From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Fri, 4 Sep 2009 15:05:29 +0000 (+0000)
Subject: changed options of read_solexa and read_fastq - undocumented
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;ds=sidebyside;h=65dca98102521647b2ccb2168b095bfc808a9c40;p=biopieces.git

changed options of read_solexa and read_fastq - undocumented

git-svn-id: http://biopieces.googlecode.com/svn/trunk@653 74ccb610-7750-0410-82ae-013aeee3265d
---

diff --git a/bp_bin/read_fastq b/bp_bin/read_fastq
index 262bfde..5173aba 100755
--- a/bp_bin/read_fastq
+++ b/bp_bin/read_fastq
@@ -40,10 +40,11 @@ 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     },
-        { long => 'quality',      short => 'q', type => 'uint',   mandatory => 'no', default => 20,    allowed => undef, disallowed => undef },
-        { long => 'skip_quality', short => 's', type => 'flag',   mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+        { 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     },
+        { long => 'convert2dec', short => 'c', type => 'flag',   mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+        { long => 'cutoff',      short => 'C', type => 'int',    mandatory => 'no', default => 20,    allowed => undef, disallowed => undef },
+        { long => 'soft_mask',   short => 's', type => 'flag',   mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
     ]   
 );
 
@@ -64,6 +65,8 @@ if ( $options->{ 'data_in' } )
     {
         if ( $record = Maasha::Fastq::fastq2biopiece( $entry ) )
         {
+            Maasha::Fastq::softmask_phred_str( $record->{ 'SEQ' }, $record->{ 'SCORES' }, $options->{ 'cutoff' } ) if $options->{ 'soft_mask' };
+
             Maasha::Biopieces::put_record( $record, $out );
         }
 
diff --git a/bp_bin/read_solexa b/bp_bin/read_solexa
index 0d93142..b7a5639 100755
--- a/bp_bin/read_solexa
+++ b/bp_bin/read_solexa
@@ -42,11 +42,11 @@ my ( $options, $in, $out, $record, $data_in, $num, $entry, @seqs, @scores, $i );
 
 $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' },
-        { long => 'format',       short => 'f', type => 'string', mandatory => 'no', default => 'octal', allowed => 'octal,decimal', disallowed => undef },
-        { long => 'quality',      short => 'q', type => 'uint',   mandatory => 'no', default => 20,      allowed => undef,           disallowed => undef },
-        { long => 'skip_quality', short => 's', type => 'flag',   mandatory => 'no', default => undef,   allowed => undef,           disallowed => undef },
+        { 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' },
+        { long => 'convert2dec', short => 'c', type => 'flag',   mandatory => 'no', default => undef,   allowed => undef, disallowed => undef },
+        { long => 'cutoff',      short => 'C', type => 'int',    mandatory => 'no', default => 20,      allowed => undef, disallowed => undef },
+        { long => 'soft_mask',   short => 's', type => 'flag',   mandatory => 'no', default => undef,   allowed => undef, disallowed => undef },
     ]   
 );
 
@@ -67,6 +67,8 @@ if ( $options->{ 'data_in' } )
     {
         if ( $record = Maasha::Fastq::fastq2biopiece( $entry ) )
         {
+            Maasha::Fastq::softmask_solexa_str( $record->{ 'SEQ' }, $record->{ 'SCORES' }, $options->{ 'cutoff' } ) if $options->{ 'soft_mask' };
+
             Maasha::Biopieces::put_record( $record, $out );
         }