/
ExampleReadFilter.scala
48 lines (43 loc) · 1.73 KB
/
ExampleReadFilter.scala
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
/*
* Copyright (c) 2012 The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.queue.qscripts.examples
import org.broadinstitute.sting.queue.QScript
import org.broadinstitute.sting.queue.extensions.gatk._
/**
* Script used for testing inclusion of a read filter
*/
class ExampleReadFilter extends QScript {
@Input(doc="The reference file for the bam files.", shortName="R")
var referenceFile: File = _
@Input(doc="Bam file to genotype.", shortName="I")
var bamFile: File = _
def script() {
val printReads = new PrintReads with BadMate
printReads.reference_sequence = referenceFile
printReads.memoryLimit = 2
printReads.input_file :+= bamFile
add(printReads)
}
}