Rename aux tag MZ to MN.

See samtools/hts-specs#714
samtools · May 9, 2023 · 6125f1c · 6125f1c
1 parent 415d2ce
commit 6125f1c
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Showing 6 changed files with 12 additions and 12 deletions.
diff --git a/sam.c b/sam.c
@@ -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;
     }

diff --git a/test/base_mods/MM-MZf1.sam → test/base_mods/MM-MNf1.sam b/test/base_mods/MM-MZf1.sam → test/base_mods/MM-MNf1.sam
@@ -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
diff --git a/test/base_mods/MM-MZf2.sam → test/base_mods/MM-MNf2.sam b/test/base_mods/MM-MZf2.sam → test/base_mods/MM-MNf2.sam
@@ -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
diff --git a/test/base_mods/MM-MZp.sam → test/base_mods/MM-MNp.sam b/test/base_mods/MM-MZp.sam → test/base_mods/MM-MNp.sam
@@ -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
diff --git a/test/base_mods/MM-multi.sam b/test/base_mods/MM-multi.sam
@@ -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
diff --git a/test/base_mods/base-mods.tst b/test/base_mods/base-mods.tst
@@ -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