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comparison 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
comparison
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37:4da2d7f0128e 38:a0925f507352
1 <tool id="sam_dump" name="Extract reads" version="1.1.0"> 1 <tool id="sam_dump" name="Extract reads" version="1.1.1">
2 <description> in SAM format from NCBI SRA.</description> 2 <description> in SAM format from NCBI SRA.</description>
3 <command> 3 <command>
4 sam-dump --log-level fatal 4 sam-dump --log-level fatal
5 #if str( $region ) != "": 5 #if str( $region ) != "":
6 --aligned-region $region 6 --aligned-region $region
7 #end if 7 #end if
8 #if str( $matepairDist ) != "": 8 #if str( $matepairDist ) != "":
9 --matepair-distance $matepairDist 9 --matepair-distance $matepairDist
10 #end if
11 #if str( $minMapq ) != "":
12 --minmapq $minMapq
10 #end if 13 #end if
11 #if $header == "yes": 14 #if $header == "yes":
12 --header 15 --header
13 #else: 16 #else:
14 --no-header 17 --no-header