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Changed the parameter names from cds to baits 

Making the usage more clear since the parameter is being used over and over to define baited
regions. Updated the headers accordingly and made it more readable.
This commit is contained in:
Mauricio Carneiro 2013-10-24 17:13:25 -04:00
parent 5d6421494b
commit 5ed47988b8
1 changed files with 12 additions and 13 deletions
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25
protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/missing/QualifyMissingIntervals.java
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@ -126,11 +126,10 @@ public final class QualifyMissingIntervals extends LocusWalker<Metrics, Metrics>
public String targetsFile; public String targetsFile;
/** /**
* List of coding sequence intervals (exons) if different from the targets file, to distinguish intervals * List of baits to distinguish untargeted intervals from those that are targeted but not covered
* that overlap the cds and intervals that don't.
*/ */
@Argument(shortName = "cds", required = false) @Argument(shortName = "baits", required = false)
public String cdsFile = null; public String baitsFile = null;
/** /**
* This value will be used to determine whether or not an interval had too high or too low GC content to be * This value will be used to determine whether or not an interval had too high or too low GC content to be
@ -183,8 +182,8 @@ public final class QualifyMissingIntervals extends LocusWalker<Metrics, Metrics>
} }
GATKReport simpleReport; GATKReport simpleReport;
GenomeLocSortedSet target; GenomeLocSortedSet targets;
GenomeLocSortedSet cds; GenomeLocSortedSet baits;
public boolean isReduceByInterval() { public boolean isReduceByInterval() {
return true; return true;
@ -192,13 +191,13 @@ public final class QualifyMissingIntervals extends LocusWalker<Metrics, Metrics>
public void initialize() { public void initialize() {
// if cds file is not provided, just use the targets file (no harm done) // if cds file is not provided, just use the targets file (no harm done)
if (cdsFile == null) if (baitsFile == null)
cdsFile = targetsFile; baitsFile = targetsFile;
simpleReport = GATKReport.newSimpleReport("QualifyMissingIntervals", "IN", "GC", "BQ", "MQ", "DP", "TP", "TS", "CD", "LN", "DS"); simpleReport = GATKReport.newSimpleReport("QualifyMissingIntervals", "INTERVAL", "GC", "BQ", "MQ", "DP", "POS_IN_TARGET", "TARGET_SIZE", "BAITED", "MISSING_SIZE", "INTERPRETATION");
final GenomeLocParser parser = getToolkit().getGenomeLocParser(); final GenomeLocParser parser = getToolkit().getGenomeLocParser();
target = new GenomeLocSortedSet(parser, IntervalUtils.intervalFileToList(parser, targetsFile)); targets = new GenomeLocSortedSet(parser, IntervalUtils.intervalFileToList(parser, targetsFile));
cds = new GenomeLocSortedSet(parser, IntervalUtils.intervalFileToList(parser, cdsFile)); baits = new GenomeLocSortedSet(parser, IntervalUtils.intervalFileToList(parser, baitsFile));
} }
public Metrics reduceInit() { public Metrics reduceInit() {
@ -241,7 +240,7 @@ public final class QualifyMissingIntervals extends LocusWalker<Metrics, Metrics>
for (Pair<GenomeLoc, Metrics> r : results) { for (Pair<GenomeLoc, Metrics> r : results) {
final GenomeLoc interval = r.getFirst(); final GenomeLoc interval = r.getFirst();
final Metrics metrics = r.getSecond(); final Metrics metrics = r.getSecond();
final List<GenomeLoc> overlappingIntervals = target.getOverlapping(interval); final List<GenomeLoc> overlappingIntervals = targets.getOverlapping(interval);
simpleReport.addRow( simpleReport.addRow(
interval.toString(), interval.toString(),
@ -251,7 +250,7 @@ public final class QualifyMissingIntervals extends LocusWalker<Metrics, Metrics>
metrics.depth(), metrics.depth(),
getPositionInTarget(interval, overlappingIntervals), getPositionInTarget(interval, overlappingIntervals),
getTargetSize(overlappingIntervals), getTargetSize(overlappingIntervals),
cds.overlaps(interval), baits.overlaps(interval),
interval.size(), interval.size(),
interpret(metrics, interval) interpret(metrics, interval)
); );