add README

README.md

@@ -0,0 +1,27 @@
+## Getting Started
+
+```sh
+wget https://github.com/lh3/dipcall/releases/download/v0.1/dipcall-0.1_x64-linux.tar.bz2
+tar -jxf dipcall-0.1_x64-linux.tar.bz2
+# for female
+dipcall.kit/run-dipcall prefix hs38.fa pat.fa.gz mat.fa.gz > prefix.mak
+# or for male, requiring PAR regions in BED
+# dipcall.kit/run-dipcall -x dipcall.kit/hs38.PAR.bed prefix hs38.fa pat.fa.gz mat.fa.gz > prefix.mak
+make -j2 -f prefix.mak
+```
+
+## Introduction
+
+Dipcall is a reference-based variant calling pipeline for a pair of phased
+haplotype assemblies. It was originally developed for constructing the
+[syndip][syndip] benchmark dataset and has been applied to other phased
+assemblies, too. Dipcall can call small variants and long INDELs as long as
+they are contained in minimap2 alignment.
+
+If you use dipcall, please cite
+
+> Li H, Bloom JM, Farjoun Y, Fleharty M, Gauthier L, Neale B, MacArthur D
+> (2018) A synthetic-diploid benchmark for accurate variant-calling evaluation.
+> Nat Methods, 15:595-597. [PMID:30013044]
+
+[syndip]: https://github.com/lh3/CHM-eval

dipcall-aux.js

@@ -1,5 +1,7 @@
 #!/usr/bin/env k8
 
+var version = "0.1";
+
 var getopt = function(args, ostr) {
 	var oli; // option letter list index
 	if (typeof(getopt.place) == 'undefined')
@@ -194,12 +196,14 @@ function main(args)
 		print("Commands:");
 		print("  samflt     filter SAM file");
 		print("  vcfpair    convert 2-sample VCF to phased VCF");
+		print("  version    print version number");
 		exit(1);
 	}
 
 	var cmd = args.shift();
 	if (cmd == 'samflt') samflt(args);
 	else if (cmd == 'vcfpair') vcfpair(args);
+	else if (cmd == 'version') print(version);
 	else throw("unrecognized command: " + cmd);
 }
 

run-dipcall

@@ -4,6 +4,8 @@ use strict;
 use warnings;
 use Getopt::Std;
 
+my $version = "0.1";
+
 my %opts = (t=>8);
 getopts("t:d:x:", \%opts);