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@SQ SN:one LN:1000
@SQ SN:two LN:500
@CO For each SAM record that has each listed aux field, performs these tests:
@CO XQ is the expected result for bam_cigar2qlen()
@CO XR is the expected result for bam_cigar2rlen()
@CO XE is the expected result for bam_endpos()
@CO (Note that these are all zero-based, while POS is one-based in SAM)
r1 0 one 50 20 8M * 0 0 ATGCATGC qqqqqqqq XQ:i:8 XR:i:8 XE:i:57
r2 0 one 100 20 50M * 0 0 ATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCAT qqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqq XQ:i:50 XR:i:50 XE:i:149
unmapped 5 two 200 0 * = 200 0 ATGCATGC qqqqqqqq XQ:i:0 XR:i:0 XE:i:200
hascigar 5 two 200 0 6M2S = 200 0 ATGCATGC qqqqqqqq XQ:i:8 XR:i:6 XE:i:200
s1 0 one 300 20 2M * 0 0 AT qq XQ:i:2 XR:i:2 XE:i:301
su1 4 * 0 0 * * 0 0 AT qq XQ:i:0 XR:i:0 XE:i:0
su2 5 two 400 0 * = 400 0 AT qq XQ:i:0 XR:i:0 XE:i:400
su3 4 one 500 0 2M * 0 0 AT qq XQ:i:2 XR:i:2 XE:i:500
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