* samtools-0.1.5-18 (r423)

[samtools.git] / bam_import.c

diff --git a/bam_import.c b/bam_import.c
index fe9af911f890bdb6a70f56e6206ea6f8923f718b..d004de3d0cb2dafb0dcf5b4e8f45b8e23dcd2b59 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"
@@ -35,6 +36,25 @@ unsigned char bam_nt16_table[256] = {
        15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15
 };
 
+unsigned short bam_char2flag_table[256] = {
+       0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
+       0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
+       0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
+       0,BAM_FREAD1,BAM_FREAD2,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
+       0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
+       BAM_FPROPER_PAIR,0,BAM_FMREVERSE,0, 0,BAM_FMUNMAP,0,0, 0,0,0,0, 0,0,0,0,
+       0,0,0,0, BAM_FDUP,0,BAM_FQCFAIL,0, 0,0,0,0, 0,0,0,0,
+       BAM_FPAIRED,0,BAM_FREVERSE,BAM_FSECONDARY, 0,BAM_FUNMAP,0,0, 0,0,0,0, 0,0,0,0,
+       0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
+       0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
+       0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
+       0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
+       0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
+       0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
+       0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
+       0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0
+};
+
 char *bam_nt16_rev_table = "=ACMGRSVTWYHKDBN";
 
 struct __tamFile_t {
@@ -98,9 +118,10 @@ bam_header_t *sam_header_read2(const char *fn)
        kstring_t *str;
        kh_ref_t *hash;
        khiter_t k;
-       hash = kh_init(ref);
+       if (fn == 0) return 0;
        fp = (strcmp(fn, "-") == 0)? gzdopen(fileno(stdin), "r") : gzopen(fn, "r");
-       assert(fp);
+       if (fp == 0) return 0;
+       hash = kh_init(ref);
        ks = ks_init(fp);
        str = (kstring_t*)calloc(1, sizeof(kstring_t));
        while (ks_getuntil(ks, 0, str, &dret) > 0) {
@@ -146,6 +167,62 @@ 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 +260,7 @@ int sam_header_parse(bam_header_t *h)
                s = r + 3;
                ++i;
        }
+       sam_header_parse_rg(h);
        return h->n_targets;
 
 header_err_ret:
@@ -238,11 +316,26 @@ int sam_read1(tamFile fp, bam_header_t *header, bam1_t *b)
                memcpy(alloc_data(b, doff + c->l_qname) + doff, str->s, c->l_qname);
                doff += c->l_qname;
        }
-       { // flag, tid, pos, qual
-               ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1; c->flag = atoi(str->s);
+       { // flag
+               long flag;
+               char *s;
+               ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1;
+               flag = strtol((char*)str->s, &s, 0);
+               if (*s) { // not the end of the string
+                       flag = 0;
+                       for (s = str->s; *s; ++s)
+                               flag |= bam_char2flag_table[(int)*s];
+               }
+               c->flag = flag;
+       }
+       { // tid, pos, qual
                ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1; c->tid = bam_get_tid(header, str->s);
-               if (c->tid < 0 && strcmp(str->s, "*"))
-                       fprintf(stderr, "[sam_read1] reference '%s' is recognized as '*'.\n", str->s);
+               if (c->tid < 0 && strcmp(str->s, "*")) {
+                       if (header->n_targets == 0) {
+                               fprintf(stderr, "[sam_read1] missing header? Abort!\n");
+                               exit(1);
+                       } else fprintf(stderr, "[sam_read1] reference '%s' is recognized as '*'.\n", str->s);
+               }
                ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1; c->pos = isdigit(str->s[0])? atoi(str->s) - 1 : -1;
                ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1; c->qual = isdigit(str->s[0])? atoi(str->s) : 0;
                if (ret < 0) return -2;
@@ -297,7 +390,7 @@ 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
@@ -395,9 +488,11 @@ int sam_read1(tamFile fp, bam_header_t *header, bam1_t *b)
 tamFile sam_open(const char *fn)
 {
        tamFile fp;
+       gzFile gzfp = (strcmp(fn, "-") == 0)? gzdopen(fileno(stdin), "r") : gzopen(fn, "r");
+       if (gzfp == 0) return 0;
        fp = (tamFile)calloc(1, sizeof(struct __tamFile_t));
        fp->str = (kstring_t*)calloc(1, sizeof(kstring_t));
-       fp->fp = (strcmp(fn, "-") == 0)? gzdopen(fileno(stdin), "r") : gzopen(fn, "r");
+       fp->fp = gzfp;
        fp->ks = ks_init(fp->fp);
        return fp;
 }