-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-# Use BWA to map sequences in the stream against a specified genome or index.
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-
-use warnings;
-use strict;
-use Data::Dumper;
-use Maasha::Biopieces;
-use Maasha::Common;
-use Maasha::Fastq;
-use Maasha::SAM;
-
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-
-my ( $options, $in, $out, $index, $tmp_dir, $tmp_fq, $tmp_sai, $tmp_sam, $fh_in, $fh_out, $record, $entry, $line, @fields, $type, @args, $arg );
-
-$options = Maasha::Biopieces::parse_options(
- [
- { long => 'genome', short => 'g', type => 'genome', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
- { long => 'index_name', short => 'i', type => 'string', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
- { long => 'mismatches', short => 'm', type => 'uint', mandatory => 'no', default => 0, allowed => "0,1,2,3", disallowed => undef },
- { long => 'max_hits', short => 'h', type => 'uint', mandatory => 'no', default => undef, allowed => undef, disallowed => 0 },
- { long => 'cpus', short => 'c', type => 'uint', mandatory => 'no', default => 1, allowed => undef, disallowed => 0 },
- ]
-);
-
-Maasha::Common::error( qq(both --index_name and --genome specified) ) if $options->{ "genome" } and $options->{ "index_name" };
-Maasha::Common::error( qq(no --index_name or --genome specified) ) if not $options->{ "genome" } and not $options->{ "index_name" };
-
-$in = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
-$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
-
-if ( defined $options->{ 'genome' } ) {
- $index = "$ENV{ 'BP_DATA' }/genomes/$options->{ 'genome' }/bowtie/$options->{ 'genome' }";
-} elsif (defined $options->{ 'index_name' } ) {
- $index = $options->{ 'index_name' };
-}
-
-$tmp_dir = Maasha::Biopieces::get_tmpdir();
-$tmp_fq = "$tmp_dir/bwa.fq";
-$tmp_sai = "$tmp_dir/bwa.fq.sai";
-$tmp_sam = "$tmp_dir/bwa.fq.sam";
-
-$fh_out = Maasha::Filesys::file_write_open( $tmp_fq );
-
-while ( $record = Maasha::Biopieces::get_record( $in ) )
-{
- if ( $entry = Maasha::Fastq::biopiece2fastq( $record ) ) {
- Maasha::Fastq::put_entry( $entry, $fh_out );
- }
-
- Maasha::Biopieces::put_record( $record, $out );
-}
-
-close $fh_out;
-
-push @args, "-t $options->{ 'cpus' }";
-push @args, "-R $options->{ 'max_hits' }" if $options->{ 'max_hits' };
-
-$arg = join " ", @args;
-
-if ( $options->{ 'verbose' } )
-{
- print STDERR qq(Running: bwa aln $arg $index $tmp_fq > $tmp_sai\n);
- Maasha::Common::run( "bwa", "aln $arg $index $tmp_fq > $tmp_sai" );
- print STDERR qq(Running: bwa samse $index $tmp_sai $tmp_fq > $tmp_sam\n);
- Maasha::Common::run( "bwa", "samse $index $tmp_sai $tmp_fq > $tmp_sam" )
-}
-else
-{
- Maasha::Common::run( "bwa", "aln $arg $index $tmp_fq > $tmp_sai 2> /dev/null" );
- Maasha::Common::run( "bwa", "samse $index $tmp_sai $tmp_fq > $tmp_sam 2> /dev/null" );
-}
-
-$fh_in = Maasha::Filesys::file_read_open( $tmp_sam );
-
-while ( $entry = Maasha::SAM::sam_entry_get( $fh_in ) )
-{
- if ( $record = Maasha::SAM::sam2biopiece( $entry ) ) {
- Maasha::Biopieces::put_record( $record, $out );
- }
-}
-
-close $fh_in;
-
-unlink $tmp_fq;
-unlink $tmp_sai;
-unlink $tmp_sam;
-
-Maasha::Biopieces::close_stream( $in );
-Maasha::Biopieces::close_stream( $out );
-
-