* samtools-0.1.5-7 (r403)

[samtools.git] / bam_import.c

diff --git a/bam_import.c b/bam_import.c
index 77e324319525b529ac456aad2e9d9f84769e7b2d..c6fbafce979d93560d80265807833a8c9972dca0 100644 (file)
--- a/bam_import.c
+++ b/bam_import.c
@@ -5,6 +5,7 @@
 #include <stdlib.h>
 #include <unistd.h>
 #include <assert.h>
+#include "kstring.h"
 #include "bam.h"
 #include "kseq.h"
 #include "khash.h"
@@ -146,6 +147,62 @@ static inline void append_text(bam_header_t *header, kstring_t *str)
        header->text[header->l_text] = 0;
 }
 
+int sam_header_parse_rg(bam_header_t *h)
+{
+       kstring_t *rgid, *rglib;
+       char *p, *q, *s, *r;
+       int n = 0;
+
+       // free
+       if (h == 0) return 0;
+       bam_strmap_destroy(h->rg2lib); h->rg2lib = 0;
+       if (h->l_text < 3) return 0;
+       // parse @RG lines
+       h->rg2lib = bam_strmap_init();
+       rgid = calloc(1, sizeof(kstring_t));
+       rglib = calloc(1, sizeof(kstring_t));
+       s = h->text;
+       while ((s = strstr(s, "@RG")) != 0) {
+               if (rgid->l && rglib->l) {
+                       bam_strmap_put(h->rg2lib, rgid->s, rglib->s);
+                       ++n;
+               }
+               rgid->l = rglib->l = 0;
+               s += 3;
+               r = s;
+               if ((p = strstr(s, "ID:")) != 0) {
+                       q = p + 3;
+                       for (p = q; *p && *p != '\t' && *p != '\r' && *p != '\n'; ++p);
+                       kputsn(q, p - q, rgid);
+               } else {
+                       fprintf(stderr, "[bam_header_parse] missing ID tag in @RG lines.\n");
+                       break;
+               }
+               if (r < p) r = p;
+               if ((p = strstr(s, "LB:")) != 0) {
+                       q = p + 3;
+                       for (p = q; *p && *p != '\t' && *p != '\r' && *p != '\n'; ++p);
+                       kputsn(q, p - q, rglib);
+               } else {
+                       fprintf(stderr, "[bam_header_parse] missing LB tag in @RG lines.\n");
+                       break;
+               }
+               if (r < p) r = p;
+               s = r + 3;
+       }
+       if (rgid->l && rglib->l) {
+               bam_strmap_put(h->rg2lib, rgid->s, rglib->s);
+               ++n;
+       }
+       free(rgid->s); free(rgid);
+       free(rglib->s); free(rglib);
+       if (n == 0) {
+               bam_strmap_destroy(h->rg2lib);
+               h->rg2lib = 0;
+       }
+       return n;
+}
+
 int sam_header_parse(bam_header_t *h)
 {
        int i;
@@ -183,6 +240,7 @@ int sam_header_parse(bam_header_t *h)
                s = r + 3;
                ++i;
        }
+       sam_header_parse_rg(h);
        return h->n_targets;
 
 header_err_ret:
@@ -301,7 +359,7 @@ int sam_read1(tamFile fp, bam_header_t *header, bam1_t *b)
                if (c->n_cigar && c->l_qseq != (int32_t)bam_cigar2qlen(c, bam1_cigar(b)))
                        parse_error(fp->n_lines, "CIGAR and sequence length are inconsistent");
                p = (uint8_t*)alloc_data(b, doff + c->l_qseq + (c->l_qseq+1)/2) + doff;
-               bzero(p, (c->l_qseq+1)/2);
+               memset(p, 0, (c->l_qseq+1)/2);
                for (i = 0; i < c->l_qseq; ++i)
                        p[i/2] |= bam_nt16_table[(int)str->s[i]] << 4*(1-i%2);
                if (ks_getuntil(ks, KS_SEP_TAB, str, &dret) < 0) return -6; // qual