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comparison indel_realigner.xml @ 4:f244b8209eb8 draft

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bug fix release
author iuc
date Mon, 25 Aug 2014 17:43:11 -0400
parents 8bcc13094767
children 35c00763cb5c
comparison
equal deleted inserted replaced
3:2553f84b8174 4:f244b8209eb8
1 <tool id="gatk2_indel_realigner" name="Indel Realigner" version="0.0.7"> 1 <tool id="gatk2_indel_realigner" name="Indel Realigner" version="@VERSION@.0">
2 <description>- perform local realignment</description> 2 <description>- perform local realignment</description>
3 <expand macro="requirements" /> 3 <expand macro="requirements" />
4 <macros> 4 <macros>
5 <import>gatk2_macros.xml</import> 5 <import>gatk2_macros.xml</import>
6 </macros> 6 </macros>
204 maxReadsForRealignment max reads allowed at an interval for realignment; if this value is exceeded, realignment is not attempted and the reads are passed to the output file(s) as-is 204 maxReadsForRealignment max reads allowed at an interval for realignment; if this value is exceeded, realignment is not attempted and the reads are passed to the output file(s) as-is
205 noOriginalAlignmentTags Don't output the original cigar or alignment start tags for each realigned read in the output bam. 205 noOriginalAlignmentTags Don't output the original cigar or alignment start tags for each realigned read in the output bam.
206 206
207 @CITATION_SECTION@ 207 @CITATION_SECTION@
208 </help> 208 </help>
209 <expand macro="citations" />
209 </tool> 210 </tool>