From e911e9fe83302e5bcd051bac5a212c3c72c92f63 Mon Sep 17 00:00:00 2001
From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Fri, 30 Oct 2009 10:55:41 +0000
Subject: [PATCH] added read_sam

git-svn-id: http://biopieces.googlecode.com/svn/trunk@724 74ccb610-7750-0410-82ae-013aeee3265d
---
 bp_bin/read_sam         | 97 +++++++++++++++++++++++++++++++++++++++++
 code_perl/Maasha/SAM.pm | 28 +++++++++++-
 2 files changed, 124 insertions(+), 1 deletion(-)
 create mode 100755 bp_bin/read_sam

diff --git a/bp_bin/read_sam b/bp_bin/read_sam
new file mode 100755
index 0000000..4096c92
--- /dev/null
+++ b/bp_bin/read_sam
@@ -0,0 +1,97 @@
+#!/usr/bin/env perl
+
+# Copyright (C) 2007-2009 Martin A. Hansen.
+
+# This program is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License
+# as published by the Free Software Foundation; either version 2
+# of the License, or (at your option) any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+
+# http://www.gnu.org/copyleft/gpl.html
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Read SAM entries from one or more files.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+use warnings;
+use strict;
+use Maasha::Biopieces;
+use Maasha::Filesys;
+use Maasha::SAM;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my ( $options, $in, $out, $record, $data_in, $num, $entry );
+
+$options = Maasha::Biopieces::parse_options(
+    [
+        { long => 'data_in', short => 'i', type => 'files!', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+        { long => 'num',     short => 'n', type => 'uint',   mandatory => 'no', default => undef, allowed => undef, disallowed => '0' },
+    ]   
+);
+
+$in  = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
+$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
+
+while ( $record = Maasha::Biopieces::get_record( $in ) ) {
+    Maasha::Biopieces::put_record( $record, $out );
+}
+
+if ( $options->{ 'data_in' } )
+{
+    $data_in = Maasha::Filesys::files_read_open( $options->{ 'data_in' } );
+
+    $num = 1;
+
+    while ( $entry = Maasha::SAM::sam_entry_get( $data_in ) ) 
+    {
+        if ( $record = Maasha::SAM::sam2biopiece( $entry ) ) {
+            Maasha::Biopieces::put_record( $record, $out );
+        }
+
+        last if $options->{ "num" } and $num == $options->{ "num" };
+
+        $num++;
+    }
+
+    close $data_in;
+}
+
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+BEGIN
+{
+    Maasha::Biopieces::status_set();
+}
+
+
+END
+{
+    Maasha::Biopieces::status_log();
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+__END__
diff --git a/code_perl/Maasha/SAM.pm b/code_perl/Maasha/SAM.pm
index 6a53274..6683973 100644
--- a/code_perl/Maasha/SAM.pm
+++ b/code_perl/Maasha/SAM.pm
@@ -59,7 +59,7 @@ use constant {
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-sub get_entry
+sub sam_entry_get
 {
     # Martin A. Hansen, September 2009.
 
@@ -87,6 +87,12 @@ sub get_entry
 }
 
 
+sub sam_entry_put
+{
+
+}
+
+
 sub sam2biopiece
 {
     # Martin A. Hansen, September 2009.
@@ -112,22 +118,42 @@ sub sam2biopiece
     $record->{ 'ISIZE' }    = $entry->[ ISIZE ];
     $record->{ 'SEQ' }      = $entry->[ SEQ ];
     $record->{ 'SCORES' }   = $entry->[ QUAL ];
+    $record->{ 'TAG' }      = $entry->[ TAG ];
+    $record->{ 'VTYPE' }    = $entry->[ VTYPE ];
+    $record->{ 'VALUE' }    = $entry->[ VALUE ];
 
     $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;
 
+    $record->{ 'READ_PAIRED' }    = $record->{ 'FLAG' } & 0x0001;
+    $record->{ 'READ_MAPPED' }    = $record->{ 'FLAG' } & 0x0002;
+    $record->{ 'Q_SEQ_UNMAPPED' } = $record->{ 'FLAG' } & 0x0004;
+    $record->{ 'MATE_UNMAPPED' }  = $record->{ 'FLAG' } & 0x0008;
+
     if ( $record->{ 'FLAG' } & 0x0010 ) {
         $record->{ 'STRAND' } = '+';
     } else {
         $record->{ 'STRAND' } = '-';
     }
 
+    $record->{ 'MATE_STRAND' }    = $record->{ 'FLAG' } & 0x0020;
+    $record->{ '1ST_READ' }       = $record->{ 'FLAG' } & 0x0040;
+    $record->{ '2ND_READ' }       = $record->{ 'FLAG' } & 0x0080;
+    $record->{ 'ALIGN_PRIMARY' }  = $record->{ 'FLAG' } & 0x0100;
+    $record->{ 'READ_FAIL' }      = $record->{ 'FLAG' } & 0x0200;
+    $record->{ 'READ_BAD' }       = $record->{ 'FLAG' } & 0x0400;
+
     return wantarray ? %{ $record } : $record;
 }
 
 
+sub biopiece2sam
+{
+
+}
+
 
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-- 
2.39.5