# HG changeset patch
# User shirish
# Date 1401803547 14400
# Node ID e20faf5be83e2c896abb00ff458ab5e1bcb1b08f
# Parent 530c9a1d75cb2f6bd6a6f082d4b43741b3e9566b
Deleted selected files
diff -r 530c9a1d75cb -r e20faf5be83e softsearch.xml
--- a/softsearch.xml Tue Jun 03 09:32:45 2014 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,57 +0,0 @@
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- complex_repository_dependency_on_softsearch
- samtools
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- 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
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diff -r 530c9a1d75cb -r e20faf5be83e tool_dependencies.xml
--- a/tool_dependencies.xml Tue Jun 03 09:32:45 2014 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,10 +0,0 @@
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