From 0372d1fe06c2167e5036fafa65be93b187cb3142 Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Tue, 10 Apr 2012 09:24:25 -0400
Subject: [PATCH] Fix for BWA -R option.

---
 tools/sr_mapping/bwa_color_wrapper.xml | 10 +++++-----
 tools/sr_mapping/bwa_wrapper.py        |  6 +++---
 tools/sr_mapping/bwa_wrapper.xml       | 10 +++++-----
 3 files changed, 13 insertions(+), 13 deletions(-)

diff --git a/tools/sr_mapping/bwa_color_wrapper.xml b/tools/sr_mapping/bwa_color_wrapper.xml
index cfd13f1ac2d..e31f5d57898 100644
--- a/tools/sr_mapping/bwa_color_wrapper.xml
+++ b/tools/sr_mapping/bwa_color_wrapper.xml
@@ -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" />
diff --git a/tools/sr_mapping/bwa_wrapper.py b/tools/sr_mapping/bwa_wrapper.py
index a6252b5b112..9026a6571bb 100644
--- a/tools/sr_mapping/bwa_wrapper.py
+++ b/tools/sr_mapping/bwa_wrapper.py
@@ -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':
diff --git a/tools/sr_mapping/bwa_wrapper.xml b/tools/sr_mapping/bwa_wrapper.xml
index aa4a97fdb07..0f25b569e8d 100644
--- a/tools/sr_mapping/bwa_wrapper.xml
+++ b/tools/sr_mapping/bwa_wrapper.xml
@@ -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" />