/usr/share/htslib-test/test/xx#tlen2.sam is in htslib-test 1.7-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 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 *****
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