From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Mon, 3 Jan 2011 12:49:50 +0000 (+0000)
Subject: misq updates
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=a1a579a01050db4df9db6d631bc22f9cf6cbf24a;p=biopieces.git

misq updates

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1199 74ccb610-7750-0410-82ae-013aeee3265d
---

diff --git a/bp_scripts/QA_Solexa_report.sh b/bp_scripts/QA_Solexa_report.sh
index 43f1ff1..e76e1d9 100755
--- a/bp_scripts/QA_Solexa_report.sh
+++ b/bp_scripts/QA_Solexa_report.sh
@@ -46,7 +46,7 @@ function pcat
 
 for fastq_file in $fastq_files; do
     base=`basename $fastq_file`
-    date=`date | sed 's/[ :]/_/g'`
+    date=`date | sed 's/[ :]/_/g' | sed 's/__/_/g'`
     tmp_dir="$HOME/QA_Solexa_report_$date"
     out_file="$tmp_dir/QA_Solexa_report_$date.txt"
     plot_scores="$tmp_dir/plot_scores.txt"
diff --git a/code_perl/Maasha/BGB/Track.pm b/code_perl/Maasha/BGB/Track.pm
index a21fa4e..f536bbb 100644
--- a/code_perl/Maasha/BGB/Track.pm
+++ b/code_perl/Maasha/BGB/Track.pm
@@ -447,7 +447,7 @@ sub feature_align
     {
         foreach $align ( split /,/, $entry->[ ALIGN ] )
         {
-            if ( $align =~ /(\d+):([ATCGN-])>([ATCGN-])/ )
+            if ( $align =~ /(\d+):([ATCGRYKMSWBDHVN-])>([ATCGRYKMSWBDHVN-])/ )
             {
                 $pos       = $1;
                 $nt_before = $2;
diff --git a/code_python/Cjung/Args.pyc b/code_python/Cjung/Args.pyc
index 4c39c4a..ddc36fc 100644
Binary files a/code_python/Cjung/Args.pyc and b/code_python/Cjung/Args.pyc differ