@HD	VN:1.17	SO:unknown
@SQ	SN:T1	LN:40
@SQ	SN:T2	LN:40
@CO	@SQ SN* LN* AH AN AS DS  M5 SP TP UR
@CO	@RG ID* BC CN DS DT FO KS LB PG PI PL PM PU SM
@CO	@PG ID* PN CL PP DS VN
@CO	this is a dummy alignment file to demonstrate different abilities of hts apis
@CO	QNAME FLAG RNAME POS MAPQ CIGAR RNEXT PNEXT TLEN SEQ QUAL [TAG:TYPE:VALUE]…
@CO	1234567890123456789012345678901234567890
@CO	AAAAACTGAAAACCCCTTTTGGGGACTGTTAACAGTTTTT	T1
@CO	TTTTCCCCACTGAAAACCCCTTTTGGGGACTGTTAACAGT	T2
@CO	ITR1-ITR2M, ITR2-ITR2M are proper pairs in T1 and T2, UNMP1 is partly mapped and pair is unmapped, UNMP2 & 3 are unmappped
@CO	A1-A2, A4-A3 are proper pairs with A4-A3 in different read order. A5 is secondary alignment
ITR1	99	T1	5	40	4M	=	33	10	ACTG	()()
ITR2	147	T2	23	49	2M	=	35	-10	TT	**
ITR2M	99	T2	35	51	2M	=	23	10	AA	&&
ITR1M	147	T1	33	37	4M	=	5	-10	ACTG	$$$$
UNMP1	73	T1	21	40	3M	*	0	5	GGG	&&1
UNMP2	141	*	0	0	*	*	0	7	AA	&&
UNMP3	77	*	0	0	*	*	0	5	GGG	&&2
A1	99	T1	25	35	6M	=	31	8	ACTGTT	******
A2	147	T1	31	33	6M	=	25	-8	ACTGTT	()()()
A3	147	T2	23	47	2M1X	=	12	-5	TTG	(((
A4	99	T2	12	50	3M	=	23	5	GAA	()(
A5	355	T1	25	35	4M	=	33	5	ACTG	PPPP
B1	99	T1	25	35	6M	=	31	8	GCTATT	******
B3	147	T2	23	47	2M1X	=	12	-5	TAG	(((
B4	99	T2	12	50	3M	=	23	5	GAT	()(
B5	355	T1	25	35	4M	=	33	5	AGTG	PPPP
