Fixed a bug in MergeBamAlignment (#1581)

- Fixed yet another bug in MergeBamAlignment: when there's a deletion in the base just beyond the 5' end of the mate, the code for clipping overhanging reads got confused and didn't clip anything. This commit fixes that.

- Added tests that specifically cover this case.

src/main/java/picard/sam/AbstractAlignmentMerger.java

@@ -832,9 +832,7 @@ private static void clip3primeEndsTo5primeEnds(final SAMRecord pos, final SAMRec
     }
 
     static int getReadPositionAtReferencePositionIgnoreSoftClips(final SAMRecord rec, final int pos) {
-        final int readPosition;
         final Cigar oldCigar = rec.getCigar();
-        final int oldStart = rec.getAlignmentStart();
         final Cigar newCigar = new Cigar();
         final List<CigarElement> cigarElements = new ArrayList<>(oldCigar.getCigarElements());
         int posShift = 0;
@@ -860,11 +858,26 @@ static int getReadPositionAtReferencePositionIgnoreSoftClips(final SAMRecord rec
         // Temporarily use the newCigar that has SOFT_CLIPs replaced with MATCH_OR_MISMATCH to get read position at reference, but ignore existence of soft-clips
         rec.setCigar(newCigar);
         // Since the read effectively got shifted forward by turning the clips into matches, the query position needs
-        // also to be moved forward bye posShift so that it's still querying the same base.
-        readPosition = SAMRecord.getReadPositionAtReferencePosition(rec, pos + posShift, false);
+        // also to be moved forward by posShift so that it's still querying the same base.
+        final int readPosition = SAMRecord.getReadPositionAtReferencePosition(rec, pos + posShift, true);
+
+        // if this returns zero, it means that there's a deletion at the position of the desired base,
+        // if the read is on the positive strand readPosition should be incremented by one to get the
+        // base __following__ the deletion rather than the one preceding it (which is what returnLastBaseIfDeleted argument in
+        // getReadPositionAtReferencePosition will do)
+        final int readPositionZeroOnDeletion = SAMRecord.getReadPositionAtReferencePosition(rec, pos + posShift, false);
+
         rec.setCigar(oldCigar);
 
-        return readPosition;
+        final boolean refPositionOnDeletion = readPositionZeroOnDeletion == 0 && readPosition != 0;
+
+        final boolean incrementReadPosition = refPositionOnDeletion &&
+                !rec.getReadNegativeStrandFlag() && // only needed for positive-strand reads
+                readPosition < rec.getReadLength(); // protection against the possibility that getReadPositionAtReferencePosition
+        // would return the last base of a read when it ends in a deletion (it currently doesn't)
+
+        return incrementReadPosition ? readPosition + 1 : readPosition;
+
     }
 
     private static void clip3PrimeEndOfRead(final SAMRecord rec, final int clipFrom, final boolean useHardClipping) {

testdata/picard/sam/MergeBamAlignment/indel_reads_aligned.sam

@@ -0,0 +1,29 @@
+@HD	VN:1.6	SO:queryname
+@SQ	SN:chr1	LN:1000	M5:17522ddd273279f4595f50fea9864734
+@PG	ID:bwa	PN:bwa	VN:0.7.15-r1140
+H2GCKCCXX150314:7:1101:10236:61064	81	chr1	490	0	4M2D147M	=	496	-147	ACAGCTGCTGTAGGGCTGGCCTAAGTCAGGCAGTTCAAGATAACCTGAAGGAGTCGAATAACATCTATCCAGTGAGTCCTGCAAGACTTCAGGCTCTTTCTCATCCAGCAGCTCCCTGCTGAGCCTGGAAAAGTGGGAAAAAGTAAAGAAT	F,<KKKFKKKKKF<FAFFAKKKKKKKKKFKFKKKAFKKKKKAKKKKKKKK<KKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKFFFAA	NM:i:2	MD:Z:4^CA147	AS:i:147	XS:i:142
+H2GCKCCXX150314:7:1101:10236:61064	161	chr1	496	0	144M7S	=	490	147	CTGCTGTAGGGCTGGCCTAAGTCAGGCAGTTCAAGATAACCTGAAGGAGTCGAATAACATCTATCCAGTGAGTCCTGCAAGACTTCAGGCTCTTTCTCATCCAGCAGCTCCCTGCTGAGCCTGGAAAAGTGGGAAAAAGTAAAGCATCTGT	AAFFFKKKFKKKKF<FKKKKAFKKKKKKKKKKKKKKKKKKKKKKKKKFKKKKKKKKKKKKKKKKKKKKKKKFKKKFKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKFFKKKFKKKKKFFKFAFFKKKAFA7AFKKA,,A,FA7F<,AFK	NM:i:0	MD:Z:144	AS:i:144	XS:i:139
+H2GCKCCXX150314:7:1101:10338:42042	97	chr1	131	22	145M6S	=	123	145	GATCCGGTCACCACTAACCATGGGCAGATCCATGGCAATGAGCTGGACTTTGTTGGGTTTTGCTATGAGAAGAGGAGGATCCAGGGCAGCTGCAAAATCAGAGAGTTTAGAGAACTCTATAAACTGGGTCGCATCGGGATCAAACCTGTCT	AAFFFKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKFKKKKKKKKKKKKKKKKKKKKKKKKKKKFFFKKKKKK7FKKKKK<KKKKK	NM:i:0	MD:Z:145	AS:i:145	XS:i:135
+H2GCKCCXX150314:7:1101:10338:42042	145	chr1	123	21	5M2D146M	=	131	-145	AGACAGGATCCGGTCACCACTAACCATGGGCAGATCCATGGCAATGAGCTGGACTTTGTTGGGTTTTGCTATGAGAAGAGGAGGATCCAGGGCAGCTGCAAAATCAGAGAGTTTAGAGAACTCTATAAACTGGGTCGCATCGGGATCAAAC	A7KA<KKFKKFFKFFKKKKKKKKKKKKKKKFKKKKKKKKKKKKKFAAKKFKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKFAKKKKFF<KFKKKKKKKKKKKFKKKKKKKKKKKKFKKKKKKKKAKKKKKKKKKKKKKKFKKFAFAA	NM:i:2	MD:Z:5^AT146	AS:i:146	XS:i:136
+H2GCKCCXX150314:7:1101:10703:6319	81	chr1	799	60	3S148M	=	799	-148	CAGGTTGGGACATTCTGAATAAGAGGTTAGTATCAGCGTTTTGCCATGTCCCCATGAACCCTGGTTCAGCCGTAGTCGTTCTGGTTCCGAACTGCATGGAGTTGTCAGTACAGGAGTCTCTTAAAGTCAAGTCTCTTGCCCTCTTTGGCTC	AFAKKKKKKKKKKKKKKKKKKKKKKKKFKKKKKKKKKAKFKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKFKKKKKKKKKKKKKKKKKKKKKKF7KKKKKKKKKKKKKKKKKKFKKKKF7KKKKKKKKKKKKKKKKKKKKKFFFAA	NM:i:0	MD:Z:148	AS:i:148	XS:i:0
+H2GCKCCXX150314:7:1101:10703:6319	161	chr1	799	60	148M1D3M	=	799	148	GTTGGGACATTCTGAATAAGAGGTTAGTATCAGCGTTTTGCCATGTCCCCATGAACCCTGGTTCAGCCGTAGTCGTTCTGGTTCCGAACTGCATGGAGTTGTCAGTACAGGAGTCTCTTAAAGTCAAGTCTCTTGCCCTCTTTGGCTCCTG	AAFFFAAKKKKKKKKKKKKKKKKKKKKKKAKKKKKKKKKKKKKKKKKKKKKKKKKKFAFKKKKFKKKAFKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKFKKKKKKKKKKKKKKKKAKKKKKKKKKKKFFKKFKKKKKKKKKA	NM:i:1	MD:Z:148^T3	AS:i:148	XS:i:0
+H2GCKCCXX150314:7:1101:11535:49813	97	chr1	044	60	151M	=	040	148	ATCAATTGCCTTATCAATTAGAAGGGCTGAATTTTGACCAAAGATCTTGCCACACTCATTACAATTGTAACGTTTTACTCCAGTATGAAGTCTACGATGGCAGGTAAGGGATGACTCCTGACTGAAGGTCTTGCCACACTCTTTACACCTG	AAFFFKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKFKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKK	NM:i:1	MD:Z:148T2	AS:i:148	XS:i:80
+H2GCKCCXX150314:7:1101:11535:49813	145	chr1	040	60	3M1D148M	=	044	-148	CAGATCAATTGCCTTATCAATTAGAAGGGCTGAATTTTGACCAAAGATCTTGCCACACTCATTACAATTGTAACGTTTTACTCCAGTATGAAGTCTACGATGGCAGGTAAGGGATGACTCCTGACTGAAGGTCTTGCCACACTCTTTACAC	KKKFKKAFKKAKKKKKFFKFKKKKKFFAKKKKKKKKFKFKKFKKKKFF<KKKFKFKFKKKKKKKKKKKKKFFFKFKKKKKKKAKAFFKKFKF<KKKKKKKKKKKKKKKKKKFKKKKKKKKKKKKKKKKKKKKKKKKFKKKKKKKKKFFAA,	NM:i:1	MD:Z:3^T148	AS:i:148	XS:i:80
+H2GCKCCXX150314:7:1101:11840:41972	81	chr1	836	60	4M1D147M	=	842	-146	GACAGGTACATGCTTAATAGAAACATATGCATTGGAAAATCAACACTGTTTGAAGGGCTTTGTTCCAGGCTGTCAGATGCATGTGGAAAGAAAAGGACAGTTAAAGTCTACTGGAAAGAAAGAGAAAAGAAACACAGACAAGGAATACGTG	#AKAAKFA<KKFKKFKKKKKKKKKKFKKKKKKKKKKKKFKKKKKKKKFKKKKKFFKKKKKKKKKKKKKKKKKKFKKKKKKKKKKKKKKKKKKKKKKKKFKKKKKAK<KKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKFFFFAA	NM:i:1	MD:Z:4^T147	AS:i:147	XS:i:0
+H2GCKCCXX150314:7:1101:11840:41972	161	chr1	842	60	146M5S	=	836	146	GTACATGCTTAATAGAAACATATGCATTGGAAAATCAACACTGTTTGAAGGGCTTTGTTCCAGGCTGTCAGATGCATGTGGAAAGAAAAGGACAGTTAAAGTCTACTGGAAAGAAAGAGAAAAGAAACACAGACAAGGAATACGTGCTGTC	AAFFFKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKFKKKKKKKKKKKKKFKKKFKKKKFKKKKKKKKKKFKFKKKKKKKKFF7FKKKKKKKKKKKKKKKKKKKKKKFFKKKKKKKKKKFKKKKKKKKKKK	NM:i:0	MD:Z:146	AS:i:146	XS:i:0
+H2GCKCCXX150314:7:1101:11931:5317	81	chr1	758	60	3S148M	=	758	-148	CAGGGGGAGATCGCCATACGTATAACCCAGTCCCTTTGGCCAGGTGACATTTGCTCTGAACTGGATGATACGAATGATGTCAGATTTGGAATCTAACATCGTGGCTGTGGAGAGGGTCAAGGAGTACTCCAAGACAGAGACAGAGGTGGGT	A<KFKKKKF7AKFKKKKKKKKKFF7KKKFKKKKKKKKF7KKKKAKKKKKKKKFKKKKKKFKKKKKKKKKKKKKKKKKKAKKKFKFKKKKKKKKKKKKKFFKKKKKKFKKKKFKKKKKKFFFKFA,KKKKKKKKKKKKKKKKKKKFA<FFAA	NM:i:0	MD:Z:148	AS:i:148	XS:i:0
+H2GCKCCXX150314:7:1101:11931:5317	161	chr1	758	60	148M1D3M	=	758	148	GGGGAGATCGCCATACGTATAACCCAGTCCCTTTGGCCAGGTGACATTTGCTCTGAACTGGATGATACGAATGATGTCAGATTTGGAATCTAACATCGTGGCTGTGGAGAGGGTCAAGGAGTACTCCAAGACAGAGACAGAGGTGGGTCTG	AAFF<FKKKKKKKKKKKKKKKKKKAFKKK,AKKKKKKAFAFKKKKKKKKKFKAFFA<FAKKFKKKKKKKKAA,FKFFKKKKKFFFKKKAFFKKKKKKKKAF7<KKKKFKKK<KKK7KKKKKKA77AFKKAKKKKKKKKK,AFK,7FFA<7A	NM:i:1	MD:Z:148^A3	AS:i:148	XS:i:19
+H2GCKCCXX150314:7:1101:12033:69942	81	chr1	063	60	3M1D148M	=	067	-148	CAGGTCCGATAGACACCAGGAAGCAACTAGCAGAGAATTTGGTAGTCATAGGTGGCACTTCTATGTTGCCAGGATTTCTCCACAGATTGCTTGCAGAAATAAGGTATTTGGTAGAAAAACCAAAATATAAAAAAGCACTTGGCACTAAGAC	<<AFAKAAKKFKFKF<FAA7FFAKKKKKKKF7KKAAKKKKFAKKKKKKKKFFKFAKKFKKKKKKFKKKFKKKKKFAFKKKAKKFFKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKFKKKKKKKKKKFK7<AKKKKKKKKKKKKKKFFFA,	NM:i:1	MD:Z:3^T148	AS:i:148	XS:i:22
+H2GCKCCXX150314:7:1101:12033:69942	161	chr1	067	60	146M5S	=	063	148	GTCCGATAGACACCAGGAAGCAACTAGCAGAGAATTTGGTAGTCATAGGTGGCACTTCTATGTTGCCAGGATTTCTCCACAGATTGCTGGCAGAAAGAAGGTATTTGGTAGAAAAACCAAAATATAAAAAAGCACTTGGAACTAAGGCGTG	,AAFFFKKKKKKKKKKKKFKKKKKKKKKKKKKAKKKKAKA7FKKKKKKKKKKFFKKFKAAKFKKKKFFKF<FKAFFFKAKFKKK,FFK7F<FKA<F7FKKKKKK7F<,A<FAFK,AA,AA,<A,<7AA7FFAFA7FK##############	NM:i:3	MD:Z:88T7T42C6	AS:i:131	XS:i:22
+H2GCKCCXX150314:7:1101:12266:70276	81	chr1	723	16	38S39M2I72M	=	817	-17	CACATGCATGCTTGTCGGTCGTTTGTGTCACATTCACCCTGTTGCAGGCGTGAATGCCGGTGGTGTTACACTCACACTGTTGTAGGAGTCCAGGTCGGTGGTGTTACACACATTCATGCTGTTGCAGGCGTGCAGGTCGGTGGTGTTACAC	#################################################################AKAF7,7,A,AAKKKAF7F7KAA7,7,FKK<KKKFKKKKKKKAKKKFKKFKFKKKKKKKKKKKKKKKKKKKKKKKKKKKKKFFFAA	NM:i:9	MD:Z:14C1G1T13T9C3C2G61	AS:i:68	XS:i:59
+H2GCKCCXX150314:7:1101:12266:70276	161	chr1	817	0	58M93S	=	723	17	GGTCGGTGGTGTTACACACATTCACACTGTTGCAGGCGTGCAGGTCGGTGGTGTTACAGTTGGGCCTTAGAAAGATTACAGGTCGTTGAGGTTACAAAAAGTCTATATCACGAGGGCAGGGGGAAGTTGATGAATAAAAAGTAAAAAGTAA	<AAAFFKKKKKKKKKKKKKKFKKKAFFKAKKKFKK7A<FFFKKFKKFF,FKKFKAFKK#############################################################################################	NM:i:0	MD:Z:58	AS:i:58	XS:i:58
+H2GCKCCXX150314:7:1101:13423:27626	97	chr1	241	0	125M26S	=	198	109	GGGTGGAGCTGAGGGTGGAAGGGGAGTGAGCTGACGCTCGGAAGGTGTCTTGAGATTATCATCCGCTGAGGGTGGAAGCGGCCCCCGCAGAGGCTCGGCAGGTGTATTGATGTTATCATCTGCTGCGGGCGGGGCTGAGGGAGGAGGGGGA	A<F<AFFKKKKAKKF<FF7,A<FK7F7FKKKKKKKKAKKF<,<AF<<F,,<AFKK,FFK77FFKKKKKFKKKKKFK<<,FKA<AF<F7<FK,F,A,,AAKFKKK<,A7K,<,,,,,,,,<AFKFK##########################	NM:i:2	MD:Z:91C19A13	AS:i:115	XS:i:111
+H2GCKCCXX150314:7:1101:13423:27626	145	chr1	198	0	40M1D111M	=	241	-109	CCGCAGACGCTCGGCAGTCGTTTAGATATTATCATCTGCCGAGGGTGGAGCTGAGGGTGGAAGGGGAGTGAGCTGACGCTCGGAAGGTGTCTTGAGATTATCATCCGCTGAGGGTGGAAGCGGCCCCCGCAGACGCTCGGCAGGTGTATTG	##########################################FFKFKKFFF7FFFKKKFFKKKKKKKKKKKKFKKK<KKKFAKKKFKKKAKKFF7,,AFFKKKKFF<KFKFF,7FFKFAFKKFKFKFKKKFKFKKKKFFKKFKKKFFFFA,	NM:i:5	MD:Z:17G0T2C1T16^T111	AS:i:124	XS:i:122
+H2GCKCCXX150314:7:1101:14672:72157	81	chr1	626	60	3M1D148M	=	630	-148	CAGGATGTAGAGGCAGCCATCGGCGTCCAGGCGGCCAGCATCACCCGTGTGCAGCCAGCCTTCCTCGTCGATGGCCTCACAAGTCTTGTCCTCCATGTTCAGGTAGCCCATGAATATGGTGCGGCCCCACAGGCAGATCTCGCCAATGCCC	##############A<KFFFKA(<,<KFA7<KFKKKKFFAFKKKKAKKKKKKKKFKAKKF7KKFKKFKKKAAFAFAKKKKKKKKKKKA7KKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKFFAAA	NM:i:2	MD:Z:3^T10A137	AS:i:143	XS:i:0
+H2GCKCCXX150314:7:1101:14672:72157	161	chr1	630	60	134M17S	=	626	148	GATGTAGAGGAAGCCATCGGCGTCCAGGCGGCCAGCATCACCCGTGTGCAGCCAGCCTTCCTCGTCGATGGCCTCACAAGTCTTGTCCTCCATGTTCAGGTAGCCCATGAATATGGTGCGGCCCCACAGGCAGAGCGCGCCAGTGCCCCGT	AAAFFKKKKKKKKKKKKKFKKKFKKKKKKKKKKKKKKFKKFKKKKKKKKKKKFKKKKKKKKKKKKKKKKKKKKKFKFKFKAFKKKKAFKFKKKKKKKKFKKKKKKKFKKKKKKKKAKKKFFKK(,F,,<AAAK##################	NM:i:0	MD:Z:134	AS:i:134	XS:i:0
+H2GCKCCXX150314:7:1101:14986:51008	97	chr1	580	60	147M1I3M	=	579	146	GCTGGGACGGGATGGGATTCTTCTCACGGCGCACGTTCTGTGGGCGGAGTGGGCGGAGCTGCCGGGGTCAGTTGGTCCAACTGTCCCGGCCTGAGGTGTCGGCCGGATCCCTCCTTCTCCCGGCGCCTCAAGCGGAAGGTGAGGGCCTGTC	AAFFFKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKFKKKKKKKKKKKKKKKKKKKKKKKKKFFKFKFKFKKFKKKAF	NM:i:2	MD:Z:80G69	AS:i:142	XS:i:0
+H2GCKCCXX150314:7:1101:14986:51008	145	chr1	579	60	4S147M	=	580	-146	GACAGGCTGGGACGGGATGGGATTCTTCTCACGGCGCACGTTCTGTGGGCGGAGTGGGCGGAGCTGCCGGGGTCAGTTGGTCCAACTGTCCCGGCCTGAGGTGTCGGCCGGATCCCTCCTTCTCCCGGCGCCTCAAGCGGAAGGTGAGGGC	AFFFFAAKFFKKKKFKFKKKKKKKKKKKKFFKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKFKKKKKKKKKKKKFKFKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKFFFAA	NM:i:1	MD:Z:81G65	AS:i:142	XS:i:0
+H2GCKCCXX150314:7:1101:15169:9659	81	chr1	043	60	4S147M	=	043	-147	ACAGCTTCTTGGAGCTTGTTTGCACACCAGCAGCCGCGCATGAGTAGTTGCCAATCTCAGCACCAAACTGCAGAGCCACGGCCACATCACAATCATCCACGCTTAGCACAGCCACCTTGTCCTTGGAGGGGCCCTGTGCACCCCCTAGGGC	AKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKFKKKKKKKKKKKKKKKFKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKFKKKA,KKKKKKKKKKKKKKAKKKFKKKKKKKKFFFAA	NM:i:0	MD:Z:147	AS:i:147	XS:i:0
+H2GCKCCXX150314:7:1101:15169:9659	161	chr1	043	60	147M2D4M	=	043	147	CTTCTTGGAGCTTGTTTGCACACCAGCAGCCGCGCATGAGTAGTTGCCAATCTCAGCACCAAACTGCAGAGCCACGGCCACATCACAATCATCCACGCTTAGCACAGCCACCTTGTCCTTGGAGGGGCCCTGTGCACCCCCTAGGGCCTGT	<AFFFKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKFKKKKKKKAFKKKKKKKKKFKFKKKKKKKFKKKKKKF<KKKKKKKKKKAKKKKKFFKKKKKKKKKKKKKKKKKKKKKKKKFKKKKFFKKKKKKKKFKKFKKFKKKKKKKKK<	NM:i:2	MD:Z:147^AT4	AS:i:147	XS:i:0
+H2GCKCCXX150314:7:1101:15291:20278	81	chr1	722	60	5M1D146M	=	728	-146	GACAGCAGTAAGAAGAGGAGGAAAAAGAGAAAACGGAGGTCCCCCTTCCCTGGTTCCCTTCTTGCCTACCTCTGGATCTGTTGGATGCAGGGCAGGACAAAGACACGCCCTCCAGCCACCATGACTGGGGGGCTTCGGCAGAACCCTGCAA	FKKKKKKKKKKKAKKKKKFFFFKKKKKKKKKKKKKKFKFKKKKKKFKKKKKKKKKKKKKKKFKKKKKKKKFKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKFFAAA	NM:i:1	MD:Z:5^A146	AS:i:146	XS:i:0
+H2GCKCCXX150314:7:1101:15291:20278	161	chr1	728	60	146M5S	=	722	146	CAGTAAGAAGAGGAGGAAAAAGAGAAAACGGAGGTCCCCCTTCCCTGGTTCCCTTCTTGCCTACCTCTGGATCTGTTGGATGCAGGGCAGGACAAAGACACGCCCTCCAGCCACCATGACTGGGGGGCTTCGGCAGAACCCTGCAACTGTC	AAAFFKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKFKKKFKKKKKKKKKKKF<FKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKFKKKKKAKAKKKKKKKAFKKKKKKKKKKK<AKKKKKKKKFA	NM:i:0	MD:Z:146	AS:i:146	XS:i:0