Add test for fixed issue #356

Added some minor comments.
biod · Oct 3, 2018 · 7619353 · 7619353
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diff --git a/BioD b/BioD
diff --git a/INSTALL.md b/INSTALL.md
@@ -12,13 +12,17 @@
 
 ## Install Sambamba from source
 
-To build Sambamba from source you can opt to install the build tools with GNU Guix
+After checking out the source from github with git submodules is is
+possibleto install the build tools with GNU Guix
 
     guix package -i gcc gdb bash ld-wrapper ldc which python2 git
 
-Even better you can create a container in the source tree and run our development setup
+Even better, with Guix, you can create a light-weight container in the source tree
+and run our development setup
 
-    guix environment -C guix --ad-hoc gcc gdb bash ld-wrapper ldc which python2 git
+    guix environment -C guix --ad-hoc gcc gdb bash ld-wrapper ldc which python git
     make clean
     make -j 4
     make check
+
+this way all dependencies are isolated.
diff --git a/test/benchmark/stats.org b/test/benchmark/stats.org
@@ -217,3 +217,41 @@ real    7m22.125s
 user    89m6.188s
 sys     2m51.228s
 #+END_SRC
+
+** Markdup
+*** 8x Intel(R) Core(TM) i7-6770HQ CPU @ 2.60GHz, 16Gb, SSD (hyperthreaded)
+
+**** sambamba 0.6.7-pre1
+
+/usr/bin/time --verbose sambamba markdup /gnu/data/in_raw.sorted.bam /gnu/data/in_raw.sorted.bam t2.bam
+finding positions of the duplicate reads in the file...
+  sorted 11286293 end pairs
+     and 156042 single ends (among them 0 unmatched pairs)
+  collecting indices of duplicate reads...   done in 1521 ms
+  found 6603388 duplicates
+collected list of positions in 0 min 16 sec
+marking duplicates...
+total time elapsed: 1 min 4 sec
+        Command being timed: "sambamba markdup /gnu/data/in_raw.sorted.bam /gnu/data/in_raw.sorted.bam t2.bam"
+        User time (seconds): 423.78
+        System time (seconds): 4.47
+        Percent of CPU this job got: 666%
+        Elapsed (wall clock) time (h:mm:ss or m:ss): 1:04.24
+        Average shared text size (kbytes): 0
+        Average unshared data size (kbytes): 0
+        Average stack size (kbytes): 0
+        Average total size (kbytes): 0
+        Maximum resident set size (kbytes): 1542764
+        Average resident set size (kbytes): 0
+        Major (requiring I/O) page faults: 0
+        Minor (reclaiming a frame) page faults: 1839470
+        Voluntary context switches: 368082
+        Involuntary context switches: 8537
+        Swaps: 0
+        File system inputs: 0
+        File system outputs: 2643840
+        Socket messages sent: 0
+        Socket messages received: 0
+        Signals delivered: 0
+        Page size (bytes): 4096
+        Exit status: 0
diff --git a/test/issue_356.sam b/test/issue_356.sam
@@ -0,0 +1,23 @@
+@HD	VN:1.3	SO:coordinate
+@SQ	SN:chr1	LN:1575
+@SQ	SN:chr2	LN:1584
+@RG	ID:foo	LB:foo	PL:ILLUMINA	SM:foo	PU:foo	CN:foo	DT:2017-12-10T00:00:00-0500	PG:foo	PM:HiSeq2500_HighOutput
+EAS56_57:6:190:289:82	69	chr1	100	0	*	=	100	0	CTCAAGGTTGTTGCAAGGGGGTCTATGTGAACAAA	<<<7<<<;<<<<<<<<8;;<7;4<;<;;;;;94<;	MF:i:192
+EAS56_57:6:190:289:82	137	chr1	100	73	35M	=	100	0	AGGGGTGCAGAGCCGAGTCACGGGGTTGCCAGCAC	<<<<<<;<<<<<<<<<<;<<;<<<<;8<6;9;;2;	MF:i:64	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_64:3:190:727:308	99	chr1	103	99	35M	=	263	195	GGTGCAGAGCCGAGTCACGGGGTTGCCAGCACAGG	<<<<<<<<<<<<<<<<<<<<<<<<<<<::<<<844	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS112_34:7:141:80:875	99	chr1	110	99	35M	=	265	190	AGCCGAGTCACGGGGTTGCCAGCACAGGGGCTTAA	<<<<<<<<<<<<<<<<<<<<<<:<<8;<<8+7;-7	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS219_FC30151:3:40:1128:1940	163	chr1	112	99	35M	=	291	214	CCGAGTCACGGGGTTGCCAGCACAGGGGCTTAACC	<<<<<<<<<<<<<<<<<<<;<<5;;<<<9;;;;7:	MF:i:18	Aq:i:70	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS51_62:5:290:319:736	69	chr1	113	0	*	=	113	0	GTTCTCAAGGTTGTTGCAAGGGGGTCTATGTGAAC	<<<<<<:7:<.<<<<7<<.<.<<.9*<4<:<4%74	MF:i:192
+EAS51_62:5:290:319:736	137	chr1	113	73	35M	=	113	0	CGAGTCACGGGGTTGCCAGCACAGGGGCTTAACCT	==;=======7====6=;==:;;====66=::27:	MF:i:64	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_597:2:132:493:921	69	chr1	119	0	*	=	119	0	GTTCTCAAGGTTGTTGCAAGGGGGTCTATGTGAAC	<<<<<<<<<<<<<<<<<<<;<<<<77;0<;;6777	MF:i:192
+B7_597:2:132:493:921	137	chr1	119	75	35M	=	119	0	ACGGGGTTGCCAGCACAGGGGCTTAACCTCTGGTG	<<<<<<<<<<<<<<<<;<<<<<<<<;<<<<;;88:	MF:i:64	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_30:7:283:799:560	163	chr1	121	66	35M	=	283	197	GGGGTTGCCAGCACAGGGGCTTAACCTCTGGTGAC	<<<<+<<<<8<<<+<<<<<;<<:07;8;7402447	MF:i:18	Aq:i:66	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS192_3:1:225:195:543	99	chr1	123	99	35M	=	299	211	GGTTGCCAGCACAGGGGCTTAACCTCTGGTGACTG	<<<<<<<<<<<<<<<<<<<<<<<9<<;::388998	MF:i:18	Aq:i:72	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+B7_589:6:114:714:317	99	chr1	126	99	35M	=	311	220	TGCCAGCACAGGGGCTTAACCTCTGGTGACTGCCA	<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<<5;<;	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_39:1:70:147:84	163	chr1	128	73	35M	=	285	192	CCAGCACAGGGGCTTAACCTCTGGTGACTGCCAGA	<<<<<<<<<<<<<<<<<<<<;<<<<<<<<<;(5<<	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS188_7:2:187:227:818	163	chr1	129	99	35M	=	290	196	CAGCACAGGGGCTTAACCTCTGGTGACTGCCAGAG	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<3<;<<	MF:i:18	Aq:i:76	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS1_97:4:77:29:126	99	chr1	131	99	35M	=	315	219	GCACAGGGGCTTAACCTCTGGTGACTGCCAGAGCT	<<<<<<<<<<3<<<<<<<;;;7<;<<449<-:977	MF:i:18	Aq:i:69	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_30:4:327:795:103	99	chr1	133	99	35M	=	302	204	ACAGGGGCTTAACCTCTGGTGACTGCCAGAGCTGC	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<;	MF:i:18	Aq:i:75	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS114_30:3:139:117:262	69	chr1	135	0	*	=	135	0	GTTCTCAAGGTTGTTGCAAGGGGGTCTATGTGAAC	<<<7<<<<<<<<<<<<<<<<<<<;<;<<<<<37;3	MF:i:192
+EAS114_30:3:139:117:262	137	chr1	135	76	35M	=	135	0	AGGGGCTTAACCTCTGGTGACTGCCAGAGCTGCTG	<<<<;<<<<<<<<<<<<<:<<<<<:<<8<<<<:<:	MF:i:64	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
+EAS219_FC30151:5:29:817:854	73	chr1	135	77	35M	=	135	0	AGGGGCTTAACCTCTGGTGACTGCCAGAGCTGCTG	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	MF:i:64	Aq:i:0	NM:i:0	UQ:i:0	H0:i:1	H1:i:0
diff --git a/test/test_suite.sh b/test/test_suite.sh
@@ -183,6 +183,13 @@ testIssue331() {
     assertEquals 0 $?
 }
 
+testIssue356(){
+    # check for missing PM tag in @RG
+    $sambamba view -S test/issue_356.sam -f bam -o $outdir/issue_356.bam
+    $sambamba view $outdir/issue_356.bam -H|grep -q "PM:HiSeq2500_HighOutput"
+    assertEquals 0 $?
+}
+
 shunit2=`which shunit2`
 if [ -x "$shunit2" ]; then
     . $shunit2
+17 −0		RELEASE-NOTES.md
+1 −0		VERSION
+2 −1		bio/sam/header.d