From ef3882f43995afb9c2ac63a04e38b99f1fde462f Mon Sep 17 00:00:00 2001
From: Ami Levy Moonshine <ami@broadinstitute.org>
Date: Thu, 11 Oct 2012 14:51:41 -0400
Subject: [PATCH] PhaseByTransmission: small typo /n.
 variantCallQC_summaryTablesOnly.R: small changes (more to come) /n
 GeneralCallingPipeline.scala: the new pipeline script. It is not as clean as
 I want it to be, but it works. I still going to work on it a little bit more.
 Also, it does not include yet: (1) the RR step (2) need better eval step (3)
 need to include other targets (currently it eork on the CEU Trio)

---
 .../sting/gatk/walkers/phasing/PhaseByTransmission.java         | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java
index 00acf854a..7ebfec49e 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java
@@ -36,7 +36,7 @@ import java.util.*;
  * <ul>
  *     <li>In parent/child pairs: If an individual genotype is missing at one site, the other one is phased if it is homozygous. No phasing probability is emitted.</li>
  *     <li>In trios: If the child is missing, parents are treated as separate individuals and phased if homozygous. No phasing probability is emitted.</li>
- *     <li>In trios: If one of the parents is missing, it is handled like a parent/child pair. Phasing is done unless both the parent and child are heterozygous and a phasing probabilitt is emitted.</li>
+ *     <li>In trios: If one of the parents is missing, it is handled like a parent/child pair. Phasing is done unless both the parent and child are heterozygous and a phasing probability is emitted.</li>
  *     <li>In trios: If two individuals are missing, the remaining individual is phased if it is homozygous. No phasing probability is emitted.</li>
  * </ul>
  *