code backup

bwa-postalt.js

@@ -207,13 +207,13 @@ function bwa_postalt(args)
 {
 	var c, opt = { a:1, b:4, o:6, e:1, verbose:3, show_pri:false, recover_mapq:true, min_mapq:10, min_sc:90, max_nm_sc:10, show_ev:false, min_pa_ratio:0.8 };
 
-	while ((c = getopt(args, 'Pqev:p:r')) != null) {
+	while ((c = getopt(args, 'Pqev:p:r:')) != null) {
 		if (c == 'v') opt.verbose = parseInt(getopt.arg);
 		else if (c == 'p') opt.pre = getopt.arg;
 		else if (c == 'P') opt.show_pri = true;
 		else if (c == 'q') opt.recover_maq = false;
 		else if (c == 'e') opt.show_ev = true;
-		else if (c == 'r') opt.min_pa_ratio = parseFloat(optarg.arg);
+		else if (c == 'r') opt.min_pa_ratio = parseFloat(getopt.arg);
 	}
 	if (opt.min_pa_ratio > 1.) opt.min_pa_ratio = 1.;
 
@@ -485,20 +485,21 @@ function bwa_postalt(args)
 		if (opt.recover_mapq && n_rpt_lifted == 1 && mapQ > 0) {
 			var l = rpt_lifted;
 			for (var i = 0; i < buf2.length; ++i) {
-				var s = buf2[i];
-				if (l[0] != s[2]) continue; // different chr
-				if (((s[1]&16) != 0) != l[1]) continue; // different strand
+				var s = buf2[i], is_ovlp = true;
+				if (l[0] != s[2]) is_ovlp = false; // different chr
+				if (((s[1]&16) != 0) != l[1]) is_ovlp = false; // different strand
 				var start = s[3] - 1, end = start;
 				while ((m = re_cigar.exec(t[5])) != null)
 					if (m[2] == 'M' || m[2] == 'D' || m[2] == 'N')
 						end += parseInt(m[1]);
+				if (!(start < l[3] && l[2] < end)) is_ovlp = false; // no overlap
 				var om = -1, pa = 10.;
 				for (var j = 11; j < s.length; ++j)
 					if ((m = /^om:i:(\d+)/.exec(s[j])) != null)
 						om = parseInt(m[1]);
 					else if ((m = /^pa:f:(\S+)/.exec(s[j])) != null)
 						pa = parseFloat(m[1]);
-				if (start < l[3] && l[2] < end) { // overlapping the lifted hit
+				if (is_ovlp) { // overlapping the lifted hit
 					if (om > 0) s[4] = om;
 					s[4] = s[4] < mapQ? s[4] : mapQ;
 				} else if (pa < opt.min_pa_ratio) { // not overlapping; has a small pa

bwt.c

@@ -305,10 +305,10 @@ int bwt_smem1a(const bwt_t *bwt, int len, const uint8_t *q, int x, int min_intv,
 		if (q[i] < 4) { // an A/C/G/T base
 			c = 3 - q[i]; // complement of q[i]
 			bwt_extend(bwt, &ik, ok, 0);
+			if (ik.x[2] < max_intv && (i - x > max_len || ik.x[2] == 1)) break;
 			if (ok[c].x[2] != ik.x[2]) { // change of the interval size
 				kv_push(bwtintv_t, *curr, ik);
 				if (ok[c].x[2] < min_intv) break; // the interval size is too small to be extended further
-				if (i - x > max_len && ik.x[2] < max_intv) break;
 			}
 			ik = ok[c]; ik.info = i + 1;
 		} else { // an ambiguous base