Fix handling of skipped lines in bcftools norm -c x

Make normalize_line() report when it skips a line due to a ref
mismatch so that normalize_vcf() knows that it has to go on
to the next one.

Failing to do this caused a crash when the first input line
was skipped because normalize_vcf() attempted to access
data via args->rbuf when nothing had been added.

The input file for the `bcftools norm -c x` did not catch this
because the line it skipped was towards the end of the file.
An extra record has been added at the front, which does trigger
the issue on the original code.

Author: daviesrob

test/norm.vcf

@@ -35,6 +35,7 @@
 ##INFO=<ID=ISTR,Number=1,Type=String,Description="Test String in INFO">
 ##INFO=<ID=END,Number=1,Type=Integer,Description="End position">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	XY00001	XY00002
+1	60	.	A	T	999	PASS	AN=4;AC=4	GT	0/0	0/1
 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	1/2:1,2,3,4,5,6:1:1e+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	1/2:1,2,3,4,5,6:1:1e+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;END=192	GT:DP	1/0:1	1/0:1
 2	101	.	ATTTTTTTTTTTTT	ATTTTTTTTTTTTTTT	999	PASS	INDEL;AN=4;AC=4;END=114	GT:DP	1/1:1	1/1:1

vcfnorm.c

@@ -2328,8 +2328,8 @@ static void destroy_data(args_t *args)
     if ( args->mseq ) free(args->seq);
 }
 
-
-static void normalize_line(args_t *args, bcf1_t *line)
+// return 0 on success, -1 if line was skipped (due to ref mismatch)
+static int normalize_line(args_t *args, bcf1_t *line)
 {
     if ( args->fai )
     {
@@ -2346,7 +2346,7 @@ static void normalize_line(args_t *args, bcf1_t *line)
             if ( ret==ERR_REF_MISMATCH && args->check_ref & CHECK_REF_SKIP )
             {
                 args->nskipped++;
-                return;
+                return -1;
             }
             if ( ret==ERR_DUP_ALLELE )
             {
@@ -2388,9 +2388,10 @@ static void normalize_line(args_t *args, bcf1_t *line)
         }
         if ( !args->filter_pass || args->atomize!=SPLIT ) break;
     }
+    return 0;
 }
 
-// return 0 on success, 1 when done
+// return 0 on success, 1 when done, -1 if line skipped
 static int split_and_normalize(args_t *args)
 {
     if ( !bcf_sr_next_line(args->files) ) return 1;
@@ -2408,8 +2409,7 @@ static int split_and_normalize(args_t *args)
     if ( args->mrows_op!=MROWS_SPLIT || line->n_allele<=2 || !args->filter_pass )
     {
         // normal operation, no splitting
-        normalize_line(args, line);
-        return 0;
+        return normalize_line(args, line);
     }
 
     // any restrictions on variant types to split?
@@ -2418,8 +2418,7 @@ static int split_and_normalize(args_t *args)
         int type = args->mrows_collapse==COLLAPSE_SNPS ? VCF_SNP : VCF_INDEL;
         if ( !(bcf_get_variant_types(line) & type) )
         {
-            normalize_line(args, line);
-            return 0;
+            return normalize_line(args, line);
         }
     }
 
@@ -2428,7 +2427,11 @@ static int split_and_normalize(args_t *args)
 
     int j;
     for (j=0; j<args->ntmp_lines; j++)
-        normalize_line(args, args->tmp_lines[j]);
+    {
+        int ret = normalize_line(args, args->tmp_lines[j]);
+        if (ret)
+            return ret;
+    }
 
     return 0;
 }
@@ -2453,7 +2456,10 @@ static void normalize_vcf(args_t *args)
         int done = 0;
         while (1)
         {
-            done = split_and_normalize(args);
+            do
+            {
+                done = split_and_normalize(args);
+            } while (done < 0); // Skipped line
             if ( done ) break;      // no more lines available
             int i = args->rbuf.f;
             int j = rbuf_last(&args->rbuf);