Fix merging of Number=G format strings

Format strings appear to be adjacently-placed-in-memory fixed-length (max_len, src_len, etc) optionally-NUL-terminated arrays, i.e., the same sort of variable-up-to-a-fixed-length strings as operated on by strncpy(). In copy_string_field(), don't copy trailing NULs. In merge_format_string(), pad the *output* string with NULs.
dlaehnemann · Feb 1, 2016 · 5d25295 · 5d25295
1 parent e0890a1
commit 5d25295
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Showing 5 changed files with 6 additions and 6 deletions.
diff --git a/test/norm.merge.out b/test/norm.merge.out
@@ -36,7 +36,7 @@
 1	105	.	TAAACCCTAAA	TAA,TAACCCTAAA	999	PASS	INDEL;AN=4;AC=2,2;DP=19;ISTR=SomeString;XRF=1e+06,2e+06,500000;XRI=1111,2222,5555;XRS=AAA,BBB,DDD;XAF=1e+06,500000;XAI=1111,5555;XAS=AAA,DDD;XGF=1e+06,2e+06,3e+06,500000,.,9e+09;XGI=1111,2222,3333,5555,.,9999;XGS=A,B,C,E,.,F	GT:PL:DP:FRF:FRI:FRS:FAF:FAI:FAS:FGF:FGI:FGS	1/2:1,2,3,4,.,6:1:1e+06,2e+06,500000:1111,2222,5555:AAAA,BBB,CC:1e+06,500000:1111,5555:A,BB:1e+06,2e+06,3e+06,500000,.,9e+09:1111,2222,3333,5555,.,9999:A,BB,CCC,EEEE,.,FFFFF	1/2:1,2,3,4,.,6:1:1e+06,2e+06,500000:1111,2222,5555:AAAA,BBB,CC:1e+06,500000:1111,5555:A,BB:1e+06,2e+06,3e+06,500000,.,9e+09:1111,2222,3333,5555,.,9999:A,BB,CCC,EEEE,.,FFFFF
 2	1	.	GGGCGTCTCATAGCTGGAGCAATGGCGAGCGCCTGGACAAGGGAGGGGAAGGGGTTCTTATTACTGACGCGGGTAGCCCCTACTGCTGTGTGGTTCCCCTATTTTTTTTTTTTTCTTTTTGAGACGGAGTCTCGCTCTGTCACCCAGGCTGGAGTGCAGTGGCACAATCTCGGCTCACTGCAAGCTCCACCT	ACGT	999	PASS	INDEL;AN=4;AC=2	GT:DP	1/0:1	1/0:1
 2	101	.	ATTTTTTTTTTTTT	ATTTTTTTTTTTTTTT	999	PASS	INDEL;AN=4;AC=4	GT:DP	1/1:1	1/1:1
-2	114	.	TC	TTCC,TTC	999	FAIL1	INDEL;AN=4;AC=2,2	GT:DP	1/2:1	1/2:1
+2	114	.	TC	TTCC,TTC	999	FAIL1	INDEL;AN=4;AC=2,2	GT:DP:FGS	1/2:1:A,BB,CCC,EEEE,.,FFFFF	1/2:1:AA,BB,CCC,EEEE,.,FFFFF
 2	115	.	C	T	999	PASS	INDEL;AN=4;AC=4	GT:DP	1/1:1	1/1:1
 20	3	.	GATG	CTATG,GACT	999	PASS	INDEL;AN=4;AC=2,2	GT	2/1	2/1
 20	5	id0001;id0002	TGGG	TAC,TG,TGGGG,AC	.	PASS	INDEL;AN=4;AC=2,2,0,0	GT:PL:DP	1/2:1,2,3,4,.,6,7,.,.,10,11,.,.,.,15:1	1/2:1,2,3,4,.,6,7,.,.,10,11,.,.,.,15:1

diff --git a/test/norm.merge.strict.out b/test/norm.merge.strict.out
@@ -36,7 +36,7 @@
 1	105	.	TAAACCCTAAA	TAA,TAACCCTAAA	999	PASS	INDEL;AN=4;AC=2,2;DP=19;ISTR=SomeString;XRF=1e+06,2e+06,500000;XRI=1111,2222,5555;XRS=AAA,BBB,DDD;XAF=1e+06,500000;XAI=1111,5555;XAS=AAA,DDD;XGF=1e+06,2e+06,3e+06,500000,.,9e+09;XGI=1111,2222,3333,5555,.,9999;XGS=A,B,C,E,.,F	GT:PL:DP:FRF:FRI:FRS:FAF:FAI:FAS:FGF:FGI:FGS	1/2:1,2,3,4,.,6:1:1e+06,2e+06,500000:1111,2222,5555:AAAA,BBB,CC:1e+06,500000:1111,5555:A,BB:1e+06,2e+06,3e+06,500000,.,9e+09:1111,2222,3333,5555,.,9999:A,BB,CCC,EEEE,.,FFFFF	1/2:1,2,3,4,.,6:1:1e+06,2e+06,500000:1111,2222,5555:AAAA,BBB,CC:1e+06,500000:1111,5555:A,BB:1e+06,2e+06,3e+06,500000,.,9e+09:1111,2222,3333,5555,.,9999:A,BB,CCC,EEEE,.,FFFFF
 2	1	.	GGGCGTCTCATAGCTGGAGCAATGGCGAGCGCCTGGACAAGGGAGGGGAAGGGGTTCTTATTACTGACGCGGGTAGCCCCTACTGCTGTGTGGTTCCCCTATTTTTTTTTTTTTCTTTTTGAGACGGAGTCTCGCTCTGTCACCCAGGCTGGAGTGCAGTGGCACAATCTCGGCTCACTGCAAGCTCCACCT	ACGT	999	PASS	INDEL;AN=4;AC=2	GT:DP	1/0:1	1/0:1
 2	101	.	ATTTTTTTTTTTTT	ATTTTTTTTTTTTTTT	999	PASS	INDEL;AN=4;AC=4	GT:DP	1/1:1	1/1:1
-2	114	.	TC	TTCC,TTC	999	PASS	INDEL;AN=4;AC=2,2	GT:DP	1/2:1	1/2:1
+2	114	.	TC	TTCC,TTC	999	PASS	INDEL;AN=4;AC=2,2	GT:DP:FGS	1/2:1:A,BB,CCC,EEEE,.,FFFFF	1/2:1:AA,BB,CCC,EEEE,.,FFFFF
 2	115	.	C	T	999	PASS	INDEL;AN=4;AC=4	GT:DP	1/1:1	1/1:1
 20	3	.	GATG	CTATG,GACT	999	PASS	INDEL;AN=4;AC=2,2	GT	2/1	2/1
 20	5	id0001;id0002	TGGG	TAC,TG,TGGGG,AC	.	PASS	INDEL;AN=4;AC=2,2,0,0	GT:PL:DP	1/2:1,2,3,4,.,6,7,.,.,10,11,.,.,.,15:1	1/2:1,2,3,4,.,6,7,.,.,10,11,.,.,.,15:1

diff --git a/test/norm.merge.vcf b/test/norm.merge.vcf
@@ -37,8 +37,8 @@
 1	105	.	TAAACCCTAAA	TAACCCTAAA	999	PASS	INDEL;AN=4;AC=2;DP=19;ISTR=SomeString;XRF=1e+06,500000;XRI=1111,5555;XRS=AAA,DDD;XAF=500000;XAI=5555;XAS=DDD;XGF=1e+06,500000,9e+09;XGI=1111,5555,9999;XGS=A,E,F	GT:PL:DP:FRF:FRI:FRS:FAF:FAI:FAS:FGF:FGI:FGS	0/1:1,4,6:1:1e+06,500000:1111,5555:AAAA,CC:500000:5555:BB:1e+06,500000,9e+09:1111,5555,9999:A,EEEE,FFFFF	0/1:1,4,6:1:1e+06,500000:1111,5555:AAAA,CC:500000:5555:BB:1e+06,500000,9e+09:1111,5555,9999:A,EEEE,FFFFF
 2	1	.	GGGCGTCTCATAGCTGGAGCAATGGCGAGCGCCTGGACAAGGGAGGGGAAGGGGTTCTTATTACTGACGCGGGTAGCCCCTACTGCTGTGTGGTTCCCCTATTTTTTTTTTTTTCTTTTTGAGACGGAGTCTCGCTCTGTCACCCAGGCTGGAGTGCAGTGGCACAATCTCGGCTCACTGCAAGCTCCACCT	ACGT	999	PASS	INDEL;AN=4;AC=2	GT:DP	1/0:1	1/0:1
 2	101	.	ATTTTTTTTTTTTT	ATTTTTTTTTTTTTTT	999	PASS	INDEL;AN=4;AC=4	GT:DP	1/1:1	1/1:1
-2	114	.	TC	TTCC	999	FAIL1	INDEL;AN=4;AC=2	GT:DP	1/0:1	1/0:1
-2	114	.	TC	TTC	999	PASS	INDEL;AN=4;AC=2	GT:DP	0/1:1	0/1:1
+2	114	.	TC	TTCC	999	FAIL1	INDEL;AN=4;AC=2	GT:DP:FGS	1/0:1:A,BB,CCC	1/0:1:AA,BB,CCC
+2	114	.	TC	TTC	999	PASS	INDEL;AN=4;AC=2	GT:DP:FGS	0/1:1:A,EEEE,FFFFF	0/1:1:AA,EEEE,FFFFF
 2	115	.	C	T	999	PASS	INDEL;AN=4;AC=4	GT:DP	1/1:1	1/1:1
 20	3	.	G	CT	999	PASS	INDEL;AN=4;AC=2	GT	0/1	0/1
 20	3	.	GATG	GACT	999	PASS	INDEL;AN=4;AC=2	GT	1/0	1/0

diff --git a/vcfmerge.c b/vcfmerge.c
@@ -858,7 +858,7 @@ int copy_string_field(char *src, int isrc, int src_len, kstring_t *dst, int idst
     }
     if ( ith_src!=isrc ) return -1; // requested field not found
     int end_src = start_src;
-    while ( end_src<src_len && src[end_src]!=',' ) end_src++;
+    while ( end_src<src_len && src[end_src] && src[end_src]!=',' ) end_src++;
 
     int nsrc_cpy = end_src - start_src;
     if ( nsrc_cpy==1 && src[start_src]=='.' ) return 0;   // don't write missing values, dst is already initialized

diff --git a/vcfnorm.c b/vcfnorm.c
@@ -1287,7 +1287,7 @@ static void merge_format_string(args_t *args, bcf1_t **lines, int nlines, bcf_fm
     {
         kstring_t *tmp = &args->tmp_str[i];
         kputsn(tmp->s,tmp->l,&str);
-        for (j=tmp->l; j<max_len; j++) kputc(0,tmp);
+        for (j=tmp->l; j<max_len; j++) kputc('\0',&str);
     }
     args->ntmp_arr2 = str.m;
     args->tmp_arr2  = (uint8_t*)str.s;