wrapper for bwa-mem
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Heng Li
parent
a5c144db4d
commit
4373a077d5
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#!/usr/bin/env perl
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use strict;
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use warnings;
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use Getopt::Std;
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my %opts = (t=>1, n=>64);
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getopts("SPADsp:R:x:t:", \%opts);
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die('
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Usage: run-bwamem [options] <idxbase> <file1> [file2]
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Options: -p STR prefix for output files [inferred from file1]
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-R STR read group header line such as \'@RG\tID:foo\tSM:bar\' [null]
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-x STR read type: pacbio, ont2d or intractg [default]
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-t INT number of threads [1]
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-P input are paired-end reads if file2 absent
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-A skip HiSeq2000/2500 PE resequencing adapter trimming (via trimadap)
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-D skip duplicate marking (via samblaster)
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-S for SAM/BAM input, don\'t shuffle
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-s sort the output alignment (more RAM)
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Note: File type is determined by the file extension of the first input sequence file.
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Recognized file extensions: fasta, fa, fastq, fq, fasta.gz, fa.gz, fastq.gz,
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fq.gz, sam, sam.gz and bam. SAM/BAM input will be converted to FASTQ.
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') if @ARGV < 2;
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warn("WARNING: many programs require read groups. Please specify with -R if you can.\n") unless defined($opts{R});
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my $idx = $ARGV[0];
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my $exepath = $0 =~/^\S+\/[^\/\s]+/? $0 : &which($0);
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my $root = $0 =~/^(\S+)\/[^\/\s]+/? $1 : undef;
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die "ERROR: failed to locate the 'bwa.kit' directory\n" if !defined($root);
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my $prefix;
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if (defined $opts{p}) {
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$prefix = $opts{p};
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} elsif ($ARGV[1] =~ /^(\S+)\.(fastq|fq|fasta|fa|mag|sam|sam\.gz|mag\.gz|fasta\.gz|fa\.gz|fastq\.gz|fq\.gz|bam)$/) {
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$prefix = $1;
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} else {
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die("ERROR: failed to identify the prefix for output. Please specify -p.\n")
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}
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my $prefix_dir = $prefix =~ /^(\S+)\/[^\/\s]+$/? $1 : ".";
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die("ERROR: directory $prefix_dir is not writable. Please specify a new output prefix with -p.\n") unless (-w $prefix_dir);
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die("ERROR: failed to locate the BWA index. Please run '$root/bwa index -p $idx ref.fa'.\n")
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unless (-f "$idx.bwt" && -f "$idx.pac" && -f "$idx.sa" && -f "$idx.ann" && -f "$idx.amb");
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if (@ARGV >= 3 && $ARGV[1] =~ /\.(bam|sam|sam\.gz)$/) {
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warn("WARNING: for SAM/BAM input, only the first sequence file is used.\n");
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@ARGV = 2;
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}
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if (defined($opts{P}) && @ARGV >= 3) {
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warn("WARNING: option -P is ignored as there are two input sequence files.\n");
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delete $opts{P};
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}
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my $size = 0;
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my $comp_ratio = 3.;
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for my $f (@ARGV[1..$#ARGV]) {
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my @a = stat($f);
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my $s = $a[7];
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$s *= $comp_ratio if $f =~ /\.(gz|bam)$/;
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$size += int($s) + 1;
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}
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my $is_pe = (defined($opts{P}) || @ARGV >= 3)? 1 : 0;
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my $is_sam = $ARGV[1] =~ /\.(sam|sam\.gz)$/? 1 : 0;
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my $is_bam = $ARGV[1] =~ /\.bam$/? 1 : 0;
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my $cmd = '';
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if ($is_sam || $is_bam) {
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my $cmd_sam2bam = $is_sam? "$root/htsbox samview -uS $ARGV[1] \\\n" : "cat $ARGV[1] \\\n";
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my $ntmps = int($size / 4e9) + 1;
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my $cmd_shuf = ($is_bam || $is_sam) && !defined($opts{S})? " | $root/htsbox bamshuf -uOn$ntmps - $prefix.shuf \\\n" : "";
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my $cmd_bam2fq = "";
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$cmd_bam2fq = " | $root/htsbox bam2fq -O " . (defined($opts{P})? "-s $prefix.out.se.fq.gz " : "") . "- \\\n";
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$cmd = $cmd_sam2bam . $cmd_shuf . $cmd_bam2fq;
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} elsif (@ARGV >= 3) {
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$cmd = " | $root/seqtk mergepe $ARGV[1] $ARGV[2] \\\n";
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} else {
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$cmd = "cat $ARGV[1] \\\n";
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}
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$cmd .= " | $root/trimadap \\\n" unless defined($opts{A});
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$cmd .= " | $root/bwa mem -t$opts{t} " . (defined($opts{x})? "-x $opts{x} " : "") . ($is_pe? "-P " : "") . (defined($opts{R})? "-R'$opts{R}' " : "") . "$ARGV[0] - 2> $prefix.log.bwamem \\\n";
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$cmd .= " | $root/samblaster 2> $prefix.log.dedup \\\n" unless defined($opts{D});
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my $has_hla = 0;
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if (-f "$ARGV[0].alt") {
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my $fh;
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open($fh, "$ARGV[0].alt") || die;
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while (<$fh>) {
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$has_hla = 1 if /^HLA-[^\s\*]+\*\d+/;
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}
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close($fh);
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my $hla_pre = $has_hla? "-p $prefix.out " : "";
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$cmd .= " | $root/k8 $root/bwa-postalt.js $hla_pre$ARGV[0].alt \\\n";
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}
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my $t_sort = $opts{t} < 4? $opts{t} : 4;
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$cmd .= defined($opts{s})? " | $root/samtools sort -@ $t_sort -m1G - $prefix.out;\n" : " | gzip -1 > $prefix.out.sam.gz;\n";
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$cmd .= "$root/run-HLA $prefix.out;\n" if ($has_hla);
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print $cmd;
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sub which
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{
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my $file = shift;
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my $path = (@_)? shift : $ENV{PATH};
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return if (!defined($path));
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foreach my $x (split(":", $path)) {
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$x =~ s/\/$//;
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return "$x/$file" if (-x "$x/$file");
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}
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return;
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}
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