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Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable

This commit is contained in:
Ryan Poplin 2011-09-15 16:26:35 -04:00
parent 2f58fdb369 fd1831b4a5
commit 2a8b8efd2f
2 changed files with 7 additions and 2 deletions
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6
public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java
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@ -43,8 +43,10 @@ import java.util.List;
* Generates an alternative reference sequence over the specified interval. * Generates an alternative reference sequence over the specified interval.
* *
* <p> * <p>
* Given variant ROD tracks, it replaces the reference bases at variation sites with the bases supplied by the ROD(s). * Given variant tracks, it replaces the reference bases at variation sites with the bases supplied by the ROD(s).
* Additionally, allows for a "snpmask" ROD to set overlapping bases to 'N'. * Additionally, allows for one or more "snpmask" VCFs to set overlapping bases to 'N'.
* Note that if there are multiple variants at a site, it takes the first one seen.
* Reference bases for each interval will be output as a separate fasta sequence (named numerically in order).
* *
* <h2>Input</h2> * <h2>Input</h2>
* <p> * <p>

3
public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReferenceWalker.java
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@ -42,6 +42,9 @@ import java.io.PrintStream;
* *
* <p> * <p>
* The output format can be partially controlled using the provided command-line arguments. * The output format can be partially controlled using the provided command-line arguments.
* Specify intervals with the usual -L argument to output only the reference bases within your intervals.
* Overlapping intervals are automatically merged; reference bases for each disjoint interval will be output as a
* separate fasta sequence (named numerically in order).
* *
* <h2>Input</h2> * <h2>Input</h2>
* <p> * <p>