Mercurial > repos > matt-shirley > sra_tools

diff sam_dump.xml @ 38:a0925f507352 draft

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bring pileup to parity with sam; fixed minMapq for sam
author Matt Shirley <mdshw5@gmail.com>
date Sun, 04 Aug 2013 23:17:53 -0400
parents 4da2d7f0128e
children 1d152e8cb375
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--- a/sam_dump.xml	Thu Aug 01 13:57:27 2013 -0400
+++ b/sam_dump.xml	Sun Aug 04 23:17:53 2013 -0400
@@ -1,4 +1,4 @@
-<tool id="sam_dump" name="Extract reads" version="1.1.0">
+<tool id="sam_dump" name="Extract reads" version="1.1.1">
   <description> in SAM format from NCBI SRA.</description>
   <command>
     sam-dump --log-level fatal 
@@ -8,6 +8,9 @@
     #if str( $matepairDist ) != "":
       --matepair-distance $matepairDist
     #end if
+    #if str( $minMapq ) != "":
+      --minmapq $minMapq
+    #end if
     #if $header == "yes":
       --header
     #else: