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GenomeAnalysisTK: better documentation of validation option. 

AlleleFrequencyWalker: output the last reference interval if it's left hanging open.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@258 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
jmaguire 2009-04-02 16:11:20 +00:00
parent 816e768a74
commit 25ace306b9
2 changed files with 39 additions and 4 deletions
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2
java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java
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@ -98,7 +98,7 @@ public class GenomeAnalysisTK extends CommandLineProgram {
protected void setupArgs() { protected void setupArgs() {
m_parser.addRequiredArg("input_file", "I", "SAM or BAM file", "INPUT_FILE"); m_parser.addRequiredArg("input_file", "I", "SAM or BAM file", "INPUT_FILE");
m_parser.addOptionalArg("maximum_reads", "M", "Maximum number of reads to process before exiting", "MAX_READS_ARG"); m_parser.addOptionalArg("maximum_reads", "M", "Maximum number of reads to process before exiting", "MAX_READS_ARG");
m_parser.addOptionalArg("validation_strictness", "S", "How strict should we be with validation", "STRICTNESS_ARG"); m_parser.addOptionalArg("validation_strictness", "S", "How strict should we be with validation (lenient|silent|strict)", "STRICTNESS_ARG");
m_parser.addOptionalArg("reference_sequence", "R", "Reference sequence file", "REF_FILE_ARG"); m_parser.addOptionalArg("reference_sequence", "R", "Reference sequence file", "REF_FILE_ARG");
m_parser.addOptionalArg("genome_region", "L", "Genome region to operation on: from chr:start-end", "REGION_STR"); m_parser.addOptionalArg("genome_region", "L", "Genome region to operation on: from chr:start-end", "REGION_STR");
m_parser.addRequiredArg("analysis_type", "T", "Type of analysis to run", "Analysis_Name"); m_parser.addRequiredArg("analysis_type", "T", "Type of analysis to run", "Analysis_Name");

41
java/src/org/broadinstitute/sting/playground/gatk/walkers/AlleleFrequencyWalker.java
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@ -18,7 +18,7 @@ import java.io.PrintStream;
public class AlleleFrequencyWalker extends LocusWalker<AlleleFrequencyEstimate, String> public class AlleleFrequencyWalker extends LocusWalker<AlleleFrequencyEstimate, String>
{ {
@Argument public int N; @Argument public int N;
@Argument public int DOWNSAMPLE; @Argument(required=false,defaultValue="0") public int DOWNSAMPLE;
@Argument public String GFF_OUTPUT_FILE; @Argument public String GFF_OUTPUT_FILE;
protected static Logger logger = Logger.getLogger(AlleleFrequencyWalker.class); protected static Logger logger = Logger.getLogger(AlleleFrequencyWalker.class);
@ -32,6 +32,18 @@ public class AlleleFrequencyWalker extends LocusWalker<AlleleFrequencyEstimate,
String bases = getBases(context); String bases = getBases(context);
double quals[][] = getOneBaseQuals(context); double quals[][] = getOneBaseQuals(context);
/*
// DEBUG: print the data for a read
{
List<SAMRecord> reads = context.getReads();
for (int i = 0; i < reads.size(); i++)
{
String cigar = reads.get(i).getCigarString();
System.out.println("DEBUG " + cigar);
}
}
*/
logger.debug(String.format("In alleleFrequnecy walker: N=%d, d=%d", N, DOWNSAMPLE)); logger.debug(String.format("In alleleFrequnecy walker: N=%d, d=%d", N, DOWNSAMPLE));
if ((DOWNSAMPLE != 0) && (DOWNSAMPLE < bases.length())) if ((DOWNSAMPLE != 0) && (DOWNSAMPLE < bases.length()))
@ -99,7 +111,8 @@ public class AlleleFrequencyWalker extends LocusWalker<AlleleFrequencyEstimate,
return alleleFreq; return alleleFreq;
} }
static public String getBases (LocusContext context) { static public String getBases (LocusContext context)
{
// Convert bases to CharArray // Convert bases to CharArray
int numReads = context.getReads().size(); //numReads(); int numReads = context.getReads().size(); //numReads();
char[] bases = new char[numReads]; char[] bases = new char[numReads];
@ -115,7 +128,8 @@ public class AlleleFrequencyWalker extends LocusWalker<AlleleFrequencyEstimate,
return new String(bases); return new String(bases);
} }
static public double[][] getOneBaseQuals (LocusContext context) { static public double[][] getOneBaseQuals (LocusContext context)
{
int numReads = context.getReads().size(); //numReads(); int numReads = context.getReads().size(); //numReads();
double[][] quals = new double[numReads][4]; double[][] quals = new double[numReads][4];
@ -472,6 +486,27 @@ public class AlleleFrequencyWalker extends LocusWalker<AlleleFrequencyEstimate,
public void onTraversalDone(String result) public void onTraversalDone(String result)
{ {
if (inside_confident_ref_interval)
{
// if we have a confident reference interval still hanging open, close it.
String tokens[] = confident_ref_interval_start.split(":");
String contig = tokens[0];
int start = Integer.parseInt(tokens[1]);
int end = last_position_considered;
double lod = confident_ref_interval_LOD_sum / confident_ref_interval_length;
output.format("%s\tCALLER\tREFERENCE\t%d\t%d\t%f\t.\t.\tLENGTH %d\n",
contig,
start,
end,
lod,
(int)(confident_ref_interval_length));
inside_confident_ref_interval = false;
}
try try
{ {
this.output.flush(); this.output.flush();