added BWA index support

[biopieces.git] / bp_bin / format_genome

diff --git a/bp_bin/format_genome b/bp_bin/format_genome
index af7de5c4ca25f3e18f5a64eeb85baff16a554055..35aa8b3af7354de14d65ef00aa444ebed767e149 100755 (executable)
--- a/bp_bin/format_genome
+++ b/bp_bin/format_genome
@@ -31,6 +31,7 @@ use strict;
 use Maasha::Fasta;
 use Maasha::Biopieces;
 use Maasha::Bowtie;
+use Maasha::BWA;
 use Maasha::NCBI;
 use Maasha::Match;
 use Maasha::UCSC;
@@ -44,7 +45,7 @@ my ( $default, $formats, $options, $in, $out, $record, $data_out, $entry,
 
 $tmp_dir = Maasha::Biopieces::get_tmpdir();
 $default = $ENV{ 'BP_DATA' };
-$formats = 'fasta,blast,vmatch,bowtie,phastcons';
+$formats = 'fasta,blast,vmatch,bowtie,bwa,phastcons';
 
 $options = Maasha::Biopieces::parse_options(
     [
@@ -64,7 +65,7 @@ $genome = $options->{ 'genome' };
 Maasha::Filesys::dir_create_if_not_exists( "$dir/genomes" );
 Maasha::Filesys::dir_create_if_not_exists( "$dir/genomes/$genome" );
 
-if ( grep { $_ =~ /fasta|blast|vmatch|bowtie/i } @{ $options->{ "formats" } } )
+if ( grep { $_ =~ /fasta|blast|vmatch|bowtie|bwa/i } @{ $options->{ "formats" } } )
 {
     if ( -f "$dir/genomes/$genome/fasta/$genome.fna" )
     {
@@ -117,6 +118,7 @@ foreach $format ( @{ $options->{ 'formats' } } )
     elsif ( $format =~ /^blat$/i )      { warn "BLAT FORMAT NOT IMPLEMENTED" }
     elsif ( $format =~ /^vmatch$/i )    { Maasha::Match::vmatch_index( "$genome.fna", $fasta_dir, "$dir/genomes/$genome/vmatch", $tmp_dir ) }
     elsif ( $format =~ /^bowtie$/i )    { Maasha::Bowtie::bowtie_index( "$fasta_dir/$genome.fna", "$dir/genomes/$genome/bowtie", $genome, $options->{ 'verbose' } ) }
+    elsif ( $format =~ /^bwa$/i )       { Maasha::BWA::bwa_index( "$fasta_dir/$genome.fna", "$dir/genomes/$genome/bwa", $genome, $options->{ 'verbose' } ) }
     elsif ( $format =~ /^phastcons$/i ) { Maasha::UCSC::phastcons_index( "$genome.pp", $phastcons_dir ) }
 
     print STDERR qq(done.\n) if $options->{ 'verbose' };