X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bp_bin%2FBGB_intersect;h=d41593e7df2ca5db6849b2597257eb48933e3e58;hb=5de6112b70b59420b245ce636a8b2e3c90acbe00;hp=b6a5bfedc931cc558fc6fc89d75ba4418d9adfde;hpb=b9062acce5ccd2ca2ebb89bec03615748c1cf20a;p=biopieces.git

diff --git a/bp_bin/BGB_intersect b/bp_bin/BGB_intersect
index b6a5bfe..d41593e 100755
--- a/bp_bin/BGB_intersect
+++ b/bp_bin/BGB_intersect
@@ -30,14 +30,14 @@ use warnings;
 use strict;
 use Data::Dumper;
 use Maasha::Biopieces;
-use Maasha::BGB::Common;
+use Maasha::BGB::Track;
 use Maasha::KISS;
 
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $user, $options, $in, $out, $record, @contigs, $contig, $track, @tracks, %hash, $fh1, $fh2, @records );
+my ( $user, $options, $in, $out, $record, @contigs, $contig, $track, @tracks, %hash, $fh1, $fh2, $entries, $entry );
 
 $user    = Maasha::Biopieces::biopiecesrc( "BGB_USER" );
 
@@ -61,15 +61,15 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
     Maasha::Biopieces::put_record( $record, $out );
 }
 
-Maasha::Common::error( qq(Bad user: "$options->{ 'user' }") ) if not grep /^$options->{ 'user' }$/, Maasha::BGB::Common::list_users();
+Maasha::Common::error( qq(Bad user: "$options->{ 'user' }") ) if not grep /^$options->{ 'user' }$/, Maasha::BGB::Track::list_users();
 
-@contigs = Maasha::BGB::Common::list_contigs( $options->{ 'user' }, $options->{ 'clade' }, $options->{ 'genome' }, $options->{ 'assembly' } );
+@contigs = Maasha::BGB::Track::list_contigs( $options->{ 'user' }, $options->{ 'clade' }, $options->{ 'genome' }, $options->{ 'assembly' } );
 
 foreach $contig ( @contigs )
 {
     undef %hash;
 
-    @tracks = Maasha::BGB::Common::list_track_dir( $options->{ 'user' }, $options->{ 'clade' }, $options->{ 'genome' }, $options->{ 'assembly' }, $contig );
+    @tracks = Maasha::BGB::Track::list_track_dir( $options->{ 'user' }, $options->{ 'clade' }, $options->{ 'genome' }, $options->{ 'assembly' }, $contig );
 
     foreach $track ( @tracks )
     {
@@ -82,12 +82,19 @@ foreach $contig ( @contigs )
 
     if ( exists $hash{ '1' } and exists $hash{ '2' } )
     {
+        print STDERR "Intersecting:\n$hash{ '1' } and\n$hash{ '2' }\n\n" if $options->{ 'verbose' };
+
         $fh1 = Maasha::Filesys::file_read_open( "$hash{ '1' }/track_data.kiss" );
         $fh2 = Maasha::Filesys::file_read_open( "$hash{ '2' }/track_data.kiss" );
 
-        @records = Maasha::KISS::kiss_intersect( $fh1, $fh2, $options->{ 'invert' } );
+        $entries = Maasha::KISS::kiss_intersect( $fh1, $fh2, $options->{ 'invert' } );
 
-        map { Maasha::Biopieces::put_record( $_, $out ) } @records;
+        foreach $entry ( @{ $entries } )
+        {
+            if ( $record = Maasha::KISS::kiss2biopiece( $entry ) ) {
+                 Maasha::Biopieces::put_record( $record, $out );
+            }
+        }
     }
 }