Add an hclen SAM filter function.

See samtools/samtools#813

(Will close issue with man page update which needs applying there)

sam.c

@@ -1255,6 +1255,26 @@ static int bam_sym_lookup(void *data, char *str, char **end,
         }
         break;
 
+    case 'h':
+        if (memcmp(str, "hclen", 5) == 0) {
+            int hclen = 0;
+            uint32_t *cigar = bam_get_cigar(b);
+            uint32_t ncigar = b->core.n_cigar;
+
+            // left
+            if (ncigar > 0 && bam_cigar_op(cigar[0]) == BAM_CHARD_CLIP)
+                hclen = bam_cigar_oplen(cigar[0]);
+
+            // right
+            if (ncigar > 1 && bam_cigar_op(cigar[ncigar-1]) == BAM_CHARD_CLIP)
+                hclen += bam_cigar_oplen(cigar[ncigar-1]);
+
+            *end = str+5;
+            res->d = hclen;
+            return 0;
+        }
+        break;
+
     case 'l':
         if (memcmp(str, "library", 7) == 0) {
             *end = str+7;

test/sam_filter/filter.tst

@@ -56,3 +56,4 @@ P func4.out   $tv -i 'filter=avg(qual) >= 20 && avg(qual) <= 30' ../ce#1000.sam
 P func5.out   $tv -i 'filter=sclen>=20' ../realn02.sam | grep -E -v '^@'
 P func6.out   $tv -i 'filter=rlen<50'   ../realn02.sam | grep -E -v '^@'
 P func7.out   $tv -i 'filter=qlen>100'   ../realn02.sam | grep -E -v '^@'
+P func8.out   $tv -i 'filter=hclen>=4'   ../c1#clip.sam | grep -E -v '^@'

test/sam_filter/func8.out

@@ -0,0 +1 @@
+s0C	0	c1	3	0	2H6M2H	*	0	0	CCGCGG	******