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 43f1ff101598cbb840152aeb405e5a4411ac03e6..e76e1d91bc969f08fc7dfea45e005d345994df41 100755 (executable)
--- 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 a21fa4e416b3d090936b57ac9dc24861a7491fc3..f536bbb3a41975c6ad3991a2dbc8d463d676a89d 100644 (file)
--- 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 (file)
Binary files a/code_python/Cjung/Args.pyc and b/code_python/Cjung/Args.pyc differ