* samtools-0.1.5-16 (r421)

 * in view and pileup, load header from FASTA index if the input is SAM.

diff --git a/bam_import.c b/bam_import.c
index a49f9e83a248f85100341c9f0c6b124b971c2e7a..d004de3d0cb2dafb0dcf5b4e8f45b8e23dcd2b59 100644 (file)
--- a/bam_import.c
+++ b/bam_import.c
@@ -118,9 +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) {

diff --git a/bam_plcmd.c b/bam_plcmd.c
index 5d5506fb5630a088f692e6f0c64e8b827f6a5329..391767ab134833f5dcc5ea914866fd7f10b97718 100644 (file)
--- a/bam_plcmd.c
+++ b/bam_plcmd.c
@@ -330,7 +330,7 @@ int bam_pileup(int argc, char *argv[])
                fprintf(stderr, "        -i        only show lines/consensus with indels\n");
                fprintf(stderr, "        -m INT    filtering reads with bits in INT [%d]\n", d->mask);
                fprintf(stderr, "        -M INT    cap mapping quality at INT [%d]\n", d->c->cap_mapQ);
-               fprintf(stderr, "        -t FILE   list of reference sequences (assume the input is in SAM)\n");
+               fprintf(stderr, "        -t FILE   list of reference sequences (force -S)\n");
                fprintf(stderr, "        -l FILE   list of sites at which pileup is output\n");
                fprintf(stderr, "        -f FILE   reference sequence in the FASTA format\n\n");
                fprintf(stderr, "        -c        output the maq consensus sequence\n");
@@ -356,6 +356,8 @@ int bam_pileup(int argc, char *argv[])
        }
        if (d->fai == 0 && (d->format & (BAM_PLF_CNS|BAM_PLF_INDEL_ONLY)))
                fprintf(stderr, "[bam_pileup] indels will not be called when -f is absent.\n");
+       if (fn_fa && is_SAM && fn_list == 0) fn_list = samfaipath(fn_fa);
+
        {
                samfile_t *fp;
                fp = is_SAM? samopen(argv[optind], "r", fn_list) : samopen(argv[optind], "rb", 0);

diff --git a/bamtk.c b/bamtk.c
index daae6ab2fd967dd1e4e0303d82b4e0e4fb299c4f..234f465116261df4e10fa0ae01e7ca0184671d65 100644 (file)
--- a/bamtk.c
+++ b/bamtk.c
@@ -4,7 +4,7 @@
 #include "bam.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.5-15 (r419)"
+#define PACKAGE_VERSION "0.1.5-16 (r421)"
 #endif
 
 int bam_taf2baf(int argc, char *argv[]);

diff --git a/misc/samtools.pl b/misc/samtools.pl
index 0b0e9d2d378e4a5965c2ecea9a4c570fa6983112..06c24dc6230c1d9baef40387574c02c9cda26d63 100755 (executable)
--- a/misc/samtools.pl
+++ b/misc/samtools.pl
@@ -229,6 +229,7 @@ sub unique {
        print $_ if (/^\@/);
        $score = $1 if (/AS:i:(\d+)/);
        my @t = split("\t");
+       next if (@t < 11);
        if ($score < 0) { # AS tag is unavailable
          my $cigar = $t[5];
          my ($mm, $go, $ge) = (0, 0, 0);

diff --git a/sam.c b/sam.c
index e8e742c80649f583b16de8fb7b1519eca9a5af10..b8e7350f3bebd70cd043bf54de02c77315092ee9 100644 (file)
--- a/sam.c
+++ b/sam.c
@@ -1,4 +1,6 @@
 #include <string.h>
+#include <unistd.h>
+#include "faidx.h"
 #include "sam.h"
 
 #define TYPE_BAM  1
@@ -152,3 +154,22 @@ int sampileup(samfile_t *fp, int mask, bam_pileup_f func, void *func_data)
        bam_destroy1(b);
        return 0;
 }
+
+char *samfaipath(const char *fn_ref)
+{
+       char *fn_list = 0;
+       fn_list = calloc(strlen(fn_ref) + 5, 1);
+       strcat(strcpy(fn_list, fn_ref), ".fai");
+       if (access(fn_list, R_OK) == -1) { // fn_list is unreadable
+               if (access(fn_ref, R_OK) == -1) {
+                       fprintf(stderr, "[samfaipath] fail to read file %s.\n", fn_ref);
+               } else {
+                       fprintf(stderr, "[samfaipath] build FASTA index...\n");
+                       if (fai_build(fn_ref) == -1) {
+                               fprintf(stderr, "[samfaipath] fail to build FASTA index.\n");
+                               free(fn_list); fn_list = 0;
+                       }
+               }
+       }
+       return fn_list;
+}

diff --git a/sam.h b/sam.h
index f06439b78a9510ea3e5e684af55ea7c64c9d77a6..0b87194e05670ba287c9debe6e22c4d79a54e353 100644 (file)
--- a/sam.h
+++ b/sam.h
@@ -51,7 +51,8 @@ extern "C" {
          @param aux auxiliary data; if mode[0]=='w', aux points to
          bam_header_t; if strcmp(mode, "rb")!=0 and @SQ header lines in SAM
          are absent, aux points the file name of the list of the reference;
-         aux is not used otherwise.
+         aux is not used otherwise. If @SQ header lines are present in SAM,
+         aux is not used, either.
 
          @return       SAM/BAM file handler
         */
@@ -88,6 +89,8 @@ extern "C" {
         */
        int sampileup(samfile_t *fp, int mask, bam_pileup_f func, void *data);
 
+       char *samfaipath(const char *fn_ref);
+
 #ifdef __cplusplus
 }
 #endif

diff --git a/sam_view.c b/sam_view.c
index 685784ddc95526626af4d7247aa734e986786b06..1776b8eb586b99b3123b8dffaeb39849179d30cc 100644 (file)
--- a/sam_view.c
+++ b/sam_view.c
@@ -3,6 +3,7 @@
 #include <stdio.h>
 #include <unistd.h>
 #include "sam.h"
+#include "faidx.h"
 
 static int g_min_mapQ = 0, g_flag_on = 0, g_flag_off = 0;
 static char *g_library, *g_rg;
@@ -38,11 +39,11 @@ int main_samview(int argc, char *argv[])
        int c, is_header = 0, is_header_only = 0, is_bamin = 1, ret = 0, is_uncompressed = 0, is_bamout = 0;
        int of_type = BAM_OFDEC, is_long_help = 0;
        samfile_t *in = 0, *out = 0;
-       char in_mode[5], out_mode[5], *fn_out = 0, *fn_list = 0;
+       char in_mode[5], out_mode[5], *fn_out = 0, *fn_list = 0, *fn_ref = 0;
 
        /* parse command-line options */
        strcpy(in_mode, "r"); strcpy(out_mode, "w");
-       while ((c = getopt(argc, argv, "Sbt:hHo:q:f:F:ul:r:xX?")) >= 0) {
+       while ((c = getopt(argc, argv, "Sbt:hHo:q:f:F:ul:r:xX?T:")) >= 0) {
                switch (c) {
                case 'S': is_bamin = 0; break;
                case 'b': is_bamout = 1; break;
@@ -59,6 +60,7 @@ int main_samview(int argc, char *argv[])
                case 'x': of_type = BAM_OFHEX; break;
                case 'X': of_type = BAM_OFSTR; break;
                case '?': is_long_help = 1; break;
+               case 'T': fn_ref = strdup(optarg); is_bamin = 0; break;
                default: return usage(is_long_help);
                }
        }
@@ -74,11 +76,19 @@ int main_samview(int argc, char *argv[])
        if (is_uncompressed) strcat(out_mode, "u");
        if (argc == optind) return usage(is_long_help);
 
+       // generate the fn_list if necessary
+       if (fn_list && fn_ref) {
+               fprintf(stderr, "[main_samview] both -t and -T are applied. -T is ignored.\n");
+       } else fn_list = samfaipath(fn_ref);
        // open file handlers
        if ((in = samopen(argv[optind], in_mode, fn_list)) == 0) {
                fprintf(stderr, "[main_samview] fail to open file for reading.\n");
                goto view_end;
        }
+       if (in->header == 0) {
+               fprintf(stderr, "[main_samview] fail to read SAM header.\n");
+               goto view_end;
+       }
        if ((out = samopen(fn_out? fn_out : "-", out_mode, in->header)) == 0) {
                fprintf(stderr, "[main_samview] fail to open file for writing.\n");
                goto view_end;
@@ -116,7 +126,7 @@ int main_samview(int argc, char *argv[])
 
 view_end:
        // close files, free and return
-       free(fn_list); free(fn_out); free(g_library); free(g_rg);
+       free(fn_list); free(fn_ref); free(fn_out); free(g_library); free(g_rg);
        samclose(in);
        samclose(out);
        return ret;
@@ -134,6 +144,7 @@ static int usage(int is_long_help)
        fprintf(stderr, "         -x       output FLAG in HEX (samtools-C specific)\n");
        fprintf(stderr, "         -X       output FLAG in stirng (samtools-C specific)\n");
        fprintf(stderr, "         -t FILE  list of reference names and lengths (force -S) [null]\n");
+       fprintf(stderr, "         -T FILE  reference sequence file (force -S) [null]\n");
        fprintf(stderr, "         -o FILE  output file name [stdout]\n");
        fprintf(stderr, "         -f INT   required flag, 0 for unset [0]\n");
        fprintf(stderr, "         -F INT   filtering flag, 0 for unset [0]\n");
@@ -153,7 +164,7 @@ static int usage(int is_long_help)
      corresponding sequence length. The `.fai' file generated by `faidx'\n\
      can be used here. This file may be empty if reads are unaligned.\n\
 \n\
-  2. SAM->BAM conversion: `samtools view -bt ref.fa.fai in.sam.gz'.\n\
+  2. SAM->BAM conversion: `samtools view -bT ref.fa in.sam.gz'.\n\
 \n\
   3. BAM->SAM conversion: `samtools view in.bam'.\n\
 \n\