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added the ability of the VCFReader to take in compressed gzipped files natively, which is really useful for the validator 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1452 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron 2009-08-21 18:40:38 +00:00
parent 647a367680
commit 0364f8e989
1 changed files with 56 additions and 19 deletions
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75
java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFReader.java
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@ -7,6 +7,7 @@ import java.nio.charset.Charset;
import java.util.*;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import java.util.zip.GZIPInputStream;
/** The VCFReader class, which given a valid vcf file, parses out the header and VCF records */
public class VCFReader implements Iterator<VCFRecord>, Iterable<VCFRecord> {
@ -32,17 +33,14 @@ public class VCFReader implements Iterator<VCFRecord>, Iterable<VCFRecord> {
* @param vcfFile the vcf file to write
*/
public VCFReader(File vcfFile) {
Charset utf8 = Charset.forName("UTF-8");
try {
mReader = new BufferedReader(
new InputStreamReader(
new FileInputStream(vcfFile),
utf8));
} catch (FileNotFoundException e) {
throw new RuntimeException("VCFReader: Unable to find VCF file: " + vcfFile, e);
}
if (vcfFile.getName().endsWith(".gz"))
openGZipFile(vcfFile);
else
openTextVersion(vcfFile);
String line = null;
// try and parse the header
try {
ArrayList<String> lines = new ArrayList<String>();
line = mReader.readLine();
@ -55,7 +53,39 @@ public class VCFReader implements Iterator<VCFRecord>, Iterable<VCFRecord> {
} catch (IOException e) {
throw new RuntimeException("VCFReader: Failed to parse VCF File on line: " + line, e);
}
}
/**
* open a g-zipped version of the VCF format
*
* @param vcfGZipFile the file to open
*/
private void openGZipFile(File vcfGZipFile) {
try {
mReader = new BufferedReader(
new InputStreamReader(new GZIPInputStream(
new FileInputStream(vcfGZipFile))));
} catch (FileNotFoundException e) {
throw new RuntimeException("VCFReader: Unable to find VCF file: " + vcfGZipFile, e);
} catch (IOException e) {
throw new RuntimeException("VCFReader: A problem occured trying to open the file using the gzipped decompressor, filename: " + vcfGZipFile, e);
}
}
/**
* open the vcf file as a text file
*
* @param vcfFile the vcf file name
*/
private void openTextVersion(File vcfFile) {
try {
mReader = new BufferedReader(
new InputStreamReader(
new FileInputStream(vcfFile),
Charset.forName("UTF-8")));
} catch (FileNotFoundException e) {
throw new RuntimeException("VCFReader: Unable to find VCF text file: " + vcfFile, e);
}
}
/** @return true if we have another VCF record to return */
@ -90,6 +120,8 @@ public class VCFReader implements Iterator<VCFRecord>, Iterable<VCFRecord> {
* package protected so that the VCFReader can access this function
*
* @param headerStrings a list of header strings
*
* @return a VCF Header created from the list of stinrgs
*/
protected VCFHeader createHeader(List<String> headerStrings) {
@ -114,7 +146,7 @@ public class VCFReader implements Iterator<VCFRecord>, Iterable<VCFRecord> {
if (str.startsWith("#") && !str.startsWith("##")) {
String[] strings = str.substring(1).split("\\s+");
for (String s : strings) {
if (headerFields.contains(s))
if (headerFields.contains(VCFHeader.HEADER_FIELDS.valueOf(s)))
throw new RuntimeException("VCFReader: Header field duplication is not allowed");
try {
headerFields.add(VCFHeader.HEADER_FIELDS.valueOf(s));
@ -135,7 +167,8 @@ public class VCFReader implements Iterator<VCFRecord>, Iterable<VCFRecord> {
/**
* create the next VCFRecord, given the input line
*
* @param line the line from the file
* @param line the line from the file
* @param mHeader the VCF header
*
* @return the VCFRecord
*/
@ -174,10 +207,12 @@ public class VCFReader implements Iterator<VCFRecord>, Iterable<VCFRecord> {
* @param genotypeString contains the phasing information, allele information, and values for genotype parameters
* @param altAlleles the alternate allele string array, which we index into based on the field parameters
* @param referenceBase the reference base
*
* @return a VCFGenotypeRecord
*/
public static VCFGenotypeRecord getVCFGenotype(String sampleName, String formatString, String genotypeString, String altAlleles[], char referenceBase) {
// parameters to create the VCF genotype record
Map<String,String> tagToValue = new HashMap<String, String>();
Map<String, String> tagToValue = new HashMap<String, String>();
VCFGenotypeRecord.PHASE phase = VCFGenotypeRecord.PHASE.UNKNOWN;
List<String> bases = new ArrayList<String>();
@ -197,15 +232,16 @@ public class VCFReader implements Iterator<VCFRecord>, Iterable<VCFRecord> {
if (!m.matches())
throw new RuntimeException("Ubable to match GT genotype flag to it's regular expression");
phase = VCFGenotypeRecord.determinePhase(m.group(2));
addAllele(m.group(1),altAlleles,referenceBase,bases);
if (m.group(3).length() > 0) addAllele(m.group(3),altAlleles,referenceBase,bases);
addAllele(m.group(1), altAlleles, referenceBase, bases);
if (m.group(3).length() > 0) addAllele(m.group(3), altAlleles, referenceBase, bases);
}
tagToValue.put(key,parse);
if (nextDivider+1 >= genotypeString.length()) nextDivider = genotypeString.length() - 1;
genotypeString = genotypeString.substring(nextDivider+1,genotypeString.length());
tagToValue.put(key, parse);
if (nextDivider + 1 >= genotypeString.length()) nextDivider = genotypeString.length() - 1;
genotypeString = genotypeString.substring(nextDivider + 1, genotypeString.length());
}
if (keyStrings.length != tagToValue.size() || genotypeString.length() > 0) throw new RuntimeException("genotype value count doesn't match the key count");
return new VCFGenotypeRecord(sampleName,tagToValue,bases,phase,referenceBase);
if (keyStrings.length != tagToValue.size() || genotypeString.length() > 0)
throw new RuntimeException("genotype value count doesn't match the key count");
return new VCFGenotypeRecord(sampleName, tagToValue, bases, phase, referenceBase);
}
@ -215,6 +251,7 @@ public class VCFReader implements Iterator<VCFRecord>, Iterable<VCFRecord> {
* @param alleleNumber the allele number, as a string
* @param altAlleles the list of alternate alleles
* @param referenceBase the reference base
* @param bases the list of bases for this genotype call
*/
private static void addAllele(String alleleNumber, String[] altAlleles, char referenceBase, List<String> bases) {
if (Integer.valueOf(alleleNumber) == 0)