Changes to Depth of Coverage:
- For speedup in large number of samples, base counts are done on a per read group level, then merged into counts on larger partitions (samples, libraries, etc) + passed all integration tests before next item - Added additional summary item, a coverage threshold. Set by (possibly multiple) -ct flags, the summary outputs will have columns for "%_bases_covered_to_X"; both per sample, and per sample per interval summary files are effected (thus md5s changed for these) NOTE: This is the last revision that will include the per-gene summary files. Once DesignFileGenerator is sufficiently general, and has integration tests, it will be moved to core and the per-gene summary from Depth of Coverage will be retired. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3437 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl
parent
0607f76a15
commit
88a06ad81f
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@ -1,5 +1,6 @@
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package org.broadinstitute.sting.gatk.walkers.coverage;
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import net.sf.samtools.SAMReadGroupRecord;
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import net.sf.samtools.SAMRecord;
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import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
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import org.broadinstitute.sting.utils.BaseUtils;
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@ -40,39 +41,67 @@ public class CoverageUtils {
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return counts;
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}
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public static String getTypeID( SAMRecord r, CoverageAggregator.AggregationType type ) {
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public static String getTypeID( SAMReadGroupRecord r, CoverageAggregator.AggregationType type ) {
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if ( type == CoverageAggregator.AggregationType.SAMPLE ) {
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return r.getReadGroup().getSample();
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return r.getSample();
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} else if ( type == CoverageAggregator.AggregationType.READGROUP ) {
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return String.format("%s_rg_%s",r.getReadGroup().getSample(),r.getReadGroup().getReadGroupId());
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return String.format("%s_rg_%s",r.getSample(),r.getReadGroupId());
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} else if ( type == CoverageAggregator.AggregationType.LIBRARY ) {
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return r.getReadGroup().getLibrary();
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return r.getLibrary();
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} else {
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throw new StingException("Invalid type ID sent to getTypeID. This is a BUG!");
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}
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}
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public static Map<CoverageAggregator.AggregationType,Map<String,int[]>>
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getBaseCountsByPartition(AlignmentContext context, int minMapQ, int maxMapQ, byte minBaseQ, byte maxBaseQ, List<CoverageAggregator.AggregationType> types) {
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Map<CoverageAggregator.AggregationType,Map<String,int[]>> countsByIDByType = new HashMap<CoverageAggregator.AggregationType,Map<String,int[]>>();
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Map<SAMReadGroupRecord,int[]> countsByRG = getBaseCountsByReadGroup(context,minMapQ,maxMapQ,minBaseQ,maxBaseQ);
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for (CoverageAggregator.AggregationType t : types ) {
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countsByIDByType.put(t,new HashMap<String,int[]>());
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}
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for (PileupElement e : context.getBasePileup()) {
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if ( e.getMappingQual() >= minMapQ && e.getMappingQual() <= maxMapQ && ( ( e.getQual() >= minBaseQ && e.getQual() <= maxBaseQ ) || e.isDeletion() ) ) {
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for (CoverageAggregator.AggregationType t : types ) {
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String id = getTypeID(e.getRead(),t);
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if ( ! countsByIDByType.get(t).keySet().contains(id) ) {
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countsByIDByType.get(t).put(id,new int[6]);
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}
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updateCounts(countsByIDByType.get(t).get(id),e);
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// iterate through the read group counts and build the type associations
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for ( Map.Entry<SAMReadGroupRecord,int[]> readGroupCountEntry : countsByRG.entrySet() ) {
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String typeID = getTypeID(readGroupCountEntry.getKey(),t);
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if ( ! countsByIDByType.keySet().contains(t) ) {
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countsByIDByType.put(t,new HashMap<String,int[]>());
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}
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if ( ! countsByIDByType.get(t).keySet().contains(typeID) ) {
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countsByIDByType.get(t).put(typeID,readGroupCountEntry.getValue().clone());
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} else {
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addCounts(countsByIDByType.get(t).get(typeID),readGroupCountEntry.getValue());
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}
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}
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}
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return countsByIDByType;
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}
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public static void addCounts(int[] updateMe, int[] leaveMeAlone ) {
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for ( int index = 0; index < leaveMeAlone.length; index++ ) {
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updateMe[index] += leaveMeAlone[index];
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}
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}
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public static Map<SAMReadGroupRecord,int[]> getBaseCountsByReadGroup(AlignmentContext context, int minMapQ, int maxMapQ, byte minBaseQ, byte maxBaseQ) {
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Map<SAMReadGroupRecord, int[]> countsByRG = new HashMap<SAMReadGroupRecord,int[]>();
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for ( PileupElement e : context.getBasePileup() ) {
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if ( e.getMappingQual() >= minMapQ && e.getMappingQual() <= maxMapQ && ( e.getQual() >= minBaseQ && e.getQual() <= maxBaseQ || e.isDeletion() ) ) {
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SAMReadGroupRecord readGroup = e.getRead().getReadGroup();
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if ( ! countsByRG.keySet().contains(readGroup) ) {
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countsByRG.put(readGroup,new int[6]);
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updateCounts(countsByRG.get(readGroup),e);
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} else {
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updateCounts(countsByRG.get(readGroup),e);
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}
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}
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}
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return countsByRG;
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}
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private static void updateCounts(int[] counts, PileupElement e) {
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if ( e.isDeletion() ) {
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counts[BaseUtils.DELETION_INDEX]++;
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@ -166,6 +166,10 @@ public class DepthOfCoverageStats {
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}
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public void update(Map<String,int[]> countsBySample) {
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if ( countsBySample == null ) {
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this.updateDepths(new HashMap<String,Integer>(1));
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return;
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}
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// todo -- do we want to do anything special regarding base count or deletion statistics?
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HashMap<String,Integer> depthBySample = new HashMap<String,Integer>();
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// todo -- needs fixing with advent of new baseutils functionality using ENUMS and handling N,D
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@ -309,4 +313,14 @@ public class DepthOfCoverageStats {
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return distribution;
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}
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public int value2bin(int value) {
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for ( int index = 0; index < binLeftEndpoints.length; index++ ) {
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if ( binLeftEndpoints[index] >= value ) {
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return index;
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}
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}
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return binLeftEndpoints.length-1;
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}
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}
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@ -104,6 +104,8 @@ public class DepthOfCoverageWalker extends LocusWalker<Map<CoverageAggregator.Ag
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File refSeqGeneList = null;
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@Argument(fullName = "outputFormat", doc = "the format of the output file (e.g. csv, table, rtable); defaults to r-readable table", required = false)
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String outputFormat = "rtable";
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@Argument(fullName = "summaryCoverageThreshold", shortName = "ct", doc = "for summary file outputs, report the % of bases coverd to >= this number. Defaults to 15; can take multiple arguments.", required = false)
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int[] coverageThresholds = {15};
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String[] OUTPUT_FORMATS = {"table","rtable","csv"};
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String[] PARTITION_TYPES = {"sample","readgroup","library"};
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@ -347,6 +349,12 @@ public class DepthOfCoverageWalker extends LocusWalker<Map<CoverageAggregator.Ag
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summaryHeader.append(separator);
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summaryHeader.append(s);
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summaryHeader.append("_granular_Q3");
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for ( int thresh : coverageThresholds ) {
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summaryHeader.append(separator);
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summaryHeader.append(s);
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summaryHeader.append("_%_above_");
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summaryHeader.append(thresh);
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}
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}
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summaryOut.printf("%s%n",summaryHeader);
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@ -446,6 +454,9 @@ public class DepthOfCoverageWalker extends LocusWalker<Map<CoverageAggregator.Ag
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targetSummary.append(formatBin(bins,median));
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targetSummary.append(separator);
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targetSummary.append(formatBin(bins,q3));
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for ( int thresh : coverageThresholds ) {
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targetSummary.append(String.format("%s%.1f",separator,getPctBasesAbove(stats.getHistograms().get(s),stats.value2bin(thresh))));
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}
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}
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@ -667,11 +678,17 @@ public class DepthOfCoverageWalker extends LocusWalker<Map<CoverageAggregator.Ag
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private void printSummary(PrintStream out, File optionalFile, DepthOfCoverageStats stats) {
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PrintStream output = getCorrectStream(out,optionalFile);
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if ( ! outputFormat.equals("csv") ) {
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output.printf("%s\t%s\t%s\t%s\t%s\t%s%n","sample_id","total","mean","granular_third_quartile","granular_median","granular_first_quartile");
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output.printf("%s\t%s\t%s\t%s\t%s\t%s","sample_id","total","mean","granular_third_quartile","granular_median","granular_first_quartile");
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} else {
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output.printf("%s,%s,%s,%s,%s,%s%n","sample_id","total","mean","granular_third_quartile","granular_median","granular_first_quartile");
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output.printf("%s,%s,%s,%s,%s,%s","sample_id","total","mean","granular_third_quartile","granular_median","granular_first_quartile");
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}
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for ( int thresh : coverageThresholds ) {
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output.printf("%s%s%d",separator,"%_bases_above_",thresh);
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}
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output.printf("%n");
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Map<String,int[]> histograms = stats.getHistograms();
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Map<String,Double> means = stats.getMeans();
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Map<String,Long> totals = stats.getTotals();
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@ -687,10 +704,16 @@ public class DepthOfCoverageWalker extends LocusWalker<Map<CoverageAggregator.Ag
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q1 = q1 == histogram.length-1 ? histogram.length-2 : q1;
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q3 = q3 == histogram.length-1 ? histogram.length-2 : q3;
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if ( ! outputFormat.equals("csv") ) {
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output.printf("%s\t%d\t%.2f\t%d\t%d\t%d%n",s,totals.get(s),means.get(s),leftEnds[q3],leftEnds[median],leftEnds[q1]);
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output.printf("%s\t%d\t%.2f\t%d\t%d\t%d",s,totals.get(s),means.get(s),leftEnds[q3],leftEnds[median],leftEnds[q1]);
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} else {
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output.printf("%s,%d,%.2f,%d,%d,%d%n",s,totals.get(s),means.get(s),leftEnds[q3],leftEnds[median],leftEnds[q1]);
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output.printf("%s,%d,%.2f,%d,%d,%d",s,totals.get(s),means.get(s),leftEnds[q3],leftEnds[median],leftEnds[q1]);
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}
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for ( int thresh : coverageThresholds ) {
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output.printf("%s%.1f",separator,getPctBasesAbove(histogram,stats.value2bin(thresh)));
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}
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output.printf("%n");
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}
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if ( ! outputFormat.equals("csv") ) {
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@ -717,6 +740,20 @@ public class DepthOfCoverageWalker extends LocusWalker<Map<CoverageAggregator.Ag
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return bin == -1 ? 0 : bin;
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}
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private double getPctBasesAbove(int[] histogram, int bin) {
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long below = 0l;
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long above = 0l;
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for ( int index = 0; index < histogram.length; index++) {
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if ( index < bin ) {
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below+=histogram[index];
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} else {
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above+=histogram[index];
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}
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}
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return 100*( (double) above )/( above + below );
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}
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private void printDepths(PrintStream stream, Map<CoverageAggregator.AggregationType,Map<String,int[]>> countsBySampleByType, Map<CoverageAggregator.AggregationType,List<String>> identifiersByType) {
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// get the depths per sample and build up the output string while tabulating total and average coverage
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StringBuilder perSampleOutput = new StringBuilder();
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@ -726,11 +763,11 @@ public class DepthOfCoverageWalker extends LocusWalker<Map<CoverageAggregator.Ag
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Map<String,int[]> countsByID = countsBySampleByType.get(type);
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for ( String s : identifiersByType.get(type) ) {
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perSampleOutput.append(separator);
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long dp = countsByID.keySet().contains(s) ? sumArray(countsByID.get(s)) : 0 ;
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long dp = (countsByID != null && countsByID.keySet().contains(s)) ? sumArray(countsByID.get(s)) : 0 ;
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perSampleOutput.append(dp);
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if ( printBaseCounts ) {
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perSampleOutput.append(separator);
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perSampleOutput.append(baseCounts(countsByID.get(s)));
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perSampleOutput.append(baseCounts(countsByID != null ? countsByID.get(s) : null ));
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}
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if ( ! depthCounted ) {
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tDepth += dp;
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@ -5,6 +5,7 @@ import org.broadinstitute.sting.commandline.Argument;
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import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
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import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
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import org.broadinstitute.sting.gatk.refdata.*;
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import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
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import org.broadinstitute.sting.gatk.refdata.utils.GATKFeatureIterator;
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import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
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import org.broadinstitute.sting.gatk.walkers.RefWalker;
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@ -23,8 +24,7 @@ import java.util.*;
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* Was written in order to annotate the Whole Exome Agilent designs at the Broad institute
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* Bind the refseq rod as -B refseq,refseq,/path/to/refGene.txt
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* Bind the interval list as -B interval_list,intervals,/path/to/intervals.interval_list
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* Bind the tcga (or other .bed) file as -B tcga,bed,/path/to/tcga.bed
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* [TCGA used as the agilent designs used both refseq and TCGA6k definitions]
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* Bind the additional files file as -B gene*,bed,/path/to/other/file.bed
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* @Author chartl
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* @Date Apr 26, 2010
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*/
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@ -32,17 +32,17 @@ public class DesignFileGeneratorWalker extends RodWalker<Long,Long> {
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private HashMap<GenomeLoc,IntervalInfoBuilder> intervalBuffer = new HashMap<GenomeLoc,IntervalInfoBuilder>();
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private HashSet<rodRefSeq> refseqBuffer = new HashSet<rodRefSeq>();
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private BEDFeature currentTCGA = null;
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private HashMap<String,BEDFeature> currentBedFeatures;
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public Long map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
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// three items to look up: interval_list, tcga, and refseq
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// three items to look up: interval_list, refseq, gene*
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if ( tracker == null ) {
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return null;
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}
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List<Object> intervalsList= tracker.getReferenceMetaData("interval_list");
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List<Object> refseqList = tracker.getReferenceMetaData("refseq");
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List<Object> tcgaList = tracker.getReferenceMetaData("tcga");
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List<GATKFeature> bedList = tracker.getGATKFeatureMetaData("gene",false);
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// put any unprocessed intervals into the interval buffer
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@ -65,10 +65,9 @@ public class DesignFileGeneratorWalker extends RodWalker<Long,Long> {
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}
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}
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// update the current tcga target
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if ( tcgaList != null && tcgaList.size() > 0 ) {
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currentTCGA = (BEDFeature) tcgaList.get(0);
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// update the bed features
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for ( GATKFeature additionalGene : bedList ) {
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currentBedFeatures.put(additionalGene.getName(),(BEDFeature) additionalGene.getUnderlyingObject());
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}
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cleanup(ref);
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@ -96,14 +95,18 @@ public class DesignFileGeneratorWalker extends RodWalker<Long,Long> {
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}
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}
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if ( currentTCGA != null &&
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interval.overlapsP(GenomeLocParser.createGenomeLoc(currentTCGA.getChr(),currentTCGA.getStart(),currentTCGA.getEnd())) &&
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!currentTCGA.getName().equals("") &&
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! intervalBuffer.get(interval).geneNames.contains("TCGA_"+currentTCGA.getName()) ) {
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for ( Map.Entry<String,BEDFeature> additionalGenes : currentBedFeatures.entrySet() ) {
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GenomeLoc entryLoc = GenomeLocParser.createGenomeLoc(additionalGenes.getValue().getChr(),additionalGenes.getValue().getStart(),additionalGenes.getValue().getEnd());
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if ( interval.overlapsP(entryLoc) &&
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! additionalGenes.getValue().getName().equals("") &&
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! intervalBuffer.get(interval).geneNames.contains(additionalGenes.getKey()+"_"+additionalGenes.getValue().getName())) {
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intervalBuffer.get(interval).update(additionalGenes.getKey()+"_"+additionalGenes.getValue().getName(),
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new ArrayList<GenomeLoc>(Arrays.asList(entryLoc)),
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null);
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nUpdate ++;
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}
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intervalBuffer.get(interval).update("TCGA_"+currentTCGA.getName().split("_f|_r")[0],
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new ArrayList<GenomeLoc>(Arrays.asList(GenomeLocParser.createGenomeLoc(currentTCGA.getChr(),currentTCGA.getStart(),currentTCGA.getEnd()))),
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new ArrayList<Integer>(Arrays.asList(Integer.parseInt(currentTCGA.getName().split("_f|_r")[1])-1)));
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}
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}
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@ -139,8 +142,11 @@ public class DesignFileGeneratorWalker extends RodWalker<Long,Long> {
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intervalBuffer.remove(interval);
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}
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if ( currentTCGA != null && GenomeLocParser.createGenomeLoc(currentTCGA.getChr(),currentTCGA.getStart(),currentTCGA.getEnd()).isBefore(ref.getLocus()) ) {
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currentTCGA = null;
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for ( Map.Entry<String,BEDFeature> entry : currentBedFeatures.entrySet() ) {
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GenomeLoc entryLoc = GenomeLocParser.createGenomeLoc(entry.getValue().getChr(),entry.getValue().getStart(),entry.getValue().getEnd());
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if ( entryLoc.isBefore(ref.getLocus()) ) {
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currentBedFeatures.remove(entry.getKey());
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}
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}
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}
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@ -182,7 +188,7 @@ class IntervalInfoBuilder {
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public void update(String gene, List<GenomeLoc> exons, List<Integer> exonNumbers) {
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if ( geneNames.contains(gene) ) {
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if ( gene.startsWith("TCGA") ) {
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if ( gene.startsWith("gene") ) {
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// exons are split up one per bed, so update the exon list for this gene
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for ( int eOff = 0; eOff < exons.size(); eOff++) {
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if ( ! exonNumbersByGene.get(gene).contains( exonNumbers.get(eOff) ) ) {
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@ -67,9 +67,9 @@ public class DepthOfCoverageB36IntegrationTest extends WalkerTest {
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spec.addAuxFile("6b15f5330414b6d4e2f6caea42139fa1", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_cumulative_coverage_counts"));
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spec.addAuxFile("cc6640d82077991dde8a2b523935cdff", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_cumulative_coverage_proportions"));
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spec.addAuxFile("0fb627234599c258a3fee1b2703e164a", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_interval_statistics"));
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spec.addAuxFile("6f6085293e8cca402ef4fe648cf06ea8", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_interval_summary"));
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spec.addAuxFile("3ad34680c216279c52c7fa0c9e078249", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_interval_summary"));
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spec.addAuxFile("347b47ef73fbd4e277704ddbd7834f69", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_statistics"));
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spec.addAuxFile("ff0c79d161259402d54d572151582697", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_summary"));
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spec.addAuxFile("65bc90b4839cb9f20e60aba4956f06a9", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_summary"));
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execute("testMapQ0Only",spec);
|
||||
}
|
||||
|
|
|
|||
|
|
@ -53,7 +53,7 @@ public class DepthOfCoverageIntegrationTest extends WalkerTest {
|
|||
String[] intervals = {"/humgen/gsa-hpprojects/GATK/data/Validation_Data/fhs_jhs_30_targts.interval_list"};
|
||||
String[] bams = {"/humgen/gsa-hpprojects/GATK/data/Validation_Data/FHS_indexed_subset.bam"};
|
||||
|
||||
String cmd = buildRootCmd(hg18,new ArrayList<String>(Arrays.asList(bams)),new ArrayList<String>(Arrays.asList(intervals))) + " -mmq 0 -mbq 0 -dels -baseCounts -pt readgroup -pt sample -pt library --outputFormat csv";
|
||||
String cmd = buildRootCmd(hg18,new ArrayList<String>(Arrays.asList(bams)),new ArrayList<String>(Arrays.asList(intervals))) + " -mmq 0 -mbq 0 -dels -baseCounts -pt readgroup -pt sample -pt library --outputFormat csv -ct 10 -ct 15 -ct 20 -ct 25";
|
||||
WalkerTestSpec spec = new WalkerTestSpec(cmd,0, new ArrayList<String>());
|
||||
|
||||
// now add the expected files that get generated
|
||||
|
|
@ -61,21 +61,21 @@ public class DepthOfCoverageIntegrationTest extends WalkerTest {
|
|||
spec.addAuxFile("e58b701b01ec0dbe75c146295434ba3b", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_cumulative_coverage_counts"));
|
||||
spec.addAuxFile("b9a7748e5aec4dc06daed893c901c00d", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_cumulative_coverage_proportions"));
|
||||
spec.addAuxFile("848e556ec7e03e9b0398d189d7cbb4ad", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_interval_statistics"));
|
||||
spec.addAuxFile("e6fc8f7a5fcc440e21de5891f3403d5d", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_interval_summary"));
|
||||
spec.addAuxFile("acd3dfb97ef64ea6547c001640acd194", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_interval_summary"));
|
||||
spec.addAuxFile("cac8e7a688d9bbe781232c61091d3237", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_statistics"));
|
||||
spec.addAuxFile("e452dfb5581a7aafaf2122c5ae497f1b", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_summary"));
|
||||
spec.addAuxFile("73c31412b75dc7014549096de7c0c609", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_summary"));
|
||||
spec.addAuxFile("38fb89e1bb52d0342f97f72e86956b79", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_cumulative_coverage_counts"));
|
||||
spec.addAuxFile("f9f2941ee39577ac2f80668e7f6b3d4b", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_cumulative_coverage_proportions"));
|
||||
spec.addAuxFile("7b9d0e93bf5b5313995be7010ef1f528", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_interval_statistics"));
|
||||
spec.addAuxFile("fd29fe0c14351e934a6fef9df1f38f7b", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_interval_summary"));
|
||||
spec.addAuxFile("8c5266ef3c0031d3b0311839b7f59245", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_interval_summary"));
|
||||
spec.addAuxFile("cc7ee5075a932dba486e78824ca34202", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_statistics"));
|
||||
spec.addAuxFile("e1653480daa2d96f7c584ed4cd20c147", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_summary"));
|
||||
spec.addAuxFile("39afa53bae210f4684951b908aa36c7d", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_summary"));
|
||||
spec.addAuxFile("529353375d23c529228b38119c51e269", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_cumulative_coverage_counts"));
|
||||
spec.addAuxFile("650ee3714da7fbad7832c9d4ad49eb51", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_cumulative_coverage_proportions"));
|
||||
spec.addAuxFile("925cc5b49286e0222bce6251d1baafc7", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_interval_statistics"));
|
||||
spec.addAuxFile("d9e812398d778f28ed12d7f3d18628e2", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_interval_summary"));
|
||||
spec.addAuxFile("7a2fc8a2fba91adfbdc90dcc0e1ef79b", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_interval_summary"));
|
||||
spec.addAuxFile("f3315551081331bc322c53b11412d707", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_statistics"));
|
||||
spec.addAuxFile("3a059ad82d945643dc4e03239c4041f5", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_summary"));
|
||||
spec.addAuxFile("455f9f0c4461bcf0b231fef704266881", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_summary"));
|
||||
|
||||
execute("testBaseOutputNoFiltering",spec);
|
||||
}
|
||||
|
|
@ -92,7 +92,7 @@ public class DepthOfCoverageIntegrationTest extends WalkerTest {
|
|||
WalkerTestSpec spec = new WalkerTestSpec(cmd,0, new ArrayList<String>());
|
||||
|
||||
spec.addAuxFile("d570c27d82a80ebd2852e9d34aff4e87",baseOutputFile);
|
||||
spec.addAuxFile("00107eea991f7379771b29dea0c859cb",createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_interval_summary"));
|
||||
spec.addAuxFile("0ee40f3e5091536c14e077b77557083a",createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_interval_summary"));
|
||||
|
||||
execute("testNoCoverageDueToFiltering",spec);
|
||||
}
|
||||
|
|
|
|||
Loading…
Reference in New Issue