From 11cdc39523e6e7efd264f0fa17973313048bca63 Mon Sep 17 00:00:00 2001
From: Yunfei Guo <yunfei.guo@bina.roche.com>
Date: Fri, 3 Mar 2017 06:49:04 -0800
Subject: [PATCH 1/2] prepare for v0.7.7 release;fix quickstart bug;disable
 illegal phase warning

---
 pom.xml                                           | 2 +-
 quickstart.sh                                     | 2 +-
 src/main/java/com/bina/varsim/util/VCFparser.java | 1 -
 3 files changed, 2 insertions(+), 3 deletions(-)

diff --git a/pom.xml b/pom.xml
index c40ea47e..5385fb7e 100644
--- a/pom.xml
+++ b/pom.xml
@@ -4,7 +4,7 @@
 
     <groupId>com.bina.varsim</groupId>
     <artifactId>varsim</artifactId>
-    <version>0.7.6</version>
+    <version>0.7.7</version>
     <packaging>jar</packaging>
 
     <name>varsim</name>
diff --git a/quickstart.sh b/quickstart.sh
index 5f635f3f..d07db869 100755
--- a/quickstart.sh
+++ b/quickstart.sh
@@ -4,7 +4,7 @@ set -x
 
 b37_source="ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz"
 dbsnp_source="ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606_b147_GRCh37p13/VCF/All_20160601.vcf.gz"
-varsim_version="0.7.1"
+varsim_version="0.7.7"
 samtools_version="1.3.1"
 
 # Download varsim
diff --git a/src/main/java/com/bina/varsim/util/VCFparser.java b/src/main/java/com/bina/varsim/util/VCFparser.java
index c99de778..af88df17 100644
--- a/src/main/java/com/bina/varsim/util/VCFparser.java
+++ b/src/main/java/com/bina/varsim/util/VCFparser.java
@@ -179,7 +179,6 @@ boolean isPhased(String geno, byte[] vals, ChrString chr) {
         }
 
         if (strangePhase) {
-            log.warn("Unrecognized phasing '" + geno + "'.");
             vals[0] = -1;
             vals[1] = -1;
             isPhased = false;

From fb11d2c3ac07eff9017af09470ba6849c6a34f96 Mon Sep 17 00:00:00 2001
From: Yunfei Guo <yunfei.guo@bina.roche.com>
Date: Fri, 3 Mar 2017 15:49:50 -0800
Subject: [PATCH 2/2] limit warnings

---
 src/main/java/com/bina/varsim/constants/Constant.java |  1 +
 src/main/java/com/bina/varsim/util/VCFparser.java     | 10 ++++++++++
 2 files changed, 11 insertions(+)

diff --git a/src/main/java/com/bina/varsim/constants/Constant.java b/src/main/java/com/bina/varsim/constants/Constant.java
index 9873628b..2ec272a7 100644
--- a/src/main/java/com/bina/varsim/constants/Constant.java
+++ b/src/main/java/com/bina/varsim/constants/Constant.java
@@ -5,4 +5,5 @@
  */
 public class Constant {
     public static final int SVLEN = 100;
+    public static final int MAX_WARNING_REPEAT = 100;
 }
diff --git a/src/main/java/com/bina/varsim/util/VCFparser.java b/src/main/java/com/bina/varsim/util/VCFparser.java
index af88df17..8722f980 100644
--- a/src/main/java/com/bina/varsim/util/VCFparser.java
+++ b/src/main/java/com/bina/varsim/util/VCFparser.java
@@ -16,6 +16,7 @@
 import java.rmi.UnexpectedException;
 import java.util.*;
 
+import static com.bina.varsim.constants.Constant.MAX_WARNING_REPEAT;
 import static com.bina.varsim.types.VCFInfo.getType;
 
 public class VCFparser extends GzFileParser<Variant> {
@@ -28,6 +29,7 @@ public class VCFparser extends GzFileParser<Variant> {
     private String sampleId = null;
     private boolean isPassFilterRequired = false;
     private boolean chromLineSeen = false;
+    private int illegalPhasingWarningCount = 0;
 
     public VCFparser() {
         sampleIndex = 10; // the first sample
@@ -179,6 +181,14 @@ boolean isPhased(String geno, byte[] vals, ChrString chr) {
         }
 
         if (strangePhase) {
+            if (illegalPhasingWarningCount < MAX_WARNING_REPEAT) {
+                log.warn("Unrecognized phasing '" + geno + "'.");
+                illegalPhasingWarningCount++;
+                if (illegalPhasingWarningCount == MAX_WARNING_REPEAT) {
+                    log.warn("Reached max number of warnings (" + MAX_WARNING_REPEAT +
+                    ") for unrecognized phasing. No more warnings.");
+                }
+            }
             vals[0] = -1;
             vals[1] = -1;
             isPhased = false;