Add 4 CRAM compliance tests from htslib

src/test/java/htsjdk/samtools/CRAMComplianceTest.java

@@ -41,14 +41,19 @@ public Object[][] getPartialVerificationData() {
                 {"c1#noseq"},       // unsigned attributes: https://github.com/samtools/htsjdk/issues/499
                 {"c1#unknown"},     // unsigned attributes: https://github.com/samtools/htsjdk/issues/499
                 {"ce#5b"},          // reads with no read bases: https://github.com/samtools/htsjdk/issues/509
+                {"ce#1000"},        // SAMRecord mismatch: https://github.com/samtools/htsjdk/issues/1189
                 {"ce#tag_depadded"},// reads with no read bases: https://github.com/samtools/htsjdk/issues/509
                 {"ce#tag_padded"},  // reads with no read bases: https://github.com/samtools/htsjdk/issues/509
                 {"ce#unmap"},       // unmapped reads with non-zero MAPQ value that is not restored
                                     // https://github.com/samtools/htsjdk/issues/714
-                {"xx#triplet"},     // the version 2.1 variant of this file has a bad insertSize, which is
-                                    // probably residual detritus from https://github.com/samtools/htsjdk/issues/364
                 {"xx#minimal"},     // cigar string "5H0M5H" is restored as "10H"
                                     // https://github.com/samtools/htsjdk/issues/713
+                {"xx#repeated"},    // SAMRecord mismatch: https://github.com/samtools/htsjdk/issues/1189
+                {"xx#tlen"},        // SAMRecord mismatch: https://github.com/samtools/htsjdk/issues/1189
+                {"xx#tlen2"},       // SAMRecord mismatch: https://github.com/samtools/htsjdk/issues/1189
+                {"xx#triplet"},     // the version 2.1 variant of this file has a bad insertSize, which is
+                                    // probably residual detritus from https://github.com/samtools/htsjdk/issues/364
+                //{"md#1"},           // fails with "offensive record" errors: https://github.com/samtools/htsjdk/issues/1187
         };
     }
 
@@ -67,6 +72,7 @@ public Object[][] getFullVerificationData() {
                 {"c1#pad1"},
                 {"c1#pad2"},
                 {"c1#pad3"},
+                {"c2#pad"},
                 {"ce#1"},
                 {"ce#2"},
                 {"ce#5"},

src/test/resources/htsjdk/samtools/cram/c2#pad.sam

@@ -0,0 +1,26 @@
+@SQ	SN:c2	LN:9
+@CO
+@CO	mpileup example from https://github.com/samtools/htslib/issues/59
+@CO	with additional Pad cigar operations
+@CO
+@CO	 c2    CC***AA**T**AA***CC
+@CO
+@CO	+s1    CT***AA**T**AA***TC
+@CO	+s1b   CT*******T*******TC
+@CO	+s2    CT*****G***G*****TC
+@CO	+s2p   CT*****G***G*****TC
+@CO	+s3    CT*****GG*GG*****TC
+@CO	+s3b   CT****CGGCGGC****TC
+@CO	+s4    CT***AAG***GAA***TC
+@CO	+s4p   CT***AAG***GAA***TC
+@CO	+s5    CTGGG*********GGGTC
+@CO
+s1	0	c2	1	0	9M	*	0	0	CTAATAATC	XXXXXXXXX
+s1b	0	c2	1	0	2M2D1M2D2M	*	0	0	CTTTC	*
+s2	0	c2	1	0	2M2D1I1D1I2D2M	*	0	0	CTGGTC	*
+s2p	0	c2	1	0	2M2D1I1P1D1P1I2D2M	*	0	0	CTGGTC	*
+s3	0	c2	1	0	2M2D2I1D2I2D2M	*	0	0	CTGGGGTC	*
+s3b	0	c2	1	0	2M1D1M2I1M2I1M1D2M	*	0	0	CTCGGCGGCTC	*
+s4	0	c2	1	0	4M1I1D1I4M	*	0	0	CTAAGGAATC	*
+s4p	0	c2	1	0	4M1I1P1D1P1I4M	*	0	0	CTAAGGAATC	*
+s5	0	c2	1	0	2M3I5D3I2M	*	0	0	CTGGGGGGTC	*

src/test/resources/htsjdk/samtools/cram/c2.fa

@@ -0,0 +1,2 @@
+>c2
+CCAATAACC

src/test/resources/htsjdk/samtools/cram/c2.fa.fai

@@ -0,0 +1 @@
+c2	9	4	9	10

src/test/resources/htsjdk/samtools/cram/md#1.sam

@@ -0,0 +1,12 @@
+@HD	VN:1.0	SO:coordinate
+@SQ	SN:a	LN:40
+x	0	a	1	255	40M	*	0	0	AAAAAAAAAACCCCCCCCYNNRGGGGGGGGTTTTTTTTTT	*	NM:i:2	MD:Z:19N0N19
+x*	0	a	1	255	40M	*	0	0	CAAAAAAAANNCCCCCCCYNNRGGGGGGGGTTTTTTTTTC	*	NM:i:6	MD:Z:0A8A0C8N0N18T0
+xIP	0	a	1	255	1I10M1I10M2I10M2P3I2P10M1I	*	0	0	NAAAAAAAAAAGCCCCCCCCCCAAGGGGGGGGGGCCCTTTTTTTTTTN	*	NM:i:12	MD:Z:18Y0N0N0R18
+xIP*	0	a	1	255	1I10M1I10M2I10M2P3I2P10M1I	*	0	0	NCAAAAAAAAAGCCCCCCCCCCAAGGGGGGGGGACCCATTTTTTTTCN	*	NM:i:16	MD:Z:0A17Y0N0N0R7G0T8T0
+xD	0	a	1	255	9M1D8M2D7M3D6M	*	0	0	AAAAAAAAACCCCCCYNNRGGGGGTTTTTT	*	NM:i:9	MD:Z:9^A6C0C0^YN0N6^GGG6
+xD*	0	a	1	255	9M1D8M2D7M3D6M	*	0	0	CAAAAAAANNCCCCCCTTGGGGGGTTTTTA	*	NM:i:13	MD:Z:0A7A0^A0C6C0^YN0N0R5^GGG5T0
+xN	0	a	1	255	10M20N10M	*	0	0	AAAAAAAAAATTTTTTTTTT	*	NM:i:0	MD:Z:20
+xN*	0	a	1	255	10M20N10M	*	0	0	CAAAAAAACCAATTTTTTTA	*	NM:i:6	MD:Z:0A7A0A0T0T7T0
+xS	0	a	11	255	5H10S20M10S5H	*	0	0	AAAAAAAAAACCCCCCCCYNNRGGGGGGGGTTTTTTTTTT	*	NM:i:2	MD:Z:9N0N9
+xS*	0	a	11	255	5H10S20M10S5H	*	0	0	CAAAATAAAACCCCCCCCYNNRGGGGGGGGTTTTATTTTC	*	NM:i:2	MD:Z:9N0N9

src/test/resources/htsjdk/samtools/cram/md.fa

@@ -0,0 +1,3 @@
+>a
+AAAAAAAAAACCCCCCCCYNNRGGGGGGGGTTTTTTTTTT
+

src/test/resources/htsjdk/samtools/cram/md.fa.fai

@@ -0,0 +1 @@
+a	40	3	40	41

src/test/resources/htsjdk/samtools/cram/xx#repeated.sam

@@ -0,0 +1,7 @@
+@SQ	SN:xx	LN:20
+S	67	xx	1	1	10M	=	11	20	AAAAAAAAAA	**********
+S	131	xx	11	1	10M	=	1	-20	TTTTTTTTTT	**********
+S	67	xx	1	1	10M	=	11	20	AAAAAAAAAA	**********
+S	131	xx	11	1	10M	=	1	-20	TTTTTTTTTT	**********
+S	67	xx	1	1	10M	=	11	20	AAAAAAAAAA	**********
+S	131	xx	11	1	10M	=	1	-20	TTTTTTTTTT	**********

src/test/resources/htsjdk/samtools/cram/xx#tlen.sam

@@ -0,0 +1,34 @@
+@CO	xx has been encoded using the SAM spec; leftmost to rightmost
+@CO	yy has been encoded using bwa/picard methods; 5' to 3'
+@CO
+@CO	00000000011111111112
+@CO	12345678901234567890
+@CO	AAAAAAAAAATTTTTTTTTT
+@CO	1>>>>          <<<<2   x1
+@CO	
+@CO	      1>>>>    	       x2
+@CO	         <<<<2
+@CO	
+@CO	         1>>>>	       x3 (7..15 vs 10..11)
+@CO	      <<<<2
+@CO	
+@CO	<<<<2          1>>>>   x4 (1..20 vs 16..5)
+@CO
+@SQ	SN:xx	LN:20
+@SQ	SN:yy	LN:20
+x1	99	xx	1	1	5M	=	16	20	AAAAA	*****
+x1	147	xx	16	1	5M	=	1	-20	TTTTT	*****
+x2	99	xx	7	1	5M	=	10	8	AAAAT	*****
+x2	147	xx	10	1	5M	=	7	-8	ATTTT	*****
+x3	147	xx	7	1	5M	=	10	8	AAAAT	*****
+x3	99	xx	10	1	5M	=	7	-8	ATTTT	*****
+x4	147	xx	1	1	5M	=	16	20	AAAAA	*****
+x4	99	xx	16	1	5M	=	1	-20	TTTTT	*****
+y1	99	yy	1	1	5M	=	16	20	AAAAA	*****
+y1	147	yy	16	1	5M	=	1	-20	TTTTT	*****
+y2	99	yy	7	1	5M	=	10	8	AAAAT	*****
+y2	147	yy	10	1	5M	=	7	-8	ATTTT	*****
+y3	147	yy	7	1	5M	=	10	-2	AAAAT	*****
+y3	99	yy	10	1	5M	=	7	2	ATTTT	*****
+y4	147	yy	1	1	5M	=	16	10	AAAAA	*****
+y4	99	yy	16	1	5M	=	1	-10	TTTTT	*****

src/test/resources/htsjdk/samtools/cram/xx#tlen2.sam

@@ -0,0 +1,36 @@
+@CO	As per xx#tlen.sam but every read is unsorted with partner
+@CO	
+@CO	xx has been encoded using the SAM spec; leftmost to rightmost
+@CO	yy has been encoded using bwa/picard methods; 5' to 3'
+@CO
+@CO	00000000011111111112
+@CO	12345678901234567890
+@CO	AAAAAAAAAATTTTTTTTTT
+@CO	1>>>>          <<<<2   x1
+@CO	
+@CO	      1>>>>    	       x2
+@CO	         <<<<2
+@CO	
+@CO	         1>>>>	       x3 (7..15 vs 10..11)
+@CO	      <<<<2
+@CO	
+@CO	<<<<2          1>>>>   x4 (1..20 vs 16..5)
+@CO
+@SQ	SN:xx	LN:20
+@SQ	SN:yy	LN:20
+x1	147	xx	16	1	5M	=	1	-20	TTTTT	*****
+x1	99	xx	1	1	5M	=	16	20	AAAAA	*****
+x2	147	xx	10	1	5M	=	7	-8	ATTTT	*****
+x2	99	xx	7	1	5M	=	10	8	AAAAT	*****
+x3	99	xx	10	1	5M	=	7	-8	ATTTT	*****
+x3	147	xx	7	1	5M	=	10	8	AAAAT	*****
+x4	99	xx	16	1	5M	=	1	-20	TTTTT	*****
+x4	147	xx	1	1	5M	=	16	20	AAAAA	*****
+y1	147	yy	16	1	5M	=	1	-20	TTTTT	*****
+y1	99	yy	1	1	5M	=	16	20	AAAAA	*****
+y2	147	yy	10	1	5M	=	7	-8	ATTTT	*****
+y2	99	yy	7	1	5M	=	10	8	AAAAT	*****
+y3	99	yy	10	1	5M	=	7	2	ATTTT	*****
+y3	147	yy	7	1	5M	=	10	-2	AAAAT	*****
+y4	99	yy	16	1	5M	=	1	-10	TTTTT	*****
+y4	147	yy	1	1	5M	=	16	10	AAAAA	*****