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Merge pull request #106 from broadinstitute/rp_unknown_sites_assess_as_tp_in_kb 

Changing CALLED_IN_DB_UNKNOWN_STATUS to count as TRUE_POSITIVEs in the s...
This commit is contained in:
Mark DePristo 2013-03-14 11:50:12 -07:00
parent 6d6264b108 38914384d1
commit 5d6faef50e
2 changed files with 2 additions and 2 deletions
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2
protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
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@ -149,7 +149,7 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
* The assembled haplotypes will be written as BAM to this file if requested. Really for debugging purposes only. * The assembled haplotypes will be written as BAM to this file if requested. Really for debugging purposes only.
* Note that the output here does not include uninformative reads so that not every input read is emitted to the bam. * Note that the output here does not include uninformative reads so that not every input read is emitted to the bam.
* *
* Turning on this mode may result in serious performance cost for the HC. It's really only approprate to * Turning on this mode may result in serious performance cost for the HC. It's really only appropriate to
* use in specific areas where you want to better understand why the HC is making specific calls. * use in specific areas where you want to better understand why the HC is making specific calls.
* *
* The reads are written out containing a HC tag (integer) that encodes which haplotype each read best matches * The reads are written out containing a HC tag (integer) that encodes which haplotype each read best matches

2
public/java/src/org/broadinstitute/sting/utils/activeregion/ActivityProfile.java
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@ -259,7 +259,7 @@ public class ActivityProfile {
* Can be overridden by subclasses to transform states in any way * Can be overridden by subclasses to transform states in any way
* *
* There's no particular contract for the output states, except that they can never refer to states * There's no particular contract for the output states, except that they can never refer to states
* beyond the current end of the stateList unless the explictly include preceding states before * beyond the current end of the stateList unless the explicitly include preceding states before
* the reference. So for example if the current state list is [1, 2, 3] this function could return * the reference. So for example if the current state list is [1, 2, 3] this function could return
* [1,2,3,4,5] but not [1,2,3,5]. * [1,2,3,4,5] but not [1,2,3,5].
* *