Hello Peter and all,
Peter Cock wrote, On 07/28/2011 05:08 PM:
> It concerns me that you're doing this for both "fastqillumina" format
> (good) and "fastqsolexa" (bad). Treating the later as fastqillumina
> would give negative scores and probably cause trouble. Unless BWA
> copes but if so it is a poor choice of argument name?
>
> In the XML wrapper you've not updated the help text for the
> FASTQ parameters to indicate it would now accept Illumina
> FASTQ as well as Sanger FASTQ.
>
> Peter
>
> P.S. It is a patch file, but it has extension xml??
These are all valid comments, here's an updated patch (with a ".patch"
extension :) ).
Thanks!
-gordon
diff -r 9ece46045d15 tools/sr_mapping/bwa_wrapper.py
--- a/tools/sr_mapping/bwa_wrapper.py Thu Jul 28 11:50:56 2011 -0400
+++ b/tools/sr_mapping/bwa_wrapper.py Thu Jul 28 17:23:38 2011 -0400
@@ -75,6 +75,7 @@
parser.add_option( '-D', '--dbkey', dest='dbkey', help='Dbkey for reference genome' )
parser.add_option( '-X', '--do_not_build_index', dest='do_not_build_index', action='store_true', help="Don't build index" )
parser.add_option( '-H', '--suppressHeader', dest='suppressHeader', help='Suppress header' )
+ parser.add_option( '-I', '--illumina1.3', dest='illumina13qual', help='Input FASTQ files have Illuina 1.3 quality scores' )
(options, args) = parser.parse_args()
# output version # of tool
@@ -163,10 +164,14 @@
stop_err( 'Error indexing reference sequence. ' + str( e ) )
else:
ref_file_name = options.ref
+ if options.illumina13qual:
+ illumina_quals = "-I"
+ else:
+ illumina_quals = ""
# set up aligning and generate aligning command options
if options.params == 'pre_set':
- aligning_cmds = '-t %s %s' % ( options.threads, color_space )
+ aligning_cmds = '-t %s %s %s' % ( options.threads, color_space, illumina_quals )
gen_alignment_cmds = ''
else:
if options.maxEditDist != '0':
@@ -185,11 +190,11 @@
noIterSearch = '-N'
else:
noIterSearch = ''
- aligning_cmds = '-n %s -o %s -e %s -d %s -i %s %s -k %s -t %s -M %s -O %s -E %s %s %s %s' % \
+ aligning_cmds = '-n %s -o %s -e %s -d %s -i %s %s -k %s -t %s -M %s -O %s -E %s %s %s %s %s' % \
( editDist, options.maxGapOpens, options.maxGapExtens, options.disallowLongDel,
options.disallowIndel, seed, options.maxEditDistSeed, options.threads,
options.mismatchPenalty, options.gapOpenPenalty, options.gapExtensPenalty,
- suboptAlign, noIterSearch, color_space )
+ suboptAlign, noIterSearch, color_space, illumina_quals )
if options.genAlignType == 'paired':
gen_alignment_cmds = '-a %s -o %s' % ( options.maxInsertSize, options.maxOccurPairing )
if options.outputTopNDisc:
diff -r 9ece46045d15 tools/sr_mapping/bwa_wrapper.xml
--- a/tools/sr_mapping/bwa_wrapper.xml Thu Jul 28 11:50:56 2011 -0400
+++ b/tools/sr_mapping/bwa_wrapper.xml Thu Jul 28 17:23:38 2011 -0400
@@ -5,6 +5,10 @@
bwa_wrapper.py
--threads="4"
+ #if $input1.ext == "fastqillumina":
+ --illumina1.3
+ #end if
+
## reference source
--fileSource=$genomeSource.refGenomeSource
#if $genomeSource.refGenomeSource == "history":
@@ -93,11 +97,11 @@
<option value="paired">Paired-end</option>
</param>
<when value="single">
- <param name="input1" type="data" format="fastqsanger" label="FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33" />
+ <param name="input1" type="data" format="fastqsanger,fastqillumina" label="FASTQ file" help="FASTQ with either Sanger-scaled quality values (fastqsanger) or Illumina-scaled quality values (fastqillumina)" />
</when>
<when value="paired">
- <param name="input1" type="data" format="fastqsanger" label="Forward FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33" />
- <param name="input2" type="data" format="fastqsanger" label="Reverse FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33" />
+ <param name="input1" type="data" format="fastqsanger,fastqillumina" label="Forward FASTQ file" help="FASTQ with either Sanger-scaled quality values (fastqsanger) or Illumina-scaled quality values (fastqillumina)" />
+ <param name="input2" type="data" format="fastqsanger,fastqillumina" label="Reverse FASTQ file" help="FASTQ with either Sanger-scaled quality values (fastqsanger) or Illumina-scaled quality values (fastqillumina)" />
</when>
</conditional>
<conditional name="params">
@@ -324,7 +328,7 @@
**Input formats**
-BWA accepts files in Sanger FASTQ format. Use the FASTQ Groomer to prepare your files.
+BWA accepts files in either Sanger FASTQ format (galaxy type *fastqsanger*) or Illumina FASTQ format (galaxy type *fastqillumina*).
------
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