* This revision is SERIOUSLY BUGGY. Please NOT use it.

[samtools.git] / sam_view.c

diff --git a/sam_view.c b/sam_view.c
index 685784ddc95526626af4d7247aa734e986786b06..105b532b4d562e04a652af43761a23a92572d06d 100644 (file)
--- a/sam_view.c
+++ b/sam_view.c
@@ -2,7 +2,9 @@
 #include <string.h>
 #include <stdio.h>
 #include <unistd.h>
+#include "sam_header.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;
@@ -16,7 +18,7 @@ static inline int __g_skip_aln(const bam_header_t *h, const bam1_t *b)
                if (s) {
                        if (g_rg && strcmp(g_rg, (char*)(s + 1)) == 0) return 0;
                        if (g_library) {
-                               const char *p = bam_strmap_get(h->rg2lib, (char*)(s + 1));
+                               const char *p = sam_tbl_get(h->rg2lib, (const char*)(s + 1));
                                return (p && strcmp(p, g_library) == 0)? 0 : 1;
                        } return 1;
                } else return 1;
@@ -38,11 +40,11 @@ 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 +61,7 @@ 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 +77,17 @@ 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 == 0 && fn_ref) 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 the 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 +125,7 @@ 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;
@@ -132,8 +141,9 @@ static int usage(int is_long_help)
        fprintf(stderr, "         -S       input is SAM\n");
        fprintf(stderr, "         -u       uncompressed BAM output (force -b)\n");
        fprintf(stderr, "         -x       output FLAG in HEX (samtools-C specific)\n");
-       fprintf(stderr, "         -X       output FLAG in stirng (samtools-C specific)\n");
+       fprintf(stderr, "         -X       output FLAG in string (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 +163,7 @@ 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\