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Hide deletion arguments in ASEReadCounter

This commit is contained in:
Geraldine Van der Auwera 2016-05-27 11:59:54 -04:00
parent 81d4eaea29
commit 3cc7d7e56d
1 changed files with 5 additions and 4 deletions
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9
public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/rnaseq/ASEReadCounter.java
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@ -90,7 +90,7 @@ import java.util.List;
* </ul>
* <h3>Caveat</h3>
* <ul>
* <li>This tool will only process biallelic sites. If your callset contains multiallelic sites, they will be ignored.
* <li>This tool will only process biallelic SNP sites. If your callset contains multiallelic sites, they will be ignored.
* Optionally, you can subset your callset to just biallelic variants using e.g.
* <a href="org_broadinstitute_gatk_tools_walkers_variantutils_SelectVariants.php">SelectVariants</a>
* with the option "-restrictAllelesTo BIALLELIC".</li>
@ -139,19 +139,20 @@ public class ASEReadCounter extends LocusWalker<String, Integer> {
public CoverageUtils.CountPileupType countType = CoverageUtils.CountPileupType.COUNT_FRAGMENTS_REQUIRE_SAME_BASE;
/**
* Available options are csv, table, rtable. By default, the format is an r-readable table.
* Available options are csv, table, rtable. By default, the format is rtable (an r-readable table).
*/
@Argument(fullName = "outputFormat", doc = "Format of the output file, can be CSV, TABLE, RTABLE", required = false)
public OUTPUT_FORMAT outputFormat = OUTPUT_FORMAT.RTABLE;
// Hiding these argument pending reevaluation (currently don't seem to work and aren't tested)
/**
* Consider a spanning deletion as contributing to coverage. Also enables deletion counts in per-base output.
*/
@Advanced
@Hidden
@Argument(fullName = "includeDeletions", shortName = "dels", doc = "Include information on deletions", required = false)
public boolean includeDeletions = false;
@Advanced
@Hidden
@Argument(fullName = "ignoreDeletionSites", doc = "Ignore sites consisting only of deletions", required = false)
public boolean ignoreDeletionSites = false;