[med-svn] [varscan] 02/05: Imported Upstream version 2.3.7+dfsg
Andreas Tille
tille at debian.org
Tue Sep 16 12:45:52 UTC 2014
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tille pushed a commit to branch master
in repository varscan.
commit f0352e739424f103b734d2b9aa9e683bb4a34848
Author: Andreas Tille <tille at debian.org>
Date: Tue Sep 16 14:20:59 2014 +0200
Imported Upstream version 2.3.7+dfsg
---
net/sf/varscan/CallMpileup.java | 63 +++++++++++++++++++++++------------------
net/sf/varscan/CallPileup.java | 2 +-
net/sf/varscan/CopyCaller.java | 2 +-
net/sf/varscan/Copynumber.java | 4 +--
net/sf/varscan/Somatic.java | 3 +-
net/sf/varscan/Trio.java | 9 +++++-
net/sf/varscan/VarScan.java | 6 ++--
7 files changed, 53 insertions(+), 36 deletions(-)
diff --git a/net/sf/varscan/CallMpileup.java b/net/sf/varscan/CallMpileup.java
index 28590ae..ebba0b3 100644
--- a/net/sf/varscan/CallMpileup.java
+++ b/net/sf/varscan/CallMpileup.java
@@ -308,35 +308,36 @@ public class CallMpileup {
try
{
- String[] lineContents = line.split("\t");
-
- // Verify expected pileup format //
-
- if(lineContents.length > 5 && lineContents[0].length() > 0 && lineContents[1].length() > 0 && lineContents[2].length() > 0 && lineContents[3].length() > 0)
- {
- if(numBases == 1 && params.containsKey("output-vcf"))
- {
- vcfHeader += "\n" + "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT";
- if(sampleList.length() > 0)
+ String[] lineContents = line.split("\t", -1);
+
+ // Output VCF header if desired //
+
+ if(numBases == 1 && params.containsKey("output-vcf"))
+ {
+ vcfHeader += "\n" + "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT";
+ if(sampleList.length() > 0)
+ {
+ vcfHeader += "\t" + sampleList;
+ }
+ else
+ {
+ // print the VCF sample header //
+ int sampleCounter = 0;
+ for(int colCounter = 3; colCounter <= (lineContents.length - 3); colCounter += 3)
{
- vcfHeader += "\t" + sampleList;
+ sampleCounter++;
+ vcfHeader += "\tSample" + sampleCounter;
}
- else
- {
- // print the VCF sample header //
- int sampleCounter = 0;
- for(int colCounter = 3; colCounter <= (lineContents.length - 3); colCounter += 3)
- {
- sampleCounter++;
- vcfHeader += "\tSample" + sampleCounter;
- }
- }
+ }
- System.out.println(vcfHeader);
- }
+ System.out.println(vcfHeader);
+ }
+ // Verify expected pileup format //
+ if(lineContents.length > 5 && lineContents[0].length() > 0 && lineContents[1].length() > 0 && lineContents[2].length() > 0 && lineContents[3].length() > 0)
+ {
String refName = lineContents[0];
String position = lineContents[1];
String refBase = lineContents[2].toUpperCase();
@@ -564,7 +565,12 @@ public class CallMpileup {
- if(allReadDepth >= minCoverage && qualityDepth >= minCoverage)
+ if(params.containsKey("output-vcf"))
+ {
+ // Skip this if we're outputting VCF //
+
+ }
+ else if(allReadDepth >= minCoverage && qualityDepth >= minCoverage)
{
HashMap<String, String> readCounts = VarScan.getReadCounts(refBase, allReadBases, allReadQualities, minAvgQual, allMapQualities);
String positionCall = VarScan.callPosition(refBase, readCounts, "CNS", minReads2, minVarFreq, minAvgQual, pValueThreshold, minFreqForHom);
@@ -722,14 +728,17 @@ public class CallMpileup {
}
-
+ // BEGIN BUILDING OUTPUT LINE //
String outLine = refName + "\t" + position + "\t";
if(params.containsKey("output-vcf"))
{
// Calculate average sample depth //
- int avgQualityDepth = qualityDepth / (samplesRef + samplesHet + samplesHom + samplesUncalled);
+ int avgQualityDepth = 0;
+ if((samplesRef + samplesHet + samplesHom + samplesUncalled) > 0)
+ avgQualityDepth = qualityDepth / (samplesRef + samplesHet + samplesHom + samplesUncalled);
+
String refColumn = "";
String varColumn = "";
@@ -901,7 +910,7 @@ public class CallMpileup {
}
else
{
- System.err.println("Error: Invalid format for pileup at line " + numBases + "\n" + line + "\n");
+ System.err.println("Warning: Line ignored: Invalid format for pileup at line " + numBases + "\n" + line + "\n");
return;
}
diff --git a/net/sf/varscan/CallPileup.java b/net/sf/varscan/CallPileup.java
index d289312..72c6bd0 100644
--- a/net/sf/varscan/CallPileup.java
+++ b/net/sf/varscan/CallPileup.java
@@ -178,7 +178,7 @@ public class CallPileup {
try
{
- String[] lineContents = line.split("\t");
+ String[] lineContents = line.split("\t", -1);
// Verify expected pileup format //
diff --git a/net/sf/varscan/CopyCaller.java b/net/sf/varscan/CopyCaller.java
index e9b5817..0eaabff 100644
--- a/net/sf/varscan/CopyCaller.java
+++ b/net/sf/varscan/CopyCaller.java
@@ -253,7 +253,7 @@ public class CopyCaller {
int gcBin = (int) gcContent;
if(gcBin >= 0 && gcBin <= 100)
{
- gcLogSum[gcBin] += logratio;
+ gcLogSum[gcBin] += (float) logratio;
gcLogNum[gcBin]++;
}
}
diff --git a/net/sf/varscan/Copynumber.java b/net/sf/varscan/Copynumber.java
index 83c3186..443c8ae 100644
--- a/net/sf/varscan/Copynumber.java
+++ b/net/sf/varscan/Copynumber.java
@@ -735,7 +735,7 @@ public class Copynumber {
String tumorQualities = "";
// Pileup Files have 6-7 columns //
- if(normalContents.length <= 7)
+ if(normalContents.length >= 6 && normalContents.length <= 7)
{
pileupDepthNormal = Integer.parseInt(normalContents[3]);
normalQualities = normalContents[5];
@@ -748,7 +748,7 @@ public class Copynumber {
}
// Pileup Files have 6-7 columns //
- if(tumorContents.length <= 7)
+ if(tumorContents.length >= 6 && tumorContents.length <= 7)
{
tumorQualities = tumorContents[5];
pileupDepthTumor = Integer.parseInt(tumorContents[3]);
diff --git a/net/sf/varscan/Somatic.java b/net/sf/varscan/Somatic.java
index 25bb198..f652dd3 100644
--- a/net/sf/varscan/Somatic.java
+++ b/net/sf/varscan/Somatic.java
@@ -43,6 +43,7 @@ public class Somatic {
"\t--min-coverage - Minimum coverage in normal and tumor to call variant [8]\n" +
"\t--min-coverage-normal - Minimum coverage in normal to call somatic [8]\n" +
"\t--min-coverage-tumor - Minimum coverage in tumor to call somatic [6]\n" +
+ "\t--min-avg-qual - Minimum Phred quality to count a base [15]\n" +
"\t--min-var-freq - Minimum variant frequency to call a heterozygote [0.10]\n" +
"\t--min-freq-for-hom\tMinimum frequency to call homozygote [0.75]\n" +
"\t--normal-purity - Estimated purity (non-tumor content) of normal sample [1.00]\n" +
@@ -334,7 +335,7 @@ public class Somatic {
try
{
- String[] lineContents = line.split("\t");
+ String[] lineContents = line.split("\t", -1);
// Verify expected pileup format //
diff --git a/net/sf/varscan/Trio.java b/net/sf/varscan/Trio.java
index 85d46cb..f1c0271 100644
--- a/net/sf/varscan/Trio.java
+++ b/net/sf/varscan/Trio.java
@@ -78,6 +78,7 @@ public class Trio {
double strandPvalueThreshold = 0.01;
double adjustedMinVarFreq = 0.05;
double adjustedpValueThreshold = 0.10;
+ int adjustedMinReads2 = 2;
boolean strandFilter = true;
String sampleList = "";
@@ -98,6 +99,9 @@ public class Trio {
if(params.containsKey("min-reads2"))
minReads2 = Integer.parseInt(params.get("min-reads2"));
+ if(params.containsKey("adj-min-reads2"))
+ adjustedMinReads2 = Integer.parseInt(params.get("adj-min-reads2"));
+
if(params.containsKey("min-var-freq"))
minVarFreq = Double.parseDouble(params.get("min-var-freq"));
@@ -185,6 +189,9 @@ public class Trio {
System.err.println("Min var freq:\t" + minVarFreq);
System.err.println("Min avg qual:\t" + minAvgQual);
System.err.println("P-value thresh:\t" + pValueThreshold);
+ System.err.println("Adj. min reads2:\t" + adjustedMinReads2);
+ System.err.println("Adj. var freq:\t" + adjustedMinVarFreq);
+ System.err.println("Adj. p-value:\t" + adjustedpValueThreshold);
}
catch(Exception e)
{
@@ -482,7 +489,7 @@ public class Trio {
// double adjustedMinVarFreq = minVarFreq / 2.00;
// double adjustedpValueThreshold = 0.20;
- trioCall = callTrio(refBase, fatherCounts, motherCounts, childCounts, minReads2, adjustedMinVarFreq, minAvgQual, adjustedpValueThreshold, minFreqForHom);
+ trioCall = callTrio(refBase, fatherCounts, motherCounts, childCounts, adjustedMinReads2, adjustedMinVarFreq, minAvgQual, adjustedpValueThreshold, minFreqForHom);
trioCallContents = trioCall.split("\t");
// Determine if something changed //
diff --git a/net/sf/varscan/VarScan.java b/net/sf/varscan/VarScan.java
index adf2283..3c509d5 100644
--- a/net/sf/varscan/VarScan.java
+++ b/net/sf/varscan/VarScan.java
@@ -1,7 +1,7 @@
/**
* @(#)VarScan.java
*
- * Copyright (c) 2009-2010 Daniel C. Koboldt and Washington University in St. Louis
+ * Copyright (c) 2009-2013 Daniel C. Koboldt and Washington University in St. Louis
*
* COPYRIGHT
*/
@@ -478,8 +478,8 @@ public class VarScan {
}
else
{
- System.err.println("File not found: " + args[1] + "\n");
- System.exit(10);
+// System.err.println("File not found: " + args[1] + "\n");
+// System.exit(10);
}
}
--
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