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Rename aux tag MZ to MN. #1612

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May 9, 2023
Merged

Rename aux tag MZ to MN. #1612

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4 changes: 2 additions & 2 deletions sam.c
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Original file line number Diff line number Diff line change
Expand Up @@ -6225,12 +6225,12 @@ int bam_parse_basemod(const bam1_t *b, hts_base_mod_state *state) {
return -1;
}

uint8_t *mi = bam_aux_get(b, "MZ");
uint8_t *mi = bam_aux_get(b, "MN");
if (mi && bam_aux2i(mi) != b->core.l_qseq) {
// bam_aux2i with set errno = EINVAL and return 0 if the tag
// isn't integer, but 0 will be a seq-length mismatch anyway so
// triggers an error here too.
hts_log_error("%s: MM/MZ data length is incompatible with"
hts_log_error("%s: MM/MN data length is incompatible with"
" SEQ length", bam_get_qname(b));
return -1;
}
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4 changes: 2 additions & 2 deletions test/base_mods/MM-MZf1.sam → test/base_mods/MM-MNf1.sam
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
@SQ SN:I LN:999
r1 0 I 1 0 36M * 0 0 AGCTCTCCAGAGTCGNACGCCATYCGCGCGCCACCA DF?GCH88.EG8.7@E9G8A?H9.:C?8,@,,9F@A Mm:Z:C+m,2,2,1,4,1;C+h,6,7;N+n,15,2; Ml:B:C,128,153,179,204,230,159,6,215,240 MZ:i:37
r1 0 I 1 0 36M * 0 0 AGCTCTCCAGAGTCGNACGCCATYCGCGCGCCACCA DF?GCH88.EG8.7@E9G8A?H9.:C?8,@,,9F@A Mm:Z:C+m,2,2,1,4,1;C+h,6,7;N+n,15,2; Ml:B:C,128,153,179,204,230,159,6,215,240 MN:i:37
r1- 16 I 1 0 36M * 0 0 AGCTCTCCAGAGTCGNACGCCATYCGCGCGCCACCA DF?GCH88.EG8.7@E9G8A?H9.:C?8,@,,9F@A Mm:Z:G-m,0,1,4,1,2;G-h,0,7;N-n,17,2; Ml:B:C,230,204,179,153,128,6,159,240,215
r2 0 I 4 0 3S33M * 0 0 AGCTCTCCAGAGTCGNACGCCATYCGCGCGCCACCA DF?GCH88.EG8.7@E9G8A?H9.:C?8,@,,9F@A Mm:Z:C+m,2,2,1,4,1;C+h,6,7;N+n,15,2; Ml:B:C,128,153,179,204,230,159,6,215,240
r3 0 I 11 0 10S20M6S * 0 0 AGCTCTCCAGAGTCGNACGCCATYCGCGCGCCACCA DF?GCH88.EG8.7@E9G8A?H9.:C?8,@,,9F@A Mm:Z:C+mh,2,2,0,0,4,1;N+n,15,2; Ml:B:C,128,0,153,0,0,159,179,0,204,0,230,6,215,240 MZ:i:36
r3 0 I 11 0 10S20M6S * 0 0 AGCTCTCCAGAGTCGNACGCCATYCGCGCGCCACCA DF?GCH88.EG8.7@E9G8A?H9.:C?8,@,,9F@A Mm:Z:C+mh,2,2,0,0,4,1;N+n,15,2; Ml:B:C,128,0,153,0,0,159,179,0,204,0,230,6,215,240 MN:i:36
4 changes: 2 additions & 2 deletions test/base_mods/MM-MZf2.sam → test/base_mods/MM-MNf2.sam
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
@SQ SN:I LN:999
r1 0 I 1 0 36M * 0 0 AGCTCTCCAGAGTCGNACGCCATYCGCGCGCCACCA DF?GCH88.EG8.7@E9G8A?H9.:C?8,@,,9F@A Mm:Z:C+m,2,2,1,4,1;C+h,6,7;N+n,15,2; Ml:B:C,128,153,179,204,230,159,6,215,240 MZ:i:36
r1 0 I 1 0 36M * 0 0 AGCTCTCCAGAGTCGNACGCCATYCGCGCGCCACCA DF?GCH88.EG8.7@E9G8A?H9.:C?8,@,,9F@A Mm:Z:C+m,2,2,1,4,1;C+h,6,7;N+n,15,2; Ml:B:C,128,153,179,204,230,159,6,215,240 MN:i:36
r1- 16 I 1 0 36M * 0 0 AGCTCTCCAGAGTCGNACGCCATYCGCGCGCCACCA DF?GCH88.EG8.7@E9G8A?H9.:C?8,@,,9F@A Mm:Z:G-m,0,1,4,1,2;G-h,0,7;N-n,17,2; Ml:B:C,230,204,179,153,128,6,159,240,215
r2 0 I 4 0 3S33M * 0 0 AGCTCTCCAGAGTCGNACGCCATYCGCGCGCCACCA DF?GCH88.EG8.7@E9G8A?H9.:C?8,@,,9F@A Mm:Z:C+m,2,2,1,4,1;C+h,6,7;N+n,15,2; Ml:B:C,128,153,179,204,230,159,6,215,240
r3 0 I 11 0 10S20M6S * 0 0 AGCTCTCCAGAGTCGNACGCCATYCGCGCGCCACCA DF?GCH88.EG8.7@E9G8A?H9.:C?8,@,,9F@A Mm:Z:C+mh,2,2,0,0,4,1;N+n,15,2; Ml:B:C,128,0,153,0,0,159,179,0,204,0,230,6,215,240 MZ:f:36
r3 0 I 11 0 10S20M6S * 0 0 AGCTCTCCAGAGTCGNACGCCATYCGCGCGCCACCA DF?GCH88.EG8.7@E9G8A?H9.:C?8,@,,9F@A Mm:Z:C+mh,2,2,0,0,4,1;N+n,15,2; Ml:B:C,128,0,153,0,0,159,179,0,204,0,230,6,215,240 MN:f:36
4 changes: 2 additions & 2 deletions test/base_mods/MM-MZp.sam → test/base_mods/MM-MNp.sam
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
@SQ SN:I LN:999
r1 0 I 1 0 36M * 0 0 AGCTCTCCAGAGTCGNACGCCATYCGCGCGCCACCA DF?GCH88.EG8.7@E9G8A?H9.:C?8,@,,9F@A Mm:Z:C+m,2,2,1,4,1;C+h,6,7;N+n,15,2; Ml:B:C,128,153,179,204,230,159,6,215,240 MZ:i:36
r1 0 I 1 0 36M * 0 0 AGCTCTCCAGAGTCGNACGCCATYCGCGCGCCACCA DF?GCH88.EG8.7@E9G8A?H9.:C?8,@,,9F@A Mm:Z:C+m,2,2,1,4,1;C+h,6,7;N+n,15,2; Ml:B:C,128,153,179,204,230,159,6,215,240 MN:i:36
r1- 16 I 1 0 36M * 0 0 AGCTCTCCAGAGTCGNACGCCATYCGCGCGCCACCA DF?GCH88.EG8.7@E9G8A?H9.:C?8,@,,9F@A Mm:Z:G-m,0,1,4,1,2;G-h,0,7;N-n,17,2; Ml:B:C,230,204,179,153,128,6,159,240,215
r2 0 I 4 0 3S33M * 0 0 AGCTCTCCAGAGTCGNACGCCATYCGCGCGCCACCA DF?GCH88.EG8.7@E9G8A?H9.:C?8,@,,9F@A Mm:Z:C+m,2,2,1,4,1;C+h,6,7;N+n,15,2; Ml:B:C,128,153,179,204,230,159,6,215,240
r3 0 I 11 0 10S20M6S * 0 0 AGCTCTCCAGAGTCGNACGCCATYCGCGCGCCACCA DF?GCH88.EG8.7@E9G8A?H9.:C?8,@,,9F@A Mm:Z:C+mh,2,2,0,0,4,1;N+n,15,2; Ml:B:C,128,0,153,0,0,159,179,0,204,0,230,6,215,240 MZ:i:36
r3 0 I 11 0 10S20M6S * 0 0 AGCTCTCCAGAGTCGNACGCCATYCGCGCGCCACCA DF?GCH88.EG8.7@E9G8A?H9.:C?8,@,,9F@A Mm:Z:C+mh,2,2,0,0,4,1;N+n,15,2; Ml:B:C,128,0,153,0,0,159,179,0,204,0,230,6,215,240 MN:i:36
2 changes: 1 addition & 1 deletion test/base_mods/MM-multi.sam
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Expand Up @@ -3,5 +3,5 @@
@CO r2 has them combined together, for example as produced by
@CO a joint basecaller which assigns probabilities to all
@CO trained events simultaneously.
r1 0 * 0 0 * * 0 0 AGCTCTCCAGAGTCGNACGCCATYCGCGCGCCACCA * Mm:Z:C+m,2,2,1,4,1;C+h,6,7;N+n,15,2; Ml:B:C,128,153,179,204,230,159,6,215,240 MZ:i:36
r1 0 * 0 0 * * 0 0 AGCTCTCCAGAGTCGNACGCCATYCGCGCGCCACCA * Mm:Z:C+m,2,2,1,4,1;C+h,6,7;N+n,15,2; Ml:B:C,128,153,179,204,230,159,6,215,240 MN:i:36
r2 0 * 0 0 * * 0 0 AGCTCTCCAGAGTCGNACGCCATYCGCGCGCCACCA * Mm:Z:C+mh,2,2,0,0,4,1;N+n,15; Ml:B:C,77,159,103,133,128,108,154,82,179,57,204,31,240
6 changes: 3 additions & 3 deletions test/base_mods/base-mods.tst
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Expand Up @@ -45,6 +45,6 @@ P MM-pileup2.out $pileup_mod < MM-pileup2.sam

# Validation testing. We just care about exit status here, but the
# test data is a copy of MM-pileup.sam so that suffices too.
P MM-pileup.out $pileup_mod < MM-MZp.sam
F MM-pileup.out $pileup_mod < MM-MZf1.sam
F MM-pileup.out $pileup_mod < MM-MZf2.sam
P MM-pileup.out $pileup_mod < MM-MNp.sam
F MM-pileup.out $pileup_mod < MM-MNf1.sam
F MM-pileup.out $pileup_mod < MM-MNf2.sam