tid is the chromosome identifier, how to accumulate ?

htsutils.c

@@ -18,6 +18,10 @@ int parseBAM(Settings *props)
     khiter_t k;
     khash_t(pass_hash) *hptr = kh_init(pass_hash);
 
+    int32_t lasttid = 0;
+    int counttid = 0;
+
+
     uint32_t lines = 0;
     uint32_t poly = 0;
 
@@ -27,6 +31,12 @@ int parseBAM(Settings *props)
 
     while (sam_read1(fh_in, header, bam) >= 0)
     {
+        if (lasttid != bam->core.tid)
+        {
+            counttid++;
+        }
+
+
         // filter based on MAPQ
         if (props->mapq > bam->core.qual)
             continue;
@@ -52,6 +62,7 @@ int parseBAM(Settings *props)
         {
             poly++;
 
+
             // add polyBasePosition to hash
             k = kh_put(pass_hash, hptr, polyBasePosition, &absent);
             if (absent)
@@ -66,6 +77,8 @@ int parseBAM(Settings *props)
         //printf("Tail: %d|%d\tHead: %d|%d\tSeq:: ", polyTailA,polyTailT,polyHeadA,polyHeadT);
         //dumpBamSeq(bam);
         //printf("\n");
+        //printf("CHROM: %d\n", bam->core.tid);
+
 
         lines++;
         //if (lines == 1)
@@ -76,7 +89,10 @@ int parseBAM(Settings *props)
     fprintf(stderr, "BAM Lines: %d / %d\n", poly, lines);
 
     // loop through hash and print values
+
     fprintf(stderr, "HASH Size: %d\n", kh_size(hptr));
+
+    /*
     for (k = kh_begin(hptr); k != kh_end(hptr); ++k)
     {
         if (kh_exist(hptr, k))
@@ -86,6 +102,7 @@ int parseBAM(Settings *props)
             printf("%d\t%d\n", key, val);
         }
     }
+    */
 
     kh_destroy(pass_hash, hptr);
     bam_destroy1(bam);