.......	JJJI=GH
diff --git a/test/test.pl b/test/test.pl
index ef12262..003adcf 100755
--- a/test/test.pl
+++ b/test/test.pl
@@ -329,5 +329,7 @@ sub test_mpileup
     # print "$$opts{bin}samtools mpileup -gb $$opts{tmp}/mpileup.list -f $$opts{tmp}/$args{ref}.gz > $$opts{tmp}/mpileup.bcf\n";
     test_cmd($opts,out=>'dat/mpileup.out.1',cmd=>"$$opts{bin}/samtools mpileup -b $$opts{tmp}/mpileup.list -f $$opts{tmp}/mpileup.ref.fa.gz -r17:100-150 2>/dev/null");
     test_cmd($opts,out=>'dat/mpileup.out.2',cmd=>"$$opts{bin}/samtools mpileup -uvDV -b $$opts{tmp}/mpileup.list -f $$opts{tmp}/mpileup.ref.fa.gz -r17:100-600 2>/dev/null| grep -v ^##samtools | grep -v ^##ref");
+    # test that filter mask replaces (not just adds to) default mask
+    test_cmd($opts,out=>'dat/mpileup.out.3',cmd=>"$$opts{bin}/samtools mpileup -B --ff 0x14 -f $$opts{tmp}/mpileup.ref.fa.gz -r17:1050-1060 $$opts{tmp}/mpileup.1.bam 2>/dev/null | grep -v mpileup");
 }
 

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