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I asked nicely and got nothing. Then I threatened and still got nothing. So I am carrying through on my threats. Guillermo, you have a short reprieve because you were away on vacation, but let's get yours done tomorrow afternoon.

This commit is contained in:
Eric Banks 2011-09-06 21:07:49 -04:00
parent da9c8ab386
commit 1ef8a1750a
3 changed files with 11 additions and 0 deletions
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3
public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java
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@ -60,6 +60,9 @@ import java.util.*;
* and/or percentage of bases covered to or beyond a threshold. * and/or percentage of bases covered to or beyond a threshold.
* Additionally, reads and bases can be filtered by mapping or base quality score. * Additionally, reads and bases can be filtered by mapping or base quality score.
* *
* <b>If any of the command-line arguments for this tool are not clear to you,
* please email chartl at broadinstitute dot org and he will gladly explain them in more detail.</b>
*
* <h2>Input</h2> * <h2>Input</h2>
* <p> * <p>
* One or more bam files (with proper headers) to be analyzed for coverage statistics * One or more bam files (with proper headers) to be analyzed for coverage statistics

5
public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetectorWalker.java
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@ -77,6 +77,11 @@ import java.util.*;
* if even a weak evidence for the same indel, not necessarily a confident call, exists in the first sample ("Normal"), or as somatic * if even a weak evidence for the same indel, not necessarily a confident call, exists in the first sample ("Normal"), or as somatic
* if first bam has coverage at the site but no indication for an indel. In the --somatic mode, BED output contains * if first bam has coverage at the site but no indication for an indel. In the --somatic mode, BED output contains
* only somatic calls, while --verbose output contains all calls annotated with GERMLINE/SOMATIC keywords. * only somatic calls, while --verbose output contains all calls annotated with GERMLINE/SOMATIC keywords.
*
* <b>If any of the general usage of this tool or any of the command-line arguments for this tool are not clear to you,
* please email asivache at broadinstitute dot org and he will gladly explain everything in more detail.</b>
*
*
*/ */
@ReadFilters({Platform454Filter.class, MappingQualityZeroFilter.class, PlatformUnitFilter.class}) @ReadFilters({Platform454Filter.class, MappingQualityZeroFilter.class, PlatformUnitFilter.class})
public class SomaticIndelDetectorWalker extends ReadWalker<Integer,Integer> { public class SomaticIndelDetectorWalker extends ReadWalker<Integer,Integer> {

3
public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java
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@ -39,6 +39,9 @@ import java.util.List;
* reasons why the site may fail validation (nearby variation, for example). * reasons why the site may fail validation (nearby variation, for example).
* </p> * </p>
* *
* <b>If any of the command-line arguments for this tool are not clear to you,
* please email chartl at broadinstitute dot org and he will gladly explain them in more detail.</b>
*
* <h2>Input</h2> * <h2>Input</h2>
* <p> * <p>
* Requires a VCF containing alleles to design amplicons towards, a VCF of variants to mask out of the amplicons, and an * Requires a VCF containing alleles to design amplicons towards, a VCF of variants to mask out of the amplicons, and an