* samtools-0.1.3-11 (r258)

[samtools.git] / bam_import.c

diff --git a/bam_import.c b/bam_import.c
index 746dc5bbbde0415911794b28d666a4a53ef86be8..9daa29f42a1676077b29f3f63ab7a7027896dbad 100644 (file)
--- a/bam_import.c
+++ b/bam_import.c
@@ -146,22 +146,27 @@ static inline void append_text(bam_header_t *header, kstring_t *str)
 }
 int sam_read1(tamFile fp, bam_header_t *header, bam1_t *b)
 {
-       int ret, doff, doff0, dret;
+       int ret, doff, doff0, dret, z = 0;
        bam1_core_t *c = &b->core;
        kstring_t *str = fp->str;
        kstream_t *ks = fp->ks;
 
        while ((ret = ks_getuntil(fp->ks, KS_SEP_TAB, str, &dret)) >= 0 && str->s[0] == '@') { // skip header
+               z += str->l + 1;
                str->s[str->l] = dret; // note that str->s is NOT null terminated!!
                append_text(header, str);
                if (dret != '\n') {
                        ret = ks_getuntil(fp->ks, '\n', str, &dret);
+                       z += str->l + 1;
                        str->s[str->l] = '\n'; // NOT null terminated!!
                        append_text(header, str);
                }
                ++fp->n_lines;
        }
-       while (ret == 0) ret = ks_getuntil(fp->ks, KS_SEP_TAB, str, &dret); // special consideration for "\r\n"
+       while (ret == 0) { // special consideration for "\r\n" and empty lines
+               ret = ks_getuntil(fp->ks, KS_SEP_TAB, str, &dret);
+               if (ret >= 0) z += str->l + 1;
+       }
        if (ret < 0) return -1;
        ++fp->n_lines;
        doff = 0;
@@ -172,10 +177,10 @@ int sam_read1(tamFile fp, bam_header_t *header, bam1_t *b)
                doff += c->l_qname;
        }
        { // flag, tid, pos, qual
-               ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); c->flag = atoi(str->s);
-               ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); c->tid = bam_get_tid(header, str->s);
-               ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); c->pos = isdigit(str->s[0])? atoi(str->s) - 1 : -1;
-               ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); c->qual = isdigit(str->s[0])? atoi(str->s) : 0;
+               ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1; c->flag = atoi(str->s);
+               ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1; c->tid = bam_get_tid(header, 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;
        }
        { // cigar
@@ -184,6 +189,7 @@ int sam_read1(tamFile fp, bam_header_t *header, bam1_t *b)
                long x;
                c->n_cigar = 0;
                if (ks_getuntil(ks, KS_SEP_TAB, str, &dret) < 0) return -3;
+               z += str->l + 1;
                if (str->s[0] != '*') {
                        for (s = str->s; *s; ++s) {
                                if (isalpha(*s)) ++c->n_cigar;
@@ -210,15 +216,19 @@ int sam_read1(tamFile fp, bam_header_t *header, bam1_t *b)
                } else c->bin = bam_reg2bin(c->pos, c->pos + 1);
        }
        { // mtid, mpos, isize
-               ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); c->mtid = strcmp(str->s, "=")? bam_get_tid(header, str->s) : c->tid;
-               ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); c->mpos = isdigit(str->s[0])? atoi(str->s) - 1 : -1;
-               ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); c->isize = (str->s[0] == '-' || isdigit(str->s[0]))? atoi(str->s) : 0;
+               ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1;
+               c->mtid = strcmp(str->s, "=")? bam_get_tid(header, str->s) : c->tid;
+               ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1;
+               c->mpos = isdigit(str->s[0])? atoi(str->s) - 1 : -1;
+               ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1;
+               c->isize = (str->s[0] == '-' || isdigit(str->s[0]))? atoi(str->s) : 0;
                if (ret < 0) return -4;
        }
        { // seq and qual
                int i;
                uint8_t *p;
                if (ks_getuntil(ks, KS_SEP_TAB, str, &dret) < 0) return -5; // seq
+               z += str->l + 1;
                c->l_qseq = strlen(str->s);
                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");
@@ -227,6 +237,7 @@ int sam_read1(tamFile fp, bam_header_t *header, bam1_t *b)
                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
+               z += str->l + 1;
                if (strcmp(str->s, "*") && c->l_qseq != strlen(str->s))
                        parse_error(fp->n_lines, "sequence and quality are inconsistent");
                p += (c->l_qseq+1)/2;
@@ -238,6 +249,7 @@ int sam_read1(tamFile fp, bam_header_t *header, bam1_t *b)
        if (dret != '\n' && dret != '\r') { // aux
                while (ks_getuntil(ks, KS_SEP_TAB, str, &dret) >= 0) {
                        uint8_t *s, type, key[2];
+                       z += str->l + 1;
                        if (str->l < 6 || str->s[2] != ':' || str->s[4] != ':')
                                parse_error(fp->n_lines, "missing colon in auxiliary data");
                        key[0] = str->s[0]; key[1] = str->s[1];
@@ -313,7 +325,7 @@ int sam_read1(tamFile fp, bam_header_t *header, bam1_t *b)
        }
        b->l_aux = doff - doff0;
        b->data_len = doff;
-       return 0;
+       return z;
 }
 
 tamFile sam_open(const char *fn)
@@ -336,41 +348,3 @@ void sam_close(tamFile fp)
                free(fp);
        }
 }
-
-static void taf2baf_core(const char *fntaf, const char *fnbaf, bam_header_t *header)
-{
-       bamFile fpbaf;
-       bam1_t *b;
-       tamFile fp;
-       int ret;
-
-       b = (bam1_t*)calloc(1, sizeof(bam1_t));
-       fpbaf = (strcmp(fnbaf, "-") == 0)? bam_dopen(fileno(stdout), "w") : bam_open(fnbaf, "w");
-       fp = sam_open(fntaf);
-       ret = sam_read1(fp, header, b);
-       bam_header_write(fpbaf, header);
-       if (ret >= 0) {
-               bam_write1(fpbaf, b);
-               while (sam_read1(fp, header, b) >= 0) bam_write1(fpbaf, b);
-       }
-       bam_close(fpbaf);
-       free(b->data); free(b);
-       sam_close(fp);
-}
-
-int bam_taf2baf(int argc, char *argv[])
-{
-       int c;
-       bam_header_t *header;
-
-       while ((c = getopt(argc, argv, "")) >= 0) {
-       }
-       if (optind + 3 > argc) {
-               fprintf(stderr, "Usage: bamtk import <in.ref_list> <in.sam> <out.bam>\n");
-               return 1;
-       }
-       header = sam_header_read2(argv[optind]);
-       taf2baf_core(argv[optind+1], argv[optind+2], header);
-       bam_header_destroy(header);
-       return 0;
-}