154 lines
4.0 KiB
Java
154 lines
4.0 KiB
Java
/*
|
|
* Copyright (c) 2010 The Broad Institute
|
|
*
|
|
* Permission is hereby granted, free of charge, to any person
|
|
* obtaining a copy of this software and associated documentation
|
|
* files (the "Software"), to deal in the Software without
|
|
* restriction, including without limitation the rights to use,
|
|
* copy, modify, merge, publish, distribute, sublicense, and/or sell
|
|
* copies of the Software, and to permit persons to whom the
|
|
* Software is furnished to do so, subject to the following
|
|
* conditions:
|
|
*
|
|
* The above copyright notice and this permission notice shall be
|
|
* included in all copies or substantial portions of the Software.
|
|
*
|
|
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
|
|
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
|
|
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
|
|
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
|
|
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
|
|
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
|
|
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
|
|
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
|
|
*/
|
|
|
|
package org.broadinstitute.sting.playground.tools.vcf;
|
|
|
|
import org.broad.tribble.vcf.VCFCodec;
|
|
|
|
import java.io.*;
|
|
import java.util.zip.*;
|
|
|
|
// Edit a VCF on the fly to be on-spec.
|
|
|
|
/**
|
|
* @author jmaguire
|
|
*/
|
|
|
|
class VCFHomogenizer implements VCFCodec.LineTransform {
|
|
|
|
//my ($chr, $off, $id, $ref, $alt, $qual, $filter, $info, $format, @genotypes) = @tokens;
|
|
public String lineTransform(String input)
|
|
{
|
|
if (input == null) { return null; }
|
|
|
|
//System.out.println("input : " + input);
|
|
|
|
// Make it tab-delimited
|
|
input = input.replaceAll(" +", "\t");
|
|
|
|
/////////
|
|
// Header corrections
|
|
if (input.startsWith("##format=VCFv3.2")) { return "##format=VCRv3.2\n"; }
|
|
if (input.startsWith("#CHROM")) { return input.replaceAll("PROB", "QUAL"); }
|
|
if (input.startsWith("#")) { return input; }
|
|
|
|
/////////
|
|
// Line-level corrections
|
|
|
|
// make "nan" into "NaN"
|
|
input = input.replaceAll("nan", "NaN");
|
|
input = input.replaceAll("DB(\\;|\\s)", "DB=1$1");
|
|
input = input.replaceAll("HM2(\\;|\\s)", "HM2=1$1");
|
|
input = input.replaceAll("HM3(\\;|\\s)", "HM3=1$1");
|
|
|
|
String[] tokens = input.split("\\s+");
|
|
|
|
/////////
|
|
// Token-level corrections
|
|
|
|
// if alt is "N", make it "."
|
|
if (tokens[4].equals("N")) { tokens[4] = "."; }
|
|
if (tokens[5].equals(".")) { tokens[5] = "-1"; }
|
|
|
|
String ref = tokens[3];
|
|
String alt = tokens[4];
|
|
String[] alts = alt.split(",");
|
|
|
|
for (int i = 9; i < tokens.length; i++)
|
|
{
|
|
if (tokens[i].equals(".")) { tokens[i] = "./.:0"; }
|
|
|
|
tokens[i] = tokens[i].replaceAll(ref, "0");
|
|
if (! alt.equals("."))
|
|
{
|
|
if (alts.length == 1)
|
|
{
|
|
tokens[i] = tokens[i].replaceAll(alt, "1");
|
|
}
|
|
else
|
|
{
|
|
for (int j = 0; j < alts.length; j++)
|
|
{
|
|
tokens[i] = tokens[i].replaceAll(alts[j], "1");
|
|
}
|
|
}
|
|
}
|
|
}
|
|
|
|
/////////
|
|
// Info-level corrections
|
|
|
|
String info = tokens[7];
|
|
String new_info = "";
|
|
String[] info_tokens = info.split(";");
|
|
for (int i = 0; i < info_tokens.length; i++)
|
|
{
|
|
if (info_tokens[i].startsWith("R2="))
|
|
{
|
|
// Fix NaN's in RNaN's in R2.
|
|
String new_token = info_tokens[i].replace("NaN", "0.0");
|
|
info_tokens[i] = new_token;
|
|
}
|
|
else if (info_tokens[i].startsWith("AC="))
|
|
{
|
|
// Fix the case where AC includes the ref count first.
|
|
String[] ACs = info_tokens[i].replaceAll("^AC=", "").split(",");
|
|
if (ACs.length == alts.length+1)
|
|
{
|
|
String new_ACs = "";
|
|
for (int j = 1; j < ACs.length; j++)
|
|
{
|
|
new_ACs += ACs[j];
|
|
if (j != (ACs.length-1)) { new_ACs += ","; }
|
|
}
|
|
info_tokens[i] = "AC=" + new_ACs;
|
|
continue;
|
|
}
|
|
}
|
|
|
|
new_info += info_tokens[i];
|
|
if (i != (info_tokens.length-1)) { new_info += ";"; }
|
|
}
|
|
tokens[7] = new_info;
|
|
|
|
|
|
/////////
|
|
// Now put it back together and emit.
|
|
String output = tokens[0];
|
|
for (int i = 1; i < tokens.length; i++)
|
|
{
|
|
output = output + "\t" + tokens[i];
|
|
}
|
|
output = output + "\n";
|
|
|
|
//System.out.println("output: " + output);
|
|
|
|
return output;
|
|
}
|
|
}
|
|
|
|
|
|
|