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Fix for BWA -R option.

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Daniel Blankenberg
2012-04-10 09:24:25 -04:00
parent 163a2f39e1
commit 0372d1fe06
3 changed files with 13 additions and 13 deletions
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tools/sr_mapping/bwa_color_wrapper.xml
+5 -5
View File
@@ -1,4 +1,4 @@
<tool id="bwa_color_wrapper" name="Map with BWA for SOLiD" version="1.0.1">
<tool id="bwa_color_wrapper" name="Map with BWA for SOLiD" version="1.0.2">
<description></description>
<parallelism method="basic"></parallelism>
<command interpreter="python">
@@ -42,7 +42,7 @@
--mismatchPenalty=$params.mismatchPenalty
--gapOpenPenalty=$params.gapOpenPenalty
--gapExtensPenalty=$params.gapExtensPenalty
--suboptAlign=$params.suboptAlign
--suboptAlign="${params.suboptAlign}"
--noIterSearch=$params.noIterSearch
--outputTopN=$params.outputTopN
--outputTopNDisc=$params.outputTopNDisc
@@ -125,7 +125,7 @@
<param name="mismatchPenalty" type="integer" value="3" label="Mismatch penalty (aln -M)" help="BWA will not search for suboptimal hits with a score lower than [value]" />
<param name="gapOpenPenalty" type="integer" value="11" label="Gap open penalty (aln -O)" />
<param name="gapExtensPenalty" type="integer" value="4" label="Gap extension penalty (aln -E)" />
<param name="suboptAlign" type="boolean" truevalue="true" falsevalue="false" checked="no" label="Proceed with suboptimal alignments even if the top hit is a repeat (aln -R)" help="For paired-end reads only. By default, BWA only searches for suboptimal alignments if the top hit is unique. Using this option has no effect on accuracy for single-end reads. It is mainly designed for improving the alignment accuracy of paired-end reads. However, the pairing procedure will be slowed down, especially for very short reads (~32bp)" />
<param name="suboptAlign" type="integer" optional="True" label="Proceed with suboptimal alignments if there are no more than INT equally best hits. (aln -R)" help="For paired-end reads only. By default, BWA only searches for suboptimal alignments if the top hit is unique. Using this option has no effect on accuracy for single-end reads. It is mainly designed for improving the alignment accuracy of paired-end reads. However, the pairing procedure will be slowed down, especially for very short reads (~32bp)" />
<param name="noIterSearch" type="boolean" truevalue="true" falsevalue="false" checked="no" label="Disable iterative search (aln -N)" help="All hits with no more than maxDiff differences will be found. This mode is much slower than the default" />
<param name="outputTopN" type="integer" value="3" label="Maximum number of alignments to output in the XA tag for reads paired properly (samse/sampe -n)" help="If a read has more than INT hits, the XA tag will not be written" />
<param name="outputTopNDisc" type="integer" value="10" label="Maximum number of alignments to output in the XA tag for disconcordant read pairs (excluding singletons) (sampe -N)" help="For paired-end reads only. If a read has more than INT hits, the XA tag will not be written" />
@@ -249,7 +249,7 @@ SOLID, HELICOS, IONTORRENT and PACBIO" />
<param name="mismatchPenalty" value="3" />
<param name="gapOpenPenalty" value="11" />
<param name="gapExtensPenalty" value="4" />
<param name="suboptAlign" value="true" />
<param name="suboptAlign" value="" />
<param name="noIterSearch" value="true" />
<param name="outputTopN" value="3" />
<param name="outputTopNDisc" value="10" />
@@ -300,7 +300,7 @@ SOLID, HELICOS, IONTORRENT and PACBIO" />
<param name="mismatchPenalty" value="3" />
<param name="gapOpenPenalty" value="11" />
<param name="gapExtensPenalty" value="4" />
<param name="suboptAlign" value="true" />
<param name="suboptAlign" value="" />
<param name="noIterSearch" value="true" />
<param name="outputTopN" value="3" />
<param name="outputTopNDisc" value="10" />
tools/sr_mapping/bwa_wrapper.py
+3 -3
View File
@@ -54,7 +54,7 @@ def __main__():
parser.add_option( '-M', '--mismatchPenalty', dest='mismatchPenalty', help='Mismatch penalty' )
parser.add_option( '-O', '--gapOpenPenalty', dest='gapOpenPenalty', help='Gap open penalty' )
parser.add_option( '-E', '--gapExtensPenalty', dest='gapExtensPenalty', help='Gap extension penalty' )
parser.add_option( '-R', '--suboptAlign', dest='suboptAlign', help='Proceed with suboptimal alignments even if the top hit is a repeat' )
parser.add_option( '-R', '--suboptAlign', dest='suboptAlign', default=None, help='Proceed with suboptimal alignments even if the top hit is a repeat' )
parser.add_option( '-N', '--noIterSearch', dest='noIterSearch', help='Disable iterative search' )
parser.add_option( '-T', '--outputTopN', dest='outputTopN', help='Maximum number of alignments to output in the XA tag for reads paired properly' )
parser.add_option( '', '--outputTopNDisc', dest='outputTopNDisc', help='Maximum number of alignments to output in the XA tag for disconcordant read pairs (excluding singletons)' )
@@ -182,8 +182,8 @@ def __main__():
seed = '-l %s' % options.seed
else:
seed = ''
if options.suboptAlign == 'true':
suboptAlign = '-R'
if options.suboptAlign:
suboptAlign = '-R "%s"' % ( options.suboptAlign )
else:
suboptAlign = ''
if options.noIterSearch == 'true':
tools/sr_mapping/bwa_wrapper.xml
+5 -5
View File
@@ -1,4 +1,4 @@
<tool id="bwa_wrapper" name="Map with BWA for Illumina" version="1.2.2">
<tool id="bwa_wrapper" name="Map with BWA for Illumina" version="1.2.3">
<description></description>
<parallelism method="basic"></parallelism>
<command interpreter="python">
@@ -45,7 +45,7 @@
--mismatchPenalty=$params.mismatchPenalty
--gapOpenPenalty=$params.gapOpenPenalty
--gapExtensPenalty=$params.gapExtensPenalty
--suboptAlign=$params.suboptAlign
--suboptAlign="${params.suboptAlign}"
--noIterSearch=$params.noIterSearch
--outputTopN=$params.outputTopN
--outputTopNDisc=$params.outputTopNDisc
@@ -122,7 +122,7 @@
<param name="mismatchPenalty" type="integer" value="3" label="Mismatch penalty (aln -M)" help="BWA will not search for suboptimal hits with a score lower than [value]" />
<param name="gapOpenPenalty" type="integer" value="11" label="Gap open penalty (aln -O)" />
<param name="gapExtensPenalty" type="integer" value="4" label="Gap extension penalty (aln -E)" />
<param name="suboptAlign" type="boolean" truevalue="true" falsevalue="false" checked="no" label="Proceed with suboptimal alignments even if the top hit is a repeat (aln -R)" help="For paired-end reads only. By default, BWA only searches for suboptimal alignments if the top hit is unique. Using this option has no effect on accuracy for single-end reads. It is mainly designed for improving the alignment accuracy of paired-end reads. However, the pairing procedure will be slowed down, especially for very short reads (~32bp)" />
<param name="suboptAlign" type="integer" optional="True" label="Proceed with suboptimal alignments if there are no more than INT equally best hits. (aln -R)" help="For paired-end reads only. By default, BWA only searches for suboptimal alignments if the top hit is unique. Using this option has no effect on accuracy for single-end reads. It is mainly designed for improving the alignment accuracy of paired-end reads. However, the pairing procedure will be slowed down, especially for very short reads (~32bp)" />
<param name="noIterSearch" type="boolean" truevalue="true" falsevalue="false" checked="no" label="Disable iterative search (aln -N)" help="All hits with no more than maxDiff differences will be found. This mode is much slower than the default" />
<param name="outputTopN" type="integer" value="3" label="Maximum number of alignments to output in the XA tag for reads paired properly (samse/sampe -n)" help="If a read has more than INT hits, the XA tag will not be written" />
<param name="outputTopNDisc" type="integer" value="10" label="Maximum number of alignments to output in the XA tag for disconcordant read pairs (excluding singletons) (sampe -N)" help="For paired-end reads only. If a read has more than INT hits, the XA tag will not be written" />
@@ -226,7 +226,7 @@ SOLID, HELICOS, IONTORRENT and PACBIO" />
<param name="mismatchPenalty" value="3" />
<param name="gapOpenPenalty" value="11" />
<param name="gapExtensPenalty" value="4" />
<param name="suboptAlign" value="true" />
<param name="suboptAlign" value="" />
<param name="noIterSearch" value="true" />
<param name="outputTopN" value="3" />
<param name="outputTopNDisc" value="10" />
@@ -263,7 +263,7 @@ SOLID, HELICOS, IONTORRENT and PACBIO" />
<param name="mismatchPenalty" value="3" />
<param name="gapOpenPenalty" value="11" />
<param name="gapExtensPenalty" value="4" />
<param name="suboptAlign" value="true" />
<param name="suboptAlign" value="" />
<param name="noIterSearch" value="true" />
<param name="outputTopN" value="3" />
<param name="outputTopNDisc" value="10" />