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Document -L unmapped

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Eric Banks 2012-02-07 13:30:54 -05:00
parent 718da7757e
commit 717cd4b912
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public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
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@ -75,6 +75,7 @@ public class GATKArgumentCollection {
* Using this option one can instruct the GATK engine to traverse over only part of the genome. This argument can be specified multiple times. * Using this option one can instruct the GATK engine to traverse over only part of the genome. This argument can be specified multiple times.
* One may use samtools-style intervals either explicitly (e.g. -L chr1 or -L chr1:100-200) or listed in a file (e.g. -L myFile.intervals). * One may use samtools-style intervals either explicitly (e.g. -L chr1 or -L chr1:100-200) or listed in a file (e.g. -L myFile.intervals).
* Additionally, one may specify a rod file to traverse over the positions for which there is a record in the file (e.g. -L file.vcf). * Additionally, one may specify a rod file to traverse over the positions for which there is a record in the file (e.g. -L file.vcf).
* To specify the completely unmapped reads in the BAM file (i.e. those without a reference contig) use -L unmapped.
*/ */
@Input(fullName = "intervals", shortName = "L", doc = "One or more genomic intervals over which to operate. Can be explicitly specified on the command line or in a file (including a rod file)", required = false) @Input(fullName = "intervals", shortName = "L", doc = "One or more genomic intervals over which to operate. Can be explicitly specified on the command line or in a file (including a rod file)", required = false)
public List<IntervalBinding<Feature>> intervals = null; public List<IntervalBinding<Feature>> intervals = null;