zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Merge pull request #932 from broadinstitute/yf_fix_picard_md 

Fix the scala wrapper for Picard MarkDuplicates
This commit is contained in:
Geraldine Van der Auwera 2015-04-16 12:08:39 -04:00
parent 8329fe46d1 a7487e282a
commit bfcac455c9
1 changed files with 2 additions and 2 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

4
public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/MarkDuplicates.scala
View File

@ -37,7 +37,7 @@ import java.io.File
*/
class MarkDuplicates extends org.broadinstitute.gatk.queue.function.JavaCommandLineFunction with PicardBamFunction {
analysisName = "MarkDuplicates"
javaMainClass = "picard.sam.MarkDuplicates"
javaMainClass = "picard.sam.markduplicates.MarkDuplicates"
@Input(doc="The input SAM or BAM files to analyze. Must be coordinate sorted.", shortName = "input", fullName = "input_bam_files", required = true)
var input: Seq[File] = Nil
@ -55,7 +55,7 @@ class MarkDuplicates extends org.broadinstitute.gatk.queue.function.JavaCommandL
var REMOVE_DUPLICATES: Boolean = false
@Argument(doc = "Maximum number of file handles to keep open when spilling read ends to disk. Set this number a little lower than the per-process maximum number of file that may be open. This number can be found by executing the 'ulimit -n' command on a Unix system.", shortName = "max_file_handles", fullName ="max_file_handles_for_read_ends_maps", required=false)
var MAX_FILE_HANDLES_FOR_READ_ENDS_MAP: Int = -1;
var MAX_FILE_HANDLES_FOR_READ_ENDS_MAP: Int = -1
@Argument(doc = "This number, plus the maximum RAM available to the JVM, determine the memory footprint used by some of the sorting collections. If you are running out of memory, try reducing this number.", shortName = "sorting_ratio", fullName = "sorting_collection_size_ratio", required = false)
var SORTING_COLLECTION_SIZE_RATIO: Double = -1