* samtools-0.1.2-22

 * the field separater is TAB only, now

diff --git a/bam_import.c b/bam_import.c
index 6697a9ffb4e89e4d67e00e8a5917c1c71ea3b405..404da01eb82841c48dd62fb03ec9d7bedff51865 100644 (file)
--- a/bam_import.c
+++ b/bam_import.c
@@ -151,7 +151,7 @@ int sam_read1(tamFile fp, bam_header_t *header, bam1_t *b)
        kstring_t *str = fp->str;
        kstream_t *ks = fp->ks;
 
-       while ((ret = ks_getuntil(fp->ks, 0, str, &dret)) >= 0 && str->s[0] == '@') { // skip header
+       while ((ret = ks_getuntil(fp->ks, KS_SEP_TAB, str, &dret)) >= 0 && str->s[0] == '@') { // skip header
                str->s[str->l] = dret; // note that str->s is NOT null terminated!!
                append_text(header, str);
                if (dret != '\n') {
@@ -161,7 +161,7 @@ int sam_read1(tamFile fp, bam_header_t *header, bam1_t *b)
                }
                ++fp->n_lines;
        }
-       while (ret == 0) ret = ks_getuntil(fp->ks, 0, str, &dret); // special consideration for "\r\n"
+       while (ret == 0) ret = ks_getuntil(fp->ks, KS_SEP_TAB, str, &dret); // special consideration for "\r\n"
        if (ret < 0) return -1;
        ++fp->n_lines;
        doff = 0;
@@ -172,10 +172,10 @@ int sam_read1(tamFile fp, bam_header_t *header, bam1_t *b)
                doff += c->l_qname;
        }
        { // flag, tid, pos, qual
-               ret = ks_getuntil(ks, 0, str, &dret); c->flag = atoi(str->s);
-               ret = ks_getuntil(ks, 0, str, &dret); c->tid = bam_get_tid(header, str->s);
-               ret = ks_getuntil(ks, 0, str, &dret); c->pos = isdigit(str->s[0])? atoi(str->s) - 1 : -1;
-               ret = ks_getuntil(ks, 0, str, &dret); c->qual = isdigit(str->s[0])? atoi(str->s) : 0;
+               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;
                if (ret < 0) return -2;
        }
        { // cigar
@@ -183,7 +183,7 @@ int sam_read1(tamFile fp, bam_header_t *header, bam1_t *b)
                int i, op;
                long x;
                c->n_cigar = 0;
-               if (ks_getuntil(ks, 0, str, &dret) < 0) return -3;
+               if (ks_getuntil(ks, KS_SEP_TAB, str, &dret) < 0) return -3;
                if (str->s[0] != '*') {
                        for (s = str->s; *s; ++s) {
                                if (isalpha(*s)) ++c->n_cigar;
@@ -210,15 +210,15 @@ 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, 0, str, &dret); c->mtid = strcmp(str->s, "=")? bam_get_tid(header, str->s) : c->tid;
-               ret = ks_getuntil(ks, 0, str, &dret); c->mpos = isdigit(str->s[0])? atoi(str->s) - 1 : -1;
-               ret = ks_getuntil(ks, 0, str, &dret); c->isize = (str->s[0] == '-' || isdigit(str->s[0]))? atoi(str->s) : 0;
+               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;
                if (ret < 0) return -4;
        }
        { // seq and qual
                int i;
                uint8_t *p;
-               if (ks_getuntil(ks, 0, str, &dret) < 0) return -5; // seq
+               if (ks_getuntil(ks, KS_SEP_TAB, str, &dret) < 0) return -5; // seq
                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");
@@ -226,7 +226,7 @@ int sam_read1(tamFile fp, bam_header_t *header, bam1_t *b)
                bzero(p, (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, 0, str, &dret) < 0) return -6; // qual
+               if (ks_getuntil(ks, KS_SEP_TAB, str, &dret) < 0) return -6; // qual
                if (c->l_qseq != strlen(str->s))
                        parse_error(fp->n_lines, "sequence and quality are inconsistent");
                p += (c->l_qseq+1)/2;
@@ -235,7 +235,7 @@ int sam_read1(tamFile fp, bam_header_t *header, bam1_t *b)
        }
        doff0 = doff;
        if (dret != '\n' && dret != '\r') { // aux
-               while (ks_getuntil(ks, 0, str, &dret) >= 0) {
+               while (ks_getuntil(ks, KS_SEP_TAB, str, &dret) >= 0) {
                        uint8_t *s, type, key[2];
                        if (str->l < 6 || str->s[2] != ':' || str->s[4] != ':')
                                parse_error(fp->n_lines, "missing colon in auxiliary data");

diff --git a/bamtk.c b/bamtk.c
index 95c206f381f090dcae39ee8afd25b85c44e4f34b..a9d852d49060732f9f543e936c267ab3f9f3fe5d 100644 (file)
--- a/bamtk.c
+++ b/bamtk.c
@@ -3,7 +3,7 @@
 #include "bam.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.2-21"
+#define PACKAGE_VERSION "0.1.2-22"
 #endif
 
 int bam_taf2baf(int argc, char *argv[]);

diff --git a/kseq.h b/kseq.h
index 2875c77577152eb9a20b41fc044288f67eb124ab..e99a8abb2abf7c70ae83d4d3162d994fdbbdec30 100644 (file)
--- a/kseq.h
+++ b/kseq.h
@@ -25,6 +25,8 @@
 
 /* Contact: Heng Li <lh3@sanger.ac.uk> */
 
+/* Last Modified: 12APR2009 */
+
 #ifndef AC_KSEQ_H
 #define AC_KSEQ_H
 
@@ -32,6 +34,10 @@
 #include <string.h>
 #include <stdlib.h>
 
+#define KS_SEP_SPACE 0 // isspace(): \t, \n, \v, \f, \r
+#define KS_SEP_TAB   1 // isspace() && !' '
+#define KS_SEP_MAX   1
+
 #define __KS_TYPE(type_t)                                              \
        typedef struct __kstream_t {                            \
                char *buf;                                                              \
@@ -99,13 +105,16 @@ typedef struct __kstring_t {
                                        if (ks->end == 0) break;                                                        \
                                } else break;                                                                                   \
                        }                                                                                                                       \
-                       if (delimiter) {                                                                                        \
+                       if (delimiter > KS_SEP_MAX) {                                                           \
                                for (i = ks->begin; i < ks->end; ++i)                                   \
                                        if (ks->buf[i] == delimiter) break;                                     \
-                       } else {                                                                                                        \
+                       } else if (delimiter == KS_SEP_SPACE) {                                         \
                                for (i = ks->begin; i < ks->end; ++i)                                   \
                                        if (isspace(ks->buf[i])) break;                                         \
-                       }                                                                                                                       \
+                       } else if (delimiter == KS_SEP_TAB) {                                           \
+                               for (i = ks->begin; i < ks->end; ++i)                                   \
+                                       if (isspace(ks->buf[i]) && ks->buf[i] != ' ') break; \
+                       } else i = 0; /* never come to here! */                                         \
                        if (str->m - str->l < i - ks->begin + 1) {                                      \
                                str->m = str->l + (i - ks->begin) + 1;                                  \
                                kroundup32(str->m);                                                                             \