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varscan.patch
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varscan.patch
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diff --git a/../sequencing_workflows/VarScan.v2.4.1/net/sf/varscan/Copynumber.class b/./net/sf/varscan/Copynumber.class
index 86c2f30..50d6de4 100644
Binary files a/../sequencing_workflows/VarScan.v2.4.1/net/sf/varscan/Copynumber.class and b/./net/sf/varscan/Copynumber.class differ
diff --git a/../sequencing_workflows/VarScan.v2.4.1/net/sf/varscan/Copynumber.java b/./net/sf/varscan/Copynumber.java
index 935f118..6256147 100644
--- a/../sequencing_workflows/VarScan.v2.4.1/net/sf/varscan/Copynumber.java
+++ b/./net/sf/varscan/Copynumber.java
@@ -227,14 +227,35 @@ public class Copynumber {
int pileupDepthNormal = Integer.parseInt(lineContents[normalOffset]);
//String normalBases = lineContents[normalOffset + 1];
String normalQualities = lineContents[normalOffset + 2];
-
+
+ //test code from DWB:
+ if (pileupDepthNormal == 0 && (! lineContents[normalOffset + 2].equals("*")) && (! lineContents[normalOffset + 2].equals(""))){
+ System.err.println("Issue with normal depth:" + line);
+ return;
+ }else if (pileupDepthNormal == 0){
+ normalQualities = "*";
+ }
+
+ //end code
+
// Parse tumor, which should be second sample //
int tumorOffset = 6;
int pileupDepthTumor = Integer.parseInt(lineContents[tumorOffset]);
//String tumorBases = lineContents[tumorOffset + 1];
- String tumorQualities = lineContents[tumorOffset + 2];
-
-
+
+ //Modification from DWB to deal with parsing error resulting from samtools 1.1 etc
+ //in this output file, a string like below is produced:
+ //1 69500 T 5 .,,.^:. CabBB 0
+ //when samtools, say samtools-0.1.18 would add two * after the 0.
+
+ String tumorQualities = "*";
+
+ if ((tumorOffset + 2) == (lineContents.length-1)){
+ tumorQualities = lineContents[tumorOffset + 2];
+ }
+
+ //end modification
+
// If either sample met the minimum coverage and both had at least one read //
// if((pileupDepthNormal >= minCoverage || pileupDepthTumor >= minCoverage) && normalQualities.length() > 0)// && tumorQualities.length() > 0)
diff --git a/../sequencing_workflows/VarScan.v2.4.1/net/sf/varscan/FpFilter.class b/./net/sf/varscan/FpFilter.class
index 1e858e9..7f5e2c1 100644
Binary files a/../sequencing_workflows/VarScan.v2.4.1/net/sf/varscan/FpFilter.class and b/./net/sf/varscan/FpFilter.class differ
diff --git a/../sequencing_workflows/VarScan.v2.4.1/net/sf/varscan/FpFilter.java b/./net/sf/varscan/FpFilter.java
index ffce630..fc9fb42 100644
--- a/../sequencing_workflows/VarScan.v2.4.1/net/sf/varscan/FpFilter.java
+++ b/./net/sf/varscan/FpFilter.java
@@ -304,18 +304,7 @@ public class FpFilter {
vcfHeaderInfo += "\n##FILTER=<ID=MMQSdiff,Description=\"Mismatch quality sum difference (ref - var) > " + maxMMQSdiff + "\">";
vcfHeaderInfo += "\n##FILTER=<ID=MapQualDiff,Description=\"Mapping quality difference (ref - var) > " + maxMapQualDiff + "\">";
vcfHeaderInfo += "\n##FILTER=<ID=ReadLenDiff,Description=\"Average supporting read length difference (ref - var) > " + maxReadLenDiff + "\">";
-
- //Added by DWB to adhere to the VCF standard that all FILTERS need to be specified
-
- vcfHeaderInfo += "\n##FILTER=<ID=RefReadPos,Description=\"Minimum average read position of ref-supporting reads below " + minRefReadPos + "\">";
- vcfHeaderInfo += "\n##FILTER=<ID=RefDist3,Description=\"Minimum average distance to effective 3' end (ref) " + minRefDist3 + "\">";
- vcfHeaderInfo += "\n##FILTER=<ID=RefMMQS,Description=\"Maximum mismatch quality sum of reference-supporting reads " + maxRefMMQS + "\">";
- vcfHeaderInfo += "\n##FILTER=<ID=RefAvgRL,Description=\"Minimum average trimmed read length for ref allele " + minRefAvgRL + "\">";
- vcfHeaderInfo += "\n##FILTER=<ID=VarAvgRL,Description=\"Minimum average trimmed read length for var allele " + minVarAvgRL + "\">";
- vcfHeaderInfo += "\n##FILTER=<ID=NoReadCounts,Description=\"No read counts found \">";
-
- //end DWB mods
-
+
// Parse the infile line by line //
@@ -563,9 +552,7 @@ public class FpFilter {
refDist3 = Double.parseDouble(refContents[13]);
// ONLY APPLY THESE FILTERS IF WE HAVE 2+ REF-SUPPORTING READS //
-
- //DWB: VCF standard dicates that filters should be ';' delimited not comma delimited, fixed below for every failReason
-
+
if(refReads >= 2)
{
// Variant read position for ref-supporting reads //
@@ -573,7 +560,7 @@ public class FpFilter {
if(refPos < minRefReadPos)
{
if(failReason.length() > 0)
- failReason += ";";
+ failReason += ",";
failReason += "RefReadPos";
stats.put("numFailRefReadPos", (stats.get("numFailRefReadPos") + 1));
}
@@ -581,7 +568,7 @@ public class FpFilter {
if(refDist3 < minRefDist3)
{
if(failReason.length() > 0)
- failReason += ";";
+ failReason += ",";
failReason += "RefDist3";
stats.put("numFailRefDist3", (stats.get("numFailRefDist3") + 1));
}
@@ -591,7 +578,7 @@ public class FpFilter {
if(refReads > 0 && refMapQual < minRefMapQual)
{
if(failReason.length() > 0)
- failReason += ";";
+ failReason += ",";
failReason += "RefMapQual";
stats.put("numFailRefMapQual", (stats.get("numFailRefMapQual") + 1));
@@ -602,7 +589,7 @@ public class FpFilter {
if(refMMQS > maxRefMMQS)
{
if(failReason.length() > 0)
- failReason += ";";
+ failReason += ",";
failReason += "RefMMQS";
stats.put("numFailRefMMQS", (stats.get("numFailRefMMQS") + 1));
}
@@ -612,7 +599,7 @@ public class FpFilter {
if(!isIndel && refReads > 0 && refRL < minRefAvgRL)
{
if(failReason.length() > 0)
- failReason += ";";
+ failReason += ",";
failReason += "RefAvgRL";
stats.put("numFailRefAvgRL", (stats.get("numFailRefAvgRL") + 1));
}
@@ -634,7 +621,7 @@ public class FpFilter {
else
{
if(failReason.length() > 0)
- failReason += ";";
+ failReason += ",";
failReason += "VarCount";
stats.put("numFailVarCount", (stats.get("numFailVarCount") + 1));
}
@@ -647,7 +634,7 @@ public class FpFilter {
if(varFreq < minVarFreq)
{
if(failReason.length() > 0)
- failReason += ";";
+ failReason += ",";
failReason += "VarFreq";
stats.put("numFailVarFreq", (stats.get("numFailVarFreq") + 1));
}
@@ -656,7 +643,7 @@ public class FpFilter {
if(varPos < minVarReadPos)
{
if(failReason.length() > 0)
- failReason += ";";
+ failReason += ",";
failReason += "VarReadPos";
stats.put("numFailVarReadPos", (stats.get("numFailVarReadPos") + 1));
}
@@ -664,7 +651,7 @@ public class FpFilter {
if(varDist3 < minVarDist3)
{
if(failReason.length() > 0)
- failReason += ";";
+ failReason += ",";
failReason += "VarDist3";
stats.put("numFailVarDist3", (stats.get("numFailVarDist3") + 1));
}
@@ -675,7 +662,7 @@ public class FpFilter {
if(varMMQS > maxVarMMQS)
{
if(failReason.length() > 0)
- failReason += ";";
+ failReason += ",";
failReason += "VarMMQS";
stats.put("numFailVarMMQS", (stats.get("numFailVarMMQS") + 1));
}
@@ -686,7 +673,7 @@ public class FpFilter {
if(varReads > 0 && varMapQual < minVarMapQual)
{
if(failReason.length() > 0)
- failReason += ";";
+ failReason += ",";
failReason += "VarMapQual";
stats.put("numFailVarMapQual", (stats.get("numFailVarMapQual") + 1));
}
@@ -696,7 +683,7 @@ public class FpFilter {
if(refReads > 0 && refBaseQual < minRefBaseQual)
{
if(failReason.length() > 0)
- failReason += ";";
+ failReason += ",";
failReason += "RefBaseQual";
stats.put("numFailRefBaseQual", (stats.get("numFailRefBaseQual") + 1));
@@ -705,7 +692,7 @@ public class FpFilter {
if(!isIndel && varReads > 0 && varBaseQual < minVarBaseQual)
{
if(failReason.length() > 0)
- failReason += ";";
+ failReason += ",";
failReason += "VarBaseQual";
stats.put("numFailVarBaseQual", (stats.get("numFailVarBaseQual") + 1));
}
@@ -713,7 +700,7 @@ public class FpFilter {
if(!isIndel && varReads > 0 && varRL < minVarAvgRL)
{
if(failReason.length() > 0)
- failReason += ";";
+ failReason += ",";
failReason += "VarAvgRL";
stats.put("numFailVarAvgRL", (stats.get("numFailVarAvgRL") + 1));
}
@@ -732,7 +719,7 @@ public class FpFilter {
if(varStrandedness < minStrandedness || (1 - varStrandedness) < minStrandedness)
{
if(failReason.length() > 0)
- failReason += ";";
+ failReason += ",";
failReason += "Strand";
stats.put("numFailStrand", (stats.get("numFailStrand") + 1));
// System.err.println(positionKey + "\t" + refReadsPlus + "\t" + refReadsMinus + "\t" + refStrandedness + "\t" + varReadsPlus + "\t" + varReadsMinus + "\t" + varStrandedness);
@@ -752,7 +739,7 @@ public class FpFilter {
if(mmqsDiff > maxMMQSdiff)
{
if(failReason.length() > 0)
- failReason += ";";
+ failReason += ",";
failReason += "MMQSdiff";
stats.put("numFailMMQSdiff", (stats.get("numFailMMQSdiff") + 1));
}
@@ -766,7 +753,7 @@ public class FpFilter {
if(mapQualDiff > maxMapQualDiff)
{
if(failReason.length() > 0)
- failReason += ";";
+ failReason += ",";
failReason += "MapQualDiff";
stats.put("numFailMapQualDiff", (stats.get("numFailMapQualDiff") + 1));
}
@@ -776,14 +763,14 @@ public class FpFilter {
if(avgReadLenDiff > maxReadLenDiff)
{
if(failReason.length() > 0)
- failReason += ";";
+ failReason += ",";
failReason += "ReadLenDiff";
stats.put("numFailReadLenDiff", (stats.get("numFailReadLenDiff") + 1));
}
}
- //end DWB mods
+
// Check to see if it failed any filters. If so, mark it for failure //
if(failReason.length() > 0)
diff --git a/./test.p b/./test.p
new file mode 100644
index 0000000..7d01158
--- /dev/null
+++ b/./test.p
@@ -0,0 +1,224 @@
+diff --git a/../sequencing_workflows/VarScan.v2.4.1/net/sf/varscan/Copynumber.class b/./net/sf/varscan/Copynumber.class
+index 86c2f30..50d6de4 100644
+Binary files a/../sequencing_workflows/VarScan.v2.4.1/net/sf/varscan/Copynumber.class and b/./net/sf/varscan/Copynumber.class differ
+diff --git a/../sequencing_workflows/VarScan.v2.4.1/net/sf/varscan/Copynumber.java b/./net/sf/varscan/Copynumber.java
+index 935f118..6256147 100644
+--- a/../sequencing_workflows/VarScan.v2.4.1/net/sf/varscan/Copynumber.java
++++ b/./net/sf/varscan/Copynumber.java
+@@ -227,14 +227,35 @@ public class Copynumber {
+ int pileupDepthNormal = Integer.parseInt(lineContents[normalOffset]);
+ //String normalBases = lineContents[normalOffset + 1];
+ String normalQualities = lineContents[normalOffset + 2];
+-
++
++ //test code from DWB:
++ if (pileupDepthNormal == 0 && (! lineContents[normalOffset + 2].equals("*")) && (! lineContents[normalOffset + 2].equals(""))){
++ System.err.println("Issue with normal depth:" + line);
++ return;
++ }else if (pileupDepthNormal == 0){
++ normalQualities = "*";
++ }
++
++ //end code
++
+ // Parse tumor, which should be second sample //
+ int tumorOffset = 6;
+ int pileupDepthTumor = Integer.parseInt(lineContents[tumorOffset]);
+ //String tumorBases = lineContents[tumorOffset + 1];
+- String tumorQualities = lineContents[tumorOffset + 2];
+-
+-
++
++ //Modification from DWB to deal with parsing error resulting from samtools 1.1 etc
++ //in this output file, a string like below is produced:
++ //1 69500 T 5 .,,.^:. CabBB 0
++ //when samtools, say samtools-0.1.18 would add two * after the 0.
++
++ String tumorQualities = "*";
++
++ if ((tumorOffset + 2) == (lineContents.length-1)){
++ tumorQualities = lineContents[tumorOffset + 2];
++ }
++
++ //end modification
++
+ // If either sample met the minimum coverage and both had at least one read //
+
+ // if((pileupDepthNormal >= minCoverage || pileupDepthTumor >= minCoverage) && normalQualities.length() > 0)// && tumorQualities.length() > 0)
+diff --git a/../sequencing_workflows/VarScan.v2.4.1/net/sf/varscan/FpFilter.class b/./net/sf/varscan/FpFilter.class
+index 1e858e9..7f5e2c1 100644
+Binary files a/../sequencing_workflows/VarScan.v2.4.1/net/sf/varscan/FpFilter.class and b/./net/sf/varscan/FpFilter.class differ
+diff --git a/../sequencing_workflows/VarScan.v2.4.1/net/sf/varscan/FpFilter.java b/./net/sf/varscan/FpFilter.java
+index ffce630..fc9fb42 100644
+--- a/../sequencing_workflows/VarScan.v2.4.1/net/sf/varscan/FpFilter.java
++++ b/./net/sf/varscan/FpFilter.java
+@@ -304,18 +304,7 @@ public class FpFilter {
+ vcfHeaderInfo += "\n##FILTER=<ID=MMQSdiff,Description=\"Mismatch quality sum difference (ref - var) > " + maxMMQSdiff + "\">";
+ vcfHeaderInfo += "\n##FILTER=<ID=MapQualDiff,Description=\"Mapping quality difference (ref - var) > " + maxMapQualDiff + "\">";
+ vcfHeaderInfo += "\n##FILTER=<ID=ReadLenDiff,Description=\"Average supporting read length difference (ref - var) > " + maxReadLenDiff + "\">";
+-
+- //Added by DWB to adhere to the VCF standard that all FILTERS need to be specified
+-
+- vcfHeaderInfo += "\n##FILTER=<ID=RefReadPos,Description=\"Minimum average read position of ref-supporting reads below " + minRefReadPos + "\">";
+- vcfHeaderInfo += "\n##FILTER=<ID=RefDist3,Description=\"Minimum average distance to effective 3' end (ref) " + minRefDist3 + "\">";
+- vcfHeaderInfo += "\n##FILTER=<ID=RefMMQS,Description=\"Maximum mismatch quality sum of reference-supporting reads " + maxRefMMQS + "\">";
+- vcfHeaderInfo += "\n##FILTER=<ID=RefAvgRL,Description=\"Minimum average trimmed read length for ref allele " + minRefAvgRL + "\">";
+- vcfHeaderInfo += "\n##FILTER=<ID=VarAvgRL,Description=\"Minimum average trimmed read length for var allele " + minVarAvgRL + "\">";
+- vcfHeaderInfo += "\n##FILTER=<ID=NoReadCounts,Description=\"No read counts found \">";
+-
+- //end DWB mods
+-
++
+
+ // Parse the infile line by line //
+
+@@ -563,9 +552,7 @@ public class FpFilter {
+ refDist3 = Double.parseDouble(refContents[13]);
+
+ // ONLY APPLY THESE FILTERS IF WE HAVE 2+ REF-SUPPORTING READS //
+-
+- //DWB: VCF standard dicates that filters should be ';' delimited not comma delimited, fixed below for every failReason
+-
++
+ if(refReads >= 2)
+ {
+ // Variant read position for ref-supporting reads //
+@@ -573,7 +560,7 @@ public class FpFilter {
+ if(refPos < minRefReadPos)
+ {
+ if(failReason.length() > 0)
+- failReason += ";";
++ failReason += ",";
+ failReason += "RefReadPos";
+ stats.put("numFailRefReadPos", (stats.get("numFailRefReadPos") + 1));
+ }
+@@ -581,7 +568,7 @@ public class FpFilter {
+ if(refDist3 < minRefDist3)
+ {
+ if(failReason.length() > 0)
+- failReason += ";";
++ failReason += ",";
+ failReason += "RefDist3";
+ stats.put("numFailRefDist3", (stats.get("numFailRefDist3") + 1));
+ }
+@@ -591,7 +578,7 @@ public class FpFilter {
+ if(refReads > 0 && refMapQual < minRefMapQual)
+ {
+ if(failReason.length() > 0)
+- failReason += ";";
++ failReason += ",";
+ failReason += "RefMapQual";
+ stats.put("numFailRefMapQual", (stats.get("numFailRefMapQual") + 1));
+
+@@ -602,7 +589,7 @@ public class FpFilter {
+ if(refMMQS > maxRefMMQS)
+ {
+ if(failReason.length() > 0)
+- failReason += ";";
++ failReason += ",";
+ failReason += "RefMMQS";
+ stats.put("numFailRefMMQS", (stats.get("numFailRefMMQS") + 1));
+ }
+@@ -612,7 +599,7 @@ public class FpFilter {
+ if(!isIndel && refReads > 0 && refRL < minRefAvgRL)
+ {
+ if(failReason.length() > 0)
+- failReason += ";";
++ failReason += ",";
+ failReason += "RefAvgRL";
+ stats.put("numFailRefAvgRL", (stats.get("numFailRefAvgRL") + 1));
+ }
+@@ -634,7 +621,7 @@ public class FpFilter {
+ else
+ {
+ if(failReason.length() > 0)
+- failReason += ";";
++ failReason += ",";
+ failReason += "VarCount";
+ stats.put("numFailVarCount", (stats.get("numFailVarCount") + 1));
+ }
+@@ -647,7 +634,7 @@ public class FpFilter {
+ if(varFreq < minVarFreq)
+ {
+ if(failReason.length() > 0)
+- failReason += ";";
++ failReason += ",";
+ failReason += "VarFreq";
+ stats.put("numFailVarFreq", (stats.get("numFailVarFreq") + 1));
+ }
+@@ -656,7 +643,7 @@ public class FpFilter {
+ if(varPos < minVarReadPos)
+ {
+ if(failReason.length() > 0)
+- failReason += ";";
++ failReason += ",";
+ failReason += "VarReadPos";
+ stats.put("numFailVarReadPos", (stats.get("numFailVarReadPos") + 1));
+ }
+@@ -664,7 +651,7 @@ public class FpFilter {
+ if(varDist3 < minVarDist3)
+ {
+ if(failReason.length() > 0)
+- failReason += ";";
++ failReason += ",";
+ failReason += "VarDist3";
+ stats.put("numFailVarDist3", (stats.get("numFailVarDist3") + 1));
+ }
+@@ -675,7 +662,7 @@ public class FpFilter {
+ if(varMMQS > maxVarMMQS)
+ {
+ if(failReason.length() > 0)
+- failReason += ";";
++ failReason += ",";
+ failReason += "VarMMQS";
+ stats.put("numFailVarMMQS", (stats.get("numFailVarMMQS") + 1));
+ }
+@@ -686,7 +673,7 @@ public class FpFilter {
+ if(varReads > 0 && varMapQual < minVarMapQual)
+ {
+ if(failReason.length() > 0)
+- failReason += ";";
++ failReason += ",";
+ failReason += "VarMapQual";
+ stats.put("numFailVarMapQual", (stats.get("numFailVarMapQual") + 1));
+ }
+@@ -696,7 +683,7 @@ public class FpFilter {
+ if(refReads > 0 && refBaseQual < minRefBaseQual)
+ {
+ if(failReason.length() > 0)
+- failReason += ";";
++ failReason += ",";
+ failReason += "RefBaseQual";
+ stats.put("numFailRefBaseQual", (stats.get("numFailRefBaseQual") + 1));
+
+@@ -705,7 +692,7 @@ public class FpFilter {
+ if(!isIndel && varReads > 0 && varBaseQual < minVarBaseQual)
+ {
+ if(failReason.length() > 0)
+- failReason += ";";
++ failReason += ",";
+ failReason += "VarBaseQual";
+ stats.put("numFailVarBaseQual", (stats.get("numFailVarBaseQual") + 1));
+ }
+@@ -713,7 +700,7 @@ public class FpFilter {
+ if(!isIndel && varReads > 0 && varRL < minVarAvgRL)
+ {
+ if(failReason.length() > 0)
+- failReason += ";";
++ failReason += ",";
+ failReason += "VarAvgRL";
+ stats.put("numFailVarAvgRL", (stats.get("numFailVarAvgRL") + 1));
+ }
+@@ -732,7 +719,7 @@ public class FpFilter {
+ if(varStrandedness < minStrandedness || (1 - varStrandedness) < minStrandedness)
+ {
+ if(failReason.length() > 0)
+- failReason += ";";
++ failReason += ",";
+ failReason += "Strand";
+ stats.put("numFailStrand", (stats.get("numFailStrand") + 1));
+ // System.err.println(positionKey + "\t" + refReadsPlus + "\t" + refReadsMinus + "\t" + refStrandedness + "\t" + varReadsPlus + "\t" + varReadsMinus + "\t" + varStrandedness);
+@@ -752,7 +739,7 @@ public class FpFilter {
+ if(mmqsDiff > maxMMQSdiff)
+ {
+ if(failReason.length() > 0)
\ No newline at end of file