From 28c8e585e2a23682dccfbd87541ed94e00279c8e Mon Sep 17 00:00:00 2001
From: bow <bow@bow.web.id>
Date: Mon, 27 Oct 2014 17:07:44 +0100
Subject: [PATCH] Expose read suffix length argument to command line
---
.../nl/lumc/sasc/biopet/tools/ExtractAlignedFastq.scala | 6 +++++-
1 file changed, 5 insertions(+), 1 deletion(-)
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastq.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastq.scala
index c232f9ca0..c8c212246 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastq.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastq.scala
@@ -162,7 +162,8 @@ object ExtractAlignedFastq extends ToolCommand {
inputFastq2: File = null,
outputFastq1: File = null,
outputFastq2: File = null,
- minMapQ: Int = 0) extends AbstractArgs
+ minMapQ: Int = 0,
+ commonSuffixLength: Int = 0) extends AbstractArgs
class OptParser extends AbstractOptParser {
@@ -199,6 +200,9 @@ object ExtractAlignedFastq extends ToolCommand {
opt[Int]('Q', "min_mapq") optional() action { (x, c) =>
c.copy(minMapQ = x) } text "Minimum MAPQ of reads in target region to remove (default: 0)"
+ opt[Int]('s', "read_suffix_length") optional() action { (x, c) =>
+ c.copy(commonSuffixLength = x) } text "Length of common suffix from each read pair (default: 0)"
+
note(
"""
|This tool creates FASTQ file(s) containing reads mapped to the given alignment intervals.
--
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