From a1a579a01050db4df9db6d631bc22f9cf6cbf24a Mon Sep 17 00:00:00 2001
From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Mon, 3 Jan 2011 12:49:50 +0000
Subject: [PATCH] misq updates

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1199 74ccb610-7750-0410-82ae-013aeee3265d
---
 bp_scripts/QA_Solexa_report.sh |   2 +-
 code_perl/Maasha/BGB/Track.pm  |   2 +-
 code_python/Cjung/Args.pyc     | Bin 5375 -> 5364 bytes
 3 files changed, 2 insertions(+), 2 deletions(-)

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 4c39c4a68733e7fdac49e939fe26d08e98449439..ddc36fc600f13f1a86a119e0c8fadcd00d0064e1 100644
GIT binary patch
delta 217
zcmeyb`9+iC;wN6NjZrS%8#yxAI1LyW81yspb5kcz5HZ-iimieXO(=%rIjWG(=1Q(2
zR3Yuj3Oq+q^yy5N<~@fZqP<y;&jD4N&gLon0cb*#r381Q>YL0ZREH|Ed9Tn(RBibH
D%c4DY

delta 224
zcmeyO`CpUc;wN6N<wxtiHgaUJaTzi&FzAOCrxq1YPUP3wyp*km5nU{d<28m@8CMaC
z*hlUUXxb)=@t#8#`pB)bS(48lS=Z)7ehk|t3kmK<(>9q&s1{9V^A@2K$R>f@K6#^v
FGXQ#$LC^pI

-- 
2.39.5