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`mpileup` loses bases of alignments starting with a insertion

Open alumi opened this issue 7 years ago • 0 comments

input SAM

@SQ	SN:ref	LN:45
q001	0	ref	10	60	4I4M4D4M4I	*	0	0	ATGCATGCATGCATGC	ABCDEFGHIJKLMNOP

samtools output

ref	10	N	1	^]A	E
ref	11	N	1	T	F
ref	12	N	1	G	G
ref	13	N	1	C-4NNNN	H
ref	14	N	1	*	I
ref	15	N	1	*	I
ref	16	N	1	*	I
ref	17	N	1	*	I
ref	18	N	1	A	I
ref	19	N	1	T	J
ref	20	N	1	G	K
ref	21	N	1	C+4ATGC$	L

cljam output

ref	10	N	1	^]A	E
ref	11	N	1	T	F
ref	12	N	1	G	G
ref	13	N	1	C-4NNNN	H
ref	14	N	1	*	~
ref	15	N	1	*	~
ref	16	N	1	*	~
ref	17	N	1	*	~
ref	18	N	1	A	I
ref	19	N	1	T	J
ref	20	N	1	G	K
ref	21	N	1	C+4ATGC$	L

alumi avatar Aug 10 '18 09:08 alumi