From c6822593fba7a4ae2a86d269450fa1f3f1a93417 Mon Sep 17 00:00:00 2001
From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Wed, 30 Sep 2009 07:55:35 +0000
Subject: [PATCH] fixed bug in get_genome_seq

git-svn-id: http://biopieces.googlecode.com/svn/trunk@688 74ccb610-7750-0410-82ae-013aeee3265d
---
 bp_bin/get_genome_seq   | 27 ++++++++++++---------------
 code_perl/Maasha/SAM.pm |  2 ++
 2 files changed, 14 insertions(+), 15 deletions(-)

diff --git a/bp_bin/get_genome_seq b/bp_bin/get_genome_seq
index 0e8d1f7..e219c51 100755
--- a/bp_bin/get_genome_seq
+++ b/bp_bin/get_genome_seq
@@ -28,6 +28,7 @@
 
 use warnings;
 use strict;
+use Data::Dumper;
 use Maasha::Biopieces;
 use Maasha::Filesys;
 use Maasha::Fasta;
@@ -38,7 +39,7 @@ use Maasha::Seq;
 
 
 my ( $options, $in, $out, $record, $genome_file, $index_file, $fh, $genome,
-     $beg, $end, $len, $index_beg, $index_len, @begs, @lens, $index, $seq, $i, %lookup_hash );
+     $beg, $end, $len, $index_beg, $index_len, @begs, @lens, $index, $seq, $i );
 
 $options = Maasha::Biopieces::parse_options(
     [
@@ -66,13 +67,9 @@ if ( $options->{ "genome" } )
     $fh          = Maasha::Filesys::file_read_open( $genome_file );
     $index       = Maasha::Fasta::index_retrieve( $index_file );
 
-    shift @{ $index }; # Get rid of the file size info
-
-    map { $lookup_hash{ $_->[ 0 ] } = [ $_->[ 1 ], $_->[ 2 ] ] } @{ $index };
-
-    if ( defined $options->{ "chr" } and exists $lookup_hash{ $options->{ "chr" } } and defined $options->{ "beg" } and ( defined $options->{ "end" } or defined $options->{ "len" } ) )
+    if ( defined $options->{ "chr" } and exists $index->{ $options->{ "chr" } } and defined $options->{ "beg" } and ( defined $options->{ "end" } or defined $options->{ "len" } ) )
     {
-        ( $index_beg, $index_len ) = @{ $lookup_hash{ $options->{ "chr" } } };
+        ( $index_beg, $index_len ) = @{ $index->{ $options->{ "chr" } } };
 
         $beg = $index_beg + $options->{ "beg" } - 1;
 
@@ -112,30 +109,30 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
 {
     if ( $options->{ "genome" } and not $record->{ "SEQ" } )
     {
-        if ( $record->{ "REC_TYPE" } eq "BED" and exists $lookup_hash{ $record->{ "CHR" } } )
+        if ( $record->{ "REC_TYPE" } eq "BED" and exists $index->{ $record->{ "CHR" } } )
         {
-            ( $index_beg, $index_len ) = @{ $lookup_hash{ $record->{ "CHR" } } };
+            ( $index_beg, $index_len ) = @{ $index->{ $record->{ "CHR" } } };
         
             $beg = $record->{ "CHR_BEG" } + $index_beg;
             $len = $record->{ "CHR_END" } - $record->{ "CHR_BEG" } + 1;
         }
-        elsif ( $record->{ "REC_TYPE" } eq "PSL" and exists $lookup_hash{ $record->{ "S_ID" } } )
+        elsif ( $record->{ "REC_TYPE" } eq "PSL" and exists $index->{ $record->{ "S_ID" } } )
         {
-            ( $index_beg, $index_len ) = @{ $lookup_hash{ $record->{ "S_ID" } } };
+            ( $index_beg, $index_len ) = @{ $index->{ $record->{ "S_ID" } } };
         
             $beg = $record->{ "S_BEG" } + $index_beg;
             $len = $record->{ "S_END" } - $record->{ "S_BEG" } + 1;
         }
-        elsif ( $record->{ "REC_TYPE" } eq "VMATCH" and exists $lookup_hash{ $record->{ "S_ID" } } )
+        elsif ( $record->{ "REC_TYPE" } eq "VMATCH" and exists $index->{ $record->{ "S_ID" } } )
         {
-            ( $index_beg, $index_len ) = @{ $lookup_hash{ $record->{ "S_ID" } } };
+            ( $index_beg, $index_len ) = @{ $index->{ $record->{ "S_ID" } } };
         
             $beg = $record->{ "S_BEG" } + $index_beg;
             $len = $record->{ "S_END" } - $record->{ "S_BEG" } + 1;
         }
-        elsif ( $record->{ "REC_TYPE" } eq "BLAST" and exists $lookup_hash{ $record->{ "S_ID" } } )
+        elsif ( $record->{ "REC_TYPE" } eq "BLAST" and exists $index->{ $record->{ "S_ID" } } )
         {
-            ( $index_beg, $index_len ) = @{ $lookup_hash{ $record->{ "S_ID" } } };
+            ( $index_beg, $index_len ) = @{ $index->{ $record->{ "S_ID" } } };
         
             $beg = $record->{ "S_BEG" } + $index_beg;
             $len = $record->{ "S_END" } - $record->{ "S_BEG" } + 1;
diff --git a/code_perl/Maasha/SAM.pm b/code_perl/Maasha/SAM.pm
index 79f697d..6a53274 100644
--- a/code_perl/Maasha/SAM.pm
+++ b/code_perl/Maasha/SAM.pm
@@ -116,6 +116,8 @@ sub sam2biopiece
     $record->{ 'S_BEG' } -= 1 if $record->{ 'S_BEG' }  != 0;
     $record->{ 'S_BEG' } -= 1 if $record->{ 'S_BEG2' } != 0;
 
+    $record->{ 'S_END' } = $record->{ 'S_BEG' } + length( $record->{ 'SEQ' } ) - 1;
+
     if ( $record->{ 'FLAG' } & 0x0010 ) {
         $record->{ 'STRAND' } = '+';
     } else {
-- 
2.39.5