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Add an InputStream constructor, which is immensely useful for various reasons. 

Also a minor performance optimization.




git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2201 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
jmaguire 2009-12-01 17:25:00 +00:00
parent e581cceab6
commit adf8f1f8b3
1 changed files with 22 additions and 3 deletions
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25
java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFReader.java
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@ -38,8 +38,26 @@ public class VCFReader implements Iterator<VCFRecord>, Iterable<VCFRecord> {
else else
openTextVersion(vcfFile); openTextVersion(vcfFile);
String line = null; this.parseHeader();
}
/**
* Create a VCF reader, given a stream.
*
* @param stream the stream file read
*/
public VCFReader (InputStream stream)
{
mReader = new BufferedReader(
new InputStreamReader(
stream,
Charset.forName("UTF-8")));
this.parseHeader();
}
private void parseHeader()
{
String line = null;
// try and parse the header // try and parse the header
try { try {
ArrayList<String> lines = new ArrayList<String>(); ArrayList<String> lines = new ArrayList<String>();
@ -53,7 +71,7 @@ public class VCFReader implements Iterator<VCFRecord>, Iterable<VCFRecord> {
} catch (IOException e) { } catch (IOException e) {
throw new RuntimeException("VCFReader: Failed to parse VCF File on line: " + line, e); throw new RuntimeException("VCFReader: Failed to parse VCF File on line: " + line, e);
} }
} }
/** /**
* open a g-zipped version of the VCF format * open a g-zipped version of the VCF format
@ -190,9 +208,10 @@ public class VCFReader implements Iterator<VCFRecord>, Iterable<VCFRecord> {
String mFormatString = tokens[index]; String mFormatString = tokens[index];
List<VCFGenotypeRecord> genotypeRecords = new ArrayList<VCFGenotypeRecord>(); List<VCFGenotypeRecord> genotypeRecords = new ArrayList<VCFGenotypeRecord>();
index++; index++;
String[] alt_alleles = values.get(VCFHeader.HEADER_FIELDS.ALT).split(",");
for (String str : mHeader.getGenotypeSamples()) { for (String str : mHeader.getGenotypeSamples()) {
if (!tokens[index].equalsIgnoreCase(VCFGenotypeRecord.EMPTY_GENOTYPE)) if (!tokens[index].equalsIgnoreCase(VCFGenotypeRecord.EMPTY_GENOTYPE))
genotypeRecords.add(getVCFGenotype(str, mFormatString, tokens[index], values.get(VCFHeader.HEADER_FIELDS.ALT).split(","), values.get(VCFHeader.HEADER_FIELDS.REF).charAt(0))); genotypeRecords.add(getVCFGenotype(str, mFormatString, tokens[index], alt_alleles, values.get(VCFHeader.HEADER_FIELDS.REF).charAt(0)));
index++; index++;
} }
return new VCFRecord(values, mFormatString, genotypeRecords); return new VCFRecord(values, mFormatString, genotypeRecords);