Merge pull request #109 from yunfeiguo/v0.7.7

v0.7.7
bioinform · Mar 4, 2017 · b810218 · b810218
2 parents 4aeabe8 + fb11d2c
commit b810218
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Showing 4 changed files with 13 additions and 3 deletions.
diff --git 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
@@ -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/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
@@ -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
@@ -179,7 +181,14 @@ boolean isPhased(String geno, byte[] vals, ChrString chr) {
         }
 
         if (strangePhase) {
-            log.warn("Unrecognized phasing '" + geno + "'.");
+            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;