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Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable

This commit is contained in:
Eric Banks 2011-10-27 23:55:18 -04:00
parent 19e27d4568 cbc43683ee
commit 3d04bb5608
1 changed files with 2 additions and 84 deletions
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86
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
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@ -255,14 +255,6 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
@Argument(fullName="keepOriginalAC", shortName="keepOriginalAC", doc="Don't update the AC, AF, or AN values in the INFO field after selecting", required=false)
private boolean KEEP_ORIGINAL_CHR_COUNTS = false;
@Hidden
@Argument(fullName="keepAFSpectrum", shortName="keepAF", doc="Don't include loci found to be non-variant after the subsetting procedure", required=false)
private boolean KEEP_AF_SPECTRUM = false;
@Hidden
@Argument(fullName="afFile", shortName="afFile", doc="The output recal file used by ApplyRecalibration", required=false)
private File AF_FILE = new File("");
@Hidden
@Argument(fullName="family_structure_file", shortName="familyFile", doc="use -family unless you know what you're doing", required=false)
private File FAMILY_STRUCTURE_FILE = null;
@ -442,7 +434,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
mvSet.add(mv);
}
} catch ( FileNotFoundException e ) {
throw new UserException.CouldNotReadInputFile(AF_FILE, e);
throw new UserException.CouldNotReadInputFile(FAMILY_STRUCTURE_FILE, e);
}
if (outMVFile != null)
try {
@ -469,31 +461,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
if (SELECT_RANDOM_FRACTION) logger.info("Selecting approximately " + 100.0*fractionRandom + "% of the variants at random from the variant track");
if (KEEP_AF_SPECTRUM) {
try {
afBreakpoints = new ArrayList<Double>();
afBoosts = new ArrayList<Double>();
logger.info("Reading in AF boost table...");
boolean firstLine = false;
for ( final String line : new XReadLines( AF_FILE ) ) {
if (!firstLine) {
firstLine = true;
continue;
}
final String[] vals = line.split(" ");
double bkp = Double.valueOf(vals[0]);
double afb = Double.valueOf(vals[1]);
afBreakpoints.add(bkp);
afBoosts.add(afb);
}
bkDelta = afBreakpoints.get(0);
} catch ( FileNotFoundException e ) {
throw new UserException.CouldNotReadInputFile(AF_FILE, e);
}
}
}
/**
@ -566,61 +534,11 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
if (SELECT_RANDOM_NUMBER) {
randomlyAddVariant(++variantNumber, sub, ref.getBase());
}
else if (!SELECT_RANDOM_FRACTION || (!KEEP_AF_SPECTRUM && GenomeAnalysisEngine.getRandomGenerator().nextDouble() < fractionRandom)) {
else if (!SELECT_RANDOM_FRACTION || ( GenomeAnalysisEngine.getRandomGenerator().nextDouble() < fractionRandom)) {
vcfWriter.add(sub);
}
else {
if (SELECT_RANDOM_FRACTION && KEEP_AF_SPECTRUM ) {
// ok we have a comp VC and we need to match the AF spectrum of inputAFRodName.
// We then pick a variant with probablity AF*desiredFraction
if ( sub.hasAttribute(VCFConstants.ALLELE_FREQUENCY_KEY) ) {
String afo = sub.getAttributeAsString(VCFConstants.ALLELE_FREQUENCY_KEY, null);
double af;
double afBoost = 1.0;
if (afo.contains(",")) {
String[] afs = afo.split(",");
afs[0] = afs[0].substring(1,afs[0].length());
afs[afs.length-1] = afs[afs.length-1].substring(0,afs[afs.length-1].length()-1);
double[] afd = new double[afs.length];
for (int k=0; k < afd.length; k++)
afd[k] = Double.valueOf(afs[k]);
af = MathUtils.arrayMax(afd);
//af = Double.valueOf(afs[0]);
}
else
af = Double.valueOf(afo);
// now boost af by table read from file if desired
//double bkpt = 0.0;
int bkidx = 0;
if (!afBreakpoints.isEmpty()) {
for ( Double bkpt : afBreakpoints) {
if (af < bkpt + bkDelta)
break;
else bkidx++;
}
if (bkidx >=afBoosts.size())
bkidx = afBoosts.size()-1;
afBoost = afBoosts.get(bkidx);
//System.out.formatPrin("af:%f bkidx:%d afboost:%f\n",af,bkidx,afBoost);
}
//System.out.format("%s .. %4.4f\n",afo.toString(), af);
if (GenomeAnalysisEngine.getRandomGenerator().nextDouble() < fractionRandom * afBoost * afBoost)
vcfWriter.add(sub);
}
}
}
}
}