From eef1cee9b748a81a1b568a917432cb882000de75 Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Sat, 1 Dec 2018 18:53:03 -0500
Subject: [PATCH] r893: added paftools.js vcfpair

---
 misc/paftools.js | 102 ++++++++++++++++++++++++++++++++++++++++++++++-
 1 file changed, 101 insertions(+), 1 deletion(-)

diff --git a/misc/paftools.js b/misc/paftools.js
index 518102c..744e877 100755
--- a/misc/paftools.js
+++ b/misc/paftools.js
@@ -1,6 +1,6 @@
 #!/usr/bin/env k8
 
-var paftools_version = '2.14-r887-dirty';
+var paftools_version = '2.14-r893-dirty';
 
 /*****************************
  ***** Library functions *****
@@ -1197,6 +1197,105 @@ function paf_bedcov(args)
 	warn("# target bases overlapping regions: " + hit_len + ' (' + (100.0 * hit_len / tot_len).toFixed(2) + '%)');
 }
 
+function paf_vcfpair(args)
+{
+	var c, is_male = false, sample = 'syndip', hgver = null;
+	var PAR = { '37':[[0, 2699520], [154931043, 155260560]] };
+	while ((c = getopt(args, "ms:g:")) != null) {
+		if (c == 'm') is_male = true;
+		else if (c == 's') sample = getopt.arg;
+		else if (c == 'g') hgver = getopt.arg;
+	}
+	if (is_male && (hgver == null || PAR[hgver] == null))
+		throw("for a male, -g must be specified to properly handle PARs on chrX");
+
+	if (getopt.ind == args.length) {
+		print("Usage: paftools.js vcfpair [options] <in.pair.vcf>");
+		print("Options:");
+		print("  -m       the sample is male");
+		print("  -g STR   human genome version '37' []");
+		print("  -s STR   sample name [" + sample + "]");
+		exit(1);
+	}
+
+	var re_ctg = is_male? /^(chr)?([0-9]+|X|Y)$/ : /^(chr)?([0-9]+|X)$/;
+	var label = ['1', '2'];
+	var buf = new Bytes();
+	var file = args[getopt.ind] == '-'? new File() : new File(args[getopt.ind]);
+	while (file.readline(buf) >= 0) {
+		var m, line = buf.toString();
+		if (line.charAt(0) == '#') {
+			if (/^##(source|reference)=/.test(line)) continue;
+			if ((m = /^##contig=.*ID=([^\s,]+)/.exec(line)) != null) {
+				if (!re_ctg.test(m[1])) continue;
+			} else if (/^#CHROM/.test(line)) {
+				var t = line.split("\t");
+				--t.length;
+				t[t.length-1] = sample;
+				line = t.join("\t");
+				print('##FILTER=<ID=HET1,Description="Heterozygous in the first haplotype">');
+				print('##FILTER=<ID=HET2,Description="Heterozygous in the second haplotype">');
+				print('##FILTER=<ID=GAP1,Description="Uncalled in the first haplotype">');
+				print('##FILTER=<ID=GAP2,Description="Uncalled in the second haplotype">');
+			}
+			print(line);
+			continue;
+		}
+		var t = line.split("\t");
+		if (!re_ctg.test(t[0])) continue;
+		var GT = null, AD = null, FILTER = [], HT = [null, null];
+		for (var i = 0; i < 2; ++i) {
+			if ((m = /^(\.|[0-9]+)\/(\.|[0-9]+):(\S+)/.exec(t[9+i])) == null) {
+				warn(line);
+				throw Error("malformatted VCF");
+			}
+			var s = m[3].split(",");
+			if (AD == null) {
+				AD = [];
+				for (var j = 0; j < s.length; ++j)
+					AD[j] = 0;
+			}
+			for (var j = 0; j < s.length; ++j)
+				AD[j] += parseInt(s[j]);
+			if (m[1] == '.') {
+				FILTER.push('GAP' + label[i]);
+				HT[i] = '.';
+			} else if (m[1] != m[2]) {
+				FILTER.push('HET' + label[i]);
+				HT[i] = '.';
+			} else HT[i] = m[1];
+		}
+		--t.length;
+		// test if this is in a haploid region
+		var hap = 0, st = parseInt(t[1]), en = st + t[3].length;
+		if (is_male) {
+			if (/^(chr)?X/.test(t[0])) {
+				if (hgver != null && PAR[hgver] != null) {
+					var r = PAR[hgver], in_par = false;
+					for (var i = 0; i < r.length; ++i)
+						if (r[i][0] <= st && en <= r[i][1])
+							in_par = true;
+					hap = in_par? 0 : 2;
+				}
+			} else if (/^(chr)?Y/.test(t[0])) {
+				hap = 1;
+			}
+		}
+		// special treatment for haploid regions
+		if (hap > 0 && FILTER.length == 1) {
+			if ((hap == 2 && FILTER[0] == "GAP1") || (hap == 1 && FILTER[0] == "GAP2"))
+				FILTER.length = 0;
+		}
+		// update VCF
+		t[5] = 30; // fake QUAL
+		t[6] = FILTER.length? FILTER.join(";") : ".";
+		t[9] = HT.join("|") + ":" + AD.join(",");
+		print(t.join("\t"));
+	}
+	file.close();
+	buf.destroy();
+}
+
 /**********************
  * Conversion related *
  **********************/
@@ -2396,6 +2495,7 @@ function main(args)
 	else if (cmd == 'asmstat') paf_asmstat(args);
 	else if (cmd == 'asmgene') paf_asmgene(args);
 	else if (cmd == 'liftover' || cmd == 'liftOver') paf_liftover(args);
+	else if (cmd == 'vcfpair') paf_vcfpair(args);
 	else if (cmd == 'call') paf_call(args);
 	else if (cmd == 'mapeval') paf_mapeval(args);
 	else if (cmd == 'bedcov') paf_bedcov(args);