# HG changeset patch # User shirish # Date 1401799905 14400 # Node ID 301e116496ee156017e8e1ee5280df2edcd1d93d # Parent aeea494b66b95bc43a75c80a7d89bb6d84501edb Deleted selected files diff -r aeea494b66b9 -r 301e116496ee softsearch.xml --- a/softsearch.xml Tue Jun 03 08:29:01 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,57 +0,0 @@ - - - - ss_tool - samtools - - for structure variation - #if $source.index_source=="history" - samtools index $bam_file ; samtools faidx $source.history_fasta_file ; $inc | SoftSearch.pl -l $min_length_soft_clip -q $min_map_quality -r $min_depth_soft_clip_loc -m $min_no_discordant_read -s $no_sd_consider_discordant -b $bam_file -f $source.history_fasta_file -o $out_file1 - #else - samtools index $bam_file ; samtools faidx $source.ref_fasta.fields.path ; $inc | SoftSearch.pl -l $min_length_soft_clip -q $min_map_quality -r $min_depth_soft_clip_loc -m $min_no_discordant_read -s $no_sd_consider_discordant -b $bam_file -f $source.ref_fasta.fields.path -o $out_file1 - #end if - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff -r aeea494b66b9 -r 301e116496ee tool_dependencies.xml --- a/tool_dependencies.xml Tue Jun 03 08:29:01 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,9 +0,0 @@ - - - - - - - - -