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Refactoring the code; also, now it prints continuously instead of potentially storing one long string. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1421 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-08-13 01:32:46 +00:00
parent 2a01e71277
commit 0ec581080c
3 changed files with 75 additions and 73 deletions
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44
java/src/org/broadinstitute/sting/playground/gatk/walkers/fasta/FastaAlternateReferenceWalker.java
View File

@ -14,14 +14,13 @@ import java.util.Iterator;
@WalkerName("FastaAlternateReferenceMaker")
@Requires(value={DataSource.REFERENCE})
public class FastaAlternateReferenceWalker extends RefWalker<Pair<GenomeLoc, String>, Pair<GenomeLoc, String>> {
public class FastaAlternateReferenceWalker extends FastaReferenceWalker {
@Argument(fullName="maskSNPs", shortName="mask", doc="print 'N' at SNP sites instead of the alternate allele", required=false)
private Boolean MASK_SNPS = false;
@Argument(fullName="outputSequenomFormat", shortName="sequenom", doc="output results in sequenom format (overrides 'maskSNPs' argument)", required=false)
private Boolean SEQUENOM = false;
private StringBuffer sb = new StringBuffer();
int deletionBasesRemaining = 0;
public Pair<GenomeLoc, String> map(RefMetaDataTracker rodData, ReferenceContext ref, AlignmentContext context) {
@ -54,45 +53,4 @@ public class FastaAlternateReferenceWalker extends RefWalker<Pair<GenomeLoc, Str
// if we got here then we're just ref
return new Pair<GenomeLoc, String>(context.getLocation(), refBase);
}
public Pair<GenomeLoc, String> reduceInit() {
return new Pair<GenomeLoc, String>(null, "");
}
public Pair<GenomeLoc, String> reduce(Pair<GenomeLoc, String> value, Pair<GenomeLoc, String> sum) {
// if there is no interval to the left, then this is the first one
if ( sum.first == null ) {
sum.first = value.first;
sum.second = value.second;
}
// if the intervals don't overlap, print out the leftmost one and start a new one
// (end of contig or new interval)
else if ( value.first.getStart() != sum.first.getStop() + 1 ) {
printFasta(sum.first, sum.second);
sum.first = value.first;
sum.second = value.second;
}
// otherwise, merge them
else {
sum.first = GenomeLocParser.setStop(sum.first,value.first.getStop());
sum.second = sum.second.concat(value.second);
}
return sum;
}
public void onTraversalDone(Pair<GenomeLoc, String> sum) {
if (sum.second != null)
printFasta(sum.first, sum.second);
}
private void printFasta(GenomeLoc loc, String s) {
out.println(">" + loc);
int lines = s.length() / 60;
int currentStart = 0;
for (int i=0; i < lines; i++) {
out.println(s.substring(currentStart, currentStart+60));
currentStart += 60;
}
out.println(s.substring(currentStart));
}
}

54
java/src/org/broadinstitute/sting/playground/gatk/walkers/fasta/FastaReferenceWalker.java
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@ -12,50 +12,44 @@ import org.broadinstitute.sting.utils.Pair;
// create a fasta sequence file from a reference and intervals
@WalkerName("FastaReferenceMaker")
public class FastaReferenceWalker extends RefWalker<Pair<GenomeLoc, Character>, Pair<GenomeLoc, String>> {
public class FastaReferenceWalker extends RefWalker<Pair<GenomeLoc, String>, GenomeLoc> {
public Pair<GenomeLoc, Character> map(RefMetaDataTracker rodData, ReferenceContext ref, AlignmentContext context) {
return new Pair<GenomeLoc, Character>(context.getLocation(), ref.getBase());
}
protected FastaSequence fasta;
public Pair<GenomeLoc, String> reduceInit() {
return new Pair<GenomeLoc, String>(null, "");
public void initialize() {
fasta = new FastaSequence(out);
}
public Pair<GenomeLoc, String> reduce(Pair<GenomeLoc, Character> value, Pair<GenomeLoc, String> sum) {
public Pair<GenomeLoc, String> map(RefMetaDataTracker rodData, ReferenceContext ref, AlignmentContext context) {
return new Pair<GenomeLoc, String>(context.getLocation(), String.valueOf(ref.getBase()));
}
public GenomeLoc reduceInit() {
return null;
}
public GenomeLoc reduce(Pair<GenomeLoc, String> value, GenomeLoc sum) {
// if there is no interval to the left, then this is the first one
if ( sum.first == null ) {
sum.first = value.first;
sum.second = value.second.toString();
if ( sum == null ) {
sum = value.first;
fasta.append(value.second.toString());
}
// if the intervals don't overlap, print out the leftmost one and start a new one
// (end of contig or new interval)
else if ( value.first.getStart() != sum.first.getStop() + 1 ) {
printFasta(sum.first, sum.second);
sum.first = value.first;
sum.second = value.second.toString();
else if ( value.first.getStart() != sum.getStop() + 1 ) {
fasta.flush();
sum = value.first;
fasta.append(value.second.toString());
}
// otherwise, merge them
else {
sum.first = GenomeLocParser.setStop(sum.first,value.first.getStop());
sum.second = new String(sum.second + value.second);
sum = GenomeLocParser.setStop(sum, value.first.getStop());
fasta.append(value.second.toString());
}
return sum;
}
public void onTraversalDone(Pair<GenomeLoc, String> sum) {
if (sum.second != null)
printFasta(sum.first, sum.second);
}
private void printFasta(GenomeLoc loc, String s) {
out.println(">" + loc);
int lines = s.length() / 60;
int currentStart = 0;
for (int i=0; i < lines; i++) {
out.println(s.substring(currentStart, currentStart+60));
currentStart += 60;
}
out.println(s.substring(currentStart));
public void onTraversalDone(GenomeLoc sum) {
fasta.flush();
}
}

50
java/src/org/broadinstitute/sting/playground/gatk/walkers/fasta/FastaSequence.java 100755
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@ -0,0 +1,50 @@
package org.broadinstitute.sting.playground.gatk.walkers.fasta;
import org.broadinstitute.sting.utils.GenomeLoc;
import java.io.PrintStream;
// fasta sequence holder class
public class FastaSequence {
private PrintStream out;
private StringBuffer sb = new StringBuffer();
private long sequenceCounter = 1;
private boolean printedHeader = false;
public FastaSequence(PrintStream out) {
this.out = out;
}
public void append(String s) {
sb.append(s);
printFasta(false);
}
public void flush() {
printFasta(true);
printedHeader = false;
}
private void printFasta(boolean printAll) {
if ( sb.length() == 0 || (!printAll && sb.length() < 60) )
return;
if ( !printedHeader ) {
out.println(">" + sequenceCounter++);
printedHeader = true;
}
int lines = sb.length() / 60;
int currentStart = 0;
for (int i=0; i < lines; i++) {
out.println(sb.substring(currentStart, currentStart+60));
currentStart += 60;
}
if ( printAll ) {
out.println(sb.substring(currentStart));
sb.setLength(0);
} else {
sb.delete(0, currentStart);
}
}
}