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Removed custom output stream for file and replaced with the standard out PrintStream 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1350 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
andrewk 2009-07-30 22:36:42 +00:00
parent 2a7dfce9ae
commit 678c2533ca
1 changed files with 8 additions and 18 deletions
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26
java/src/org/broadinstitute/sting/playground/gatk/walkers/CoverageEvalWalker.java
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@ -30,29 +30,18 @@ public class CoverageEvalWalker extends LocusWalker<List<String>, String> {
@Argument(fullName="lod_threshold", shortName="lod", doc="The lod threshold on which variants should be filtered", required=false) public Double LOD_THRESHOLD = 5.0;
@Argument(fullName="format_geli", shortName="geli", doc="Output variant calls in Geli/Picard format", required=false) public boolean GELI_OUTPUT_FORMAT = false;
@Argument(fullName="variants_out", shortName="varout", doc="File to which variants should be written", required=true) public File VARIANTS_FILE;
@Argument(fullName="min_coverage", shortName="mincov", doc="Mininum coverage to downsample to", required=false) public int min_coverage=1;
@Argument(fullName="max_coverage", shortName="maxcov", doc="Maximum coverage to downsample to", required=false) public int max_coverage=20;
@Argument(fullName="downsampling_repeats", shortName="repeat", doc="Number of times to repeat downsampling at each coverage level", required=false) public int downsampling_repeats=20;
public PrintStream variantsOut;
@Argument(fullName="max_coverage", shortName="maxcov", doc="Maximum coverage to downsample to", required=false) public int max_coverage=Integer.MAX_VALUE;
@Argument(fullName="downsampling_repeats", shortName="repeat", doc="Number of times to repeat downsampling at each coverage level", required=false) public int downsampling_repeats=1;
SingleSampleGenotyper SSG;
public void initialize() {
SSG = new SingleSampleGenotyper();
SSG.VARIANTS_FILE = VARIANTS_FILE;
SSG.initialize();
try {
variantsOut = new PrintStream(VARIANTS_FILE);
} catch (FileNotFoundException e) {
err.format("Unable to open file '%s'. Perhaps the parent directory does not exist or is read-only.\n", VARIANTS_FILE.getAbsolutePath());
System.exit(-1);
}
String header = "#Sequence Position ReferenceBase NumberOfReads MaxMappingQuality BestGenotype BtrLod BtnbLod dbSNP AA AC AG AT CC CG CT GG GT TT";
variantsOut.println("DownsampledCoverage\tAvailableCoverage\tHapmapChipGenotype\tGenotypeCallType\t"+header.substring(1));
String header = "#Sequence Position ReferenceBase NumberOfReads MaxMappingQuality BestGenotype BtrLod BtnbLod AA AC AG AT CC CG CT GG GT TT";
out.println("DownsampledCoverage\tAvailableCoverage\tHapmapChipGenotype\tGenotypeCallType\t"+header.substring(1));
}
public boolean filter(RefMetaDataTracker tracker, char ref, LocusContext context) {
@ -74,10 +63,11 @@ public class CoverageEvalWalker extends LocusWalker<List<String>, String> {
int coverage_available = reads.size();
List<Integer> coverage_levels = new ArrayList<Integer>();// = {4, 7, 10, 20, Integer.MAX_VALUE};
for (int coverage = min_coverage; coverage <= max_coverage; coverage++) {
Integer this_max_coverage = Math.min(max_coverage, coverage_available);
for (int coverage = min_coverage; coverage <= this_max_coverage; coverage++) {
coverage_levels.add(coverage);
}
coverage_levels.add(coverage_available); // Run on all available reads
//coverage_levels.add(coverage_available); // Run on all available reads
// Iterate over coverage levels
for (int coverage : coverage_levels) {
@ -108,7 +98,7 @@ public class CoverageEvalWalker extends LocusWalker<List<String>, String> {
public String reduce(List<String> alleleFreqLines, String sum) {
for (String line : alleleFreqLines) {
variantsOut.println(line);
out.println(line);
}
return "";