* added bam_verbose global variable

[samtools.git] / sam_view.c

diff --git a/sam_view.c b/sam_view.c
index fbffdb4f178e3b11c53a735b6b062b7754844e16..a57961476a946831ecffaac2630a77f3ad1f6b21 100644 (file)
--- a/sam_view.c
+++ b/sam_view.c
@@ -6,6 +6,7 @@
 #include "sam_header.h"
 #include "sam.h"
 #include "faidx.h"
+#include "kstring.h"
 #include "khash.h"
 KHASH_SET_INIT_STR(rg)
 
@@ -68,6 +69,37 @@ static inline int __g_skip_aln(const bam_header_t *h, const bam1_t *b)
        return 0;
 }
 
+static char *drop_rg(char *hdtxt, rghash_t h, int *len)
+{
+       char *p = hdtxt, *q, *r, *s;
+       kstring_t str;
+       memset(&str, 0, sizeof(kstring_t));
+       while (1) {
+               int toprint = 0;
+               q = strchr(p, '\n');
+               if (q == 0) q = p + strlen(p);
+               if (q - p < 3) break; // the line is too short; then stop
+               if (strncmp(p, "@RG\t", 4) == 0) {
+                       int c;
+                       khint_t k;
+                       if ((r = strstr(p, "\tID:")) != 0) {
+                               r += 4;
+                               for (s = r; *s != '\0' && *s != '\n' && *s != '\t'; ++s);
+                               c = *s; *s = '\0';
+                               k = kh_get(rg, h, r);
+                               *s = c;
+                               if (k != kh_end(h)) toprint = 1;
+                       }
+               } else toprint = 1;
+               if (toprint) {
+                       kputsn(p, q - p, &str); kputc('\n', &str);
+               }
+               p = q + 1;
+       }
+       *len = str.l;
+       return str.s;
+}
+
 // callback function for bam_fetch() that prints nonskipped records
 static int view_func(const bam1_t *b, void *data)
 {
@@ -164,6 +196,14 @@ int main_samview(int argc, char *argv[])
                ret = 1;
                goto view_end;
        }
+       if (g_rghash) { // FIXME: I do not know what "bam_header_t::n_text" is for...
+               char *tmp;
+               int l;
+               tmp = drop_rg(in->header->text, g_rghash, &l);
+               free(in->header->text);
+               in->header->text = tmp;
+               in->header->l_text = l;
+       }
        if (!is_count && (out = samopen(fn_out? fn_out : "-", out_mode, in->header)) == 0) {
                fprintf(stderr, "[main_samview] fail to open \"%s\" for writing.\n", fn_out? fn_out : "standard output");
                ret = 1;