{
@Output
public PrintStream out;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/HaplotypeIndelErrorModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/HaplotypeIndelErrorModel.java
index 200a250f2..26023bd2f 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/HaplotypeIndelErrorModel.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/HaplotypeIndelErrorModel.java
@@ -454,8 +454,7 @@ public class HaplotypeIndelErrorModel {
// Compute log10(10^x1/2 + 10^x2/2) = log10(10^x1+x0^x2)-log10(2)
// First term is approximated by Jacobian log with table lookup.
// Second term is a constant added to both likelihoods so will be ignored
- haplotypeLikehoodMatrix[i][j] += MathUtils.softMax(readLikelihood[0],
- readLikelihood[1]);
+ haplotypeLikehoodMatrix[i][j] += MathUtils.approximateLog10SumLog10(readLikelihood[0], readLikelihood[1]);
}
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
index 6410d619d..64993b43a 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
@@ -166,18 +166,17 @@ public class PairHMMIndelErrorModel {
final double pBaseRead = (x == y)? baseMatchArray[(int)qual]:baseMismatchArray[(int)qual];
- matchMetricArray[indI][indJ] = MathUtils.softMax(matchMetricArray[im1][jm1] + pBaseRead, XMetricArray[im1][jm1] + pBaseRead,
- YMetricArray[im1][jm1] + pBaseRead);
+ matchMetricArray[indI][indJ] = pBaseRead + MathUtils.approximateLog10SumLog10(new double[]{matchMetricArray[im1][jm1], XMetricArray[im1][jm1], YMetricArray[im1][jm1]});
final double c1 = indJ == Y_METRIC_LENGTH-1 ? END_GAP_COST : currentGOP[jm1];
final double d1 = indJ == Y_METRIC_LENGTH-1 ? END_GAP_COST : currentGCP[jm1];
- XMetricArray[indI][indJ] = MathUtils.softMax(matchMetricArray[im1][indJ] + c1, XMetricArray[im1][indJ] + d1);
+ XMetricArray[indI][indJ] = MathUtils.approximateLog10SumLog10(matchMetricArray[im1][indJ] + c1, XMetricArray[im1][indJ] + d1);
// update Y array
final double c2 = indI == X_METRIC_LENGTH-1 ? END_GAP_COST : currentGOP[jm1];
final double d2 = indI == X_METRIC_LENGTH-1 ? END_GAP_COST : currentGCP[jm1];
- YMetricArray[indI][indJ] = MathUtils.softMax(matchMetricArray[indI][jm1] + c2, YMetricArray[indI][jm1] + d2);
+ YMetricArray[indI][indJ] = MathUtils.approximateLog10SumLog10(matchMetricArray[indI][jm1] + c2, YMetricArray[indI][jm1] + d2);
}
}
@@ -316,9 +315,7 @@ public class PairHMMIndelErrorModel {
final int bestI = X_METRIC_LENGTH - 1, bestJ = Y_METRIC_LENGTH - 1;
- final double bestMetric = MathUtils.softMax(matchMetricArray[bestI][bestJ],
- XMetricArray[bestI][bestJ],
- YMetricArray[bestI][bestJ]);
+ final double bestMetric = MathUtils.approximateLog10SumLog10(new double[]{ matchMetricArray[bestI][bestJ], XMetricArray[bestI][bestJ], YMetricArray[bestI][bestJ] });
/*
if (DEBUG) {
@@ -651,7 +648,7 @@ public class PairHMMIndelErrorModel {
private final static double[] getHaplotypeLikelihoods(final int numHaplotypes, final int readCounts[], final double readLikelihoods[][]) {
final double[][] haplotypeLikehoodMatrix = new double[numHaplotypes][numHaplotypes];
- // todo: MAD 09/26/11 -- I'm almost certain this calculation can be simplied to just a single loop without the intermediate NxN matrix
+ // todo: MAD 09/26/11 -- I'm almost certain this calculation can be simplified to just a single loop without the intermediate NxN matrix
for (int i=0; i < numHaplotypes; i++) {
for (int j=i; j < numHaplotypes; j++){
// combine likelihoods of haplotypeLikelihoods[i], haplotypeLikelihoods[j]
@@ -665,7 +662,7 @@ public class PairHMMIndelErrorModel {
final double li = readLikelihoods[readIdx][i];
final double lj = readLikelihoods[readIdx][j];
final int readCount = readCounts[readIdx];
- haplotypeLikehoodMatrix[i][j] += readCount * (MathUtils.softMax(li, lj) + LOG_ONE_HALF);
+ haplotypeLikehoodMatrix[i][j] += readCount * (MathUtils.approximateLog10SumLog10(li, lj) + LOG_ONE_HALF);
}
}
}
@@ -678,7 +675,7 @@ public class PairHMMIndelErrorModel {
}
}
- // renormalize so that max element is zero.
+ // renormalize so that max element is zero.
return MathUtils.normalizeFromLog10(genotypeLikelihoods, false, true);
}
}
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetectorWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetectorWalker.java
index aa9ae1517..59a7bd01a 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetectorWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetectorWalker.java
@@ -26,6 +26,10 @@
package org.broadinstitute.sting.gatk.walkers.indels;
import net.sf.samtools.*;
+import org.apache.commons.jexl2.Expression;
+import org.apache.commons.jexl2.JexlContext;
+import org.apache.commons.jexl2.JexlEngine;
+import org.apache.commons.jexl2.MapContext;
import org.broad.tribble.Feature;
import org.broadinstitute.sting.commandline.*;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
@@ -71,7 +75,7 @@ import java.util.*;
*
* This is a simple, counts-and-cutoffs based tool for calling indels from aligned (preferrably MSA cleaned) sequencing
* data. Supported output formats are: BED format, extended verbose output (tab separated), and VCF. The latter two outputs
- * include additional statistics such as mismtaches and base qualitites around the calls, read strandness (how many
+ * include additional statistics such as mismatches and base qualitites around the calls, read strandness (how many
* forward/reverse reads support ref and indel alleles) etc. It is highly recommended to use these additional
* statistics to perform post-filtering of the calls as the tool is tuned for sensitivity (in other words it will
* attempt to "call" anything remotely reasonable based only on read counts and will generate all the additional
@@ -88,6 +92,16 @@ import java.util.*;
* bam tagging is not required in this case, and tags are completely ignored if still used: all input bams will be merged
* on the fly and assumed to represent a single sample - this tool does not check for sample id in the read groups).
*
+ * Which (putative) calls will make it into the output file(s) is controlled by an expression/list of expressions passed with -filter
+ * flag: if any of the expressions evaluate to TRUE, the site will be discarded. Otherwise the putative call and all the
+ * associated statistics will be printed into the output. Expressions recognize the following variables(in paired-sample
+ * somatic mode variables are prefixed with T_ and N_ for Tumor and Normal, e.g. N_COV and T_COV are defined instead of COV):
+ * COV for coverage at the site, INDEL_F for fraction of reads supporting consensus indel at the site (wrt total coverage),
+ * INDEL_CF for fraction of reads with consensus indel wrt all reads with an indel at the site, CONS_CNT for the count of
+ * reads supporting the consensus indel at the site. Conventional arithmetic and logical operations are supported. For instance,
+ * N_COV<4||T_COV<6||T_INDEL_F<0.3||T_INDEL_CF<0.7 instructs the tool to only output indel calls with at least 30% observed
+ * allelic fraction and with consensus indel making at least 70% of all indel observations at the site, and only at the sites
+ * where tumor coverage and normal coverage are at least 6 and 4, respectively.
*
Input
*
* Tumor and normal bam files (or single sample bam file(s) in --unpaired mode).
@@ -147,30 +161,44 @@ public class SomaticIndelDetectorWalker extends ReadWalker {
doc="Lightweight bed output file (only positions and events, no stats/annotations)", required=false)
java.io.File bedOutput = null;
+ @Deprecated
@Argument(fullName="minCoverage", shortName="minCoverage",
doc="indel calls will be made only at sites with tumor coverage of minCoverage or more reads; "+
- "with --unpaired (single sample) option, this value is used for minimum sample coverage", required=false)
+ "with --unpaired (single sample) option, this value is used for minimum sample coverage. "+
+ "INSTEAD USE: T_COV {
"GENOMIC/UTR/INTRON/CODING and with the gene name", required=false)
String RefseqFileName = null;
+
+ @Argument(shortName="filter", doc="One or more logical expressions. If any of the expressions is TRUE, " +
+ "putative indel will be discarded and nothing will be printed into the output (unless genotyping "+
+ "at the specific position is explicitly requested, see -genotype). "+
+ "Default: T_COV<6||N_COV<4||T_INDEL_F<0.3||T_INDEL_CF<0.7", required=false)
+ public ArrayList FILTER_EXPRESSIONS = new ArrayList();
+
//@Argument(fullName="blacklistedLanes", shortName="BL",
// doc="Name of lanes (platform units) that should be ignored. Reads coming from these lanes will never be seen "+
// "by this application, so they will not contribute indels to consider and will not be counted.", required=false)
@@ -221,7 +256,7 @@ public class SomaticIndelDetectorWalker extends ReadWalker {
private Writer verboseWriter = null;
- private static String annGenomic = "GENOMIC";
+ private static String annGenomic = "GENOMIC\t";
private static String annIntron = "INTRON";
private static String annUTR = "UTR";
private static String annCoding = "CODING";
@@ -245,6 +280,32 @@ public class SomaticIndelDetectorWalker extends ReadWalker {
private long lastGenotypedPosition = -1; // last position on the currentGenotypeInterval, for which a call was already printed;
// can be 1 base before lastGenotyped start
+ private JexlEngine jexlEngine = new JexlEngine();
+ private ArrayList jexlExpressions = new ArrayList();
+
+ // the following arrays store indel source-specific (normal/tumor) metric names
+ // for fast access when populating JEXL expression contexts (see IndelPrecall.fillContext())
+ private final static String[] normalMetricsCassette = new String[4];
+ private final static String[] tumorMetricsCassette = new String[4];
+ private final static String[] singleMetricsCassette = new String[4];
+ private final static int C_COV=0;
+ private final static int C_CONS_CNT=1;
+ private final static int C_INDEL_F=2;
+ private final static int C_INDEL_CF=3;
+ static {
+ normalMetricsCassette[C_COV] = "N_COV";
+ tumorMetricsCassette[C_COV] = "T_COV";
+ singleMetricsCassette[C_COV] = "COV";
+ normalMetricsCassette[C_CONS_CNT] = "N_CONS_CNT";
+ tumorMetricsCassette[C_CONS_CNT] = "T_CONS_CNT";
+ singleMetricsCassette[C_CONS_CNT] = "CONS_CNT";
+ normalMetricsCassette[C_INDEL_F] = "N_INDEL_F";
+ tumorMetricsCassette[C_INDEL_F] = "T_INDEL_F";
+ singleMetricsCassette[C_INDEL_F] = "INDEL_F";
+ normalMetricsCassette[C_INDEL_CF] = "N_INDEL_CF";
+ tumorMetricsCassette[C_INDEL_CF] = "T_INDEL_CF";
+ singleMetricsCassette[C_INDEL_CF] = "INDEL_CF";
+ }
// "/humgen/gsa-scr1/GATK_Data/refGene.sorted.txt"
@@ -389,6 +450,24 @@ public class SomaticIndelDetectorWalker extends ReadWalker {
vcf_writer.writeHeader(new VCFHeader(getVCFHeaderInfo(), SampleUtils.getSAMFileSamples(getToolkit().getSAMFileHeader()))) ;
refData = new ReferenceDataSource(getToolkit().getArguments().referenceFile);
+
+ // Now initialize JEXL expressions:
+ if ( FILTER_EXPRESSIONS.size() == 0 ) {
+ if ( call_unpaired ) {
+ FILTER_EXPRESSIONS.add("COV<6||INDEL_F<0.3||INDEL_CF<0.7");
+ } else {
+ FILTER_EXPRESSIONS.add("T_COV<6||N_COV<4||T_INDEL_F<0.3||T_INDEL_CF<0.7");
+ }
+ }
+ for ( String s : FILTER_EXPRESSIONS ) {
+ try {
+ Expression e = jexlEngine.createExpression(s);
+ jexlExpressions.add(e);
+ } catch (Exception e) {
+ throw new UserException.BadArgumentValue("Filter expression", "Invalid expression used (" + s + "). Please see the JEXL docs for correct syntax.") ;
+ }
+
+ }
}
@@ -661,14 +740,26 @@ public class SomaticIndelDetectorWalker extends ReadWalker {
if ( normal_context.indelsAt(pos).size() == 0 && ! genotype ) continue;
IndelPrecall normalCall = new IndelPrecall(normal_context,pos,NQS_WIDTH);
+ JexlContext jc = new MapContext();
+ normalCall.fillContext(jc,singleMetricsCassette);
+ boolean discard_event = false;
- if ( normalCall.getCoverage() < minCoverage && ! genotype ) {
- if ( DEBUG ) {
- System.out.println("DEBUG>> Indel at "+pos+"; coverare in normal="+normalCall.getCoverage()+" (SKIPPED)");
- }
- continue; // low coverage
+ for ( Expression e : jexlExpressions ) {
+ if ( ((Boolean)e.evaluate(jc)).booleanValue() ) { discard_event=true; break; }
}
+ if ( discard_event && ! genotype ) {
+ normal_context.indelsAt(pos).clear();
+ continue; //*
+ }
+
+// if ( normalCall.getCoverage() < minCoverage && ! genotype ) {
+// if ( DEBUG ) {
+// System.out.println("DEBUG>> Indel at "+pos+"; coverare in normal="+normalCall.getCoverage()+" (SKIPPED)");
+// }
+// continue; // low coverage
+// }
+
if ( DEBUG ) System.out.println("DEBUG>> "+(normalCall.getAllVariantCount() == 0?"No Indel":"Indel")+" at "+pos);
long left = Math.max( pos-NQS_WIDTH, normal_context.getStart() );
@@ -697,24 +788,16 @@ public class SomaticIndelDetectorWalker extends ReadWalker {
location = getToolkit().getGenomeLocParser().createGenomeLoc(location.getContig(), pos);
- boolean haveCall = normalCall.isCall(); // cache the value
-
- if ( haveCall || genotype) {
- if ( haveCall ) normalCallsMade++;
- printVCFLine(vcf_writer,normalCall);
- if ( bedWriter != null ) normalCall.printBedLine(bedWriter);
- if ( verboseWriter != null ) printVerboseLine(verboseWriter, normalCall);
- lastGenotypedPosition = pos;
- }
+ if ( ! discard_event ) normalCallsMade++;
+ printVCFLine(vcf_writer,normalCall, discard_event);
+ if ( bedWriter != null ) normalCall.printBedLine(bedWriter);
+ if ( verboseWriter != null ) printVerboseLine(verboseWriter, normalCall, discard_event);
+ lastGenotypedPosition = pos;
normal_context.indelsAt(pos).clear();
// we dealt with this indel; don't want to see it again
// (we might otherwise in the case when 1) there is another indel that follows
// within MISMATCH_WIDTH bases and 2) we'd need to wait for more coverage for that next indel)
-
-// for ( IndelVariant var : variants ) {
-// System.out.print("\t"+var.getType()+"\t"+var.getBases()+"\t"+var.getCount());
-// }
}
if ( DEBUG ) System.out.println("DEBUG>> Actual shift to " + move_to + " ("+adjustedPosition+")");
@@ -829,18 +912,32 @@ public class SomaticIndelDetectorWalker extends ReadWalker {
IndelPrecall tumorCall = new IndelPrecall(tumor_context,pos,NQS_WIDTH);
IndelPrecall normalCall = new IndelPrecall(normal_context,pos,NQS_WIDTH);
- if ( tumorCall.getCoverage() < minCoverage && ! genotype ) {
- if ( DEBUG ) {
- System.out.println("DEBUG>> Indel in tumor at "+pos+"; coverare in tumor="+tumorCall.getCoverage()+" (SKIPPED)");
- }
- continue; // low coverage
+ JexlContext jc = new MapContext();
+ tumorCall.fillContext(jc,tumorMetricsCassette);
+ normalCall.fillContext(jc,normalMetricsCassette);
+ boolean discard_event = false;
+
+ for ( Expression e : jexlExpressions ) {
+ if ( ((Boolean)e.evaluate(jc)).booleanValue() ) { discard_event=true; break; }
}
- if ( normalCall.getCoverage() < minNormalCoverage && ! genotype ) {
- if ( DEBUG ) {
- System.out.println("DEBUG>> Indel in tumor at "+pos+"; coverare in normal="+normalCall.getCoverage()+" (SKIPPED)");
- }
- continue; // low coverage
+
+ if ( discard_event && ! genotype ) {
+ tumor_context.indelsAt(pos).clear();
+ normal_context.indelsAt(pos).clear();
+ continue; //*
}
+// if ( tumorCall.getCoverage() < minCoverage && ! genotype ) {
+// if ( DEBUG ) {
+// System.out.println("DEBUG>> Indel in tumor at "+pos+"; coverare in tumor="+tumorCall.getCoverage()+" (SKIPPED)");
+// }
+// continue; // low coverage
+// }
+// if ( normalCall.getCoverage() < minNormalCoverage && ! genotype ) {
+// if ( DEBUG ) {
+// System.out.println("DEBUG>> Indel in tumor at "+pos+"; coverare in normal="+normalCall.getCoverage()+" (SKIPPED)");
+// }
+// continue; // low coverage
+// }
if ( DEBUG ) {
System.out.print("DEBUG>> "+(tumorCall.getAllVariantCount() == 0?"No Indel":"Indel")+" in tumor, ");
@@ -868,32 +965,24 @@ public class SomaticIndelDetectorWalker extends ReadWalker {
if ( right > tumor_context.getStop() ) right = tumor_context.getStop(); // if indel is too close to the end of the window but we need to emit anyway (force-shift), adjust right
-// location = getToolkit().getGenomeLocParser().setStart(location,pos);
-// location = getToolkit().getGenomeLocParser().setStop(location,pos); // retrieve annotation data
-
location = getToolkit().getGenomeLocParser().createGenomeLoc(location.getContig(),pos); // retrieve annotation data
- boolean haveCall = tumorCall.isCall(); // cache the value
+// boolean haveCall = tumorCall.isCall(); // cache the value
- if ( haveCall || genotype ) {
- if ( haveCall ) tumorCallsMade++;
+ if ( ! discard_event ) tumorCallsMade++;
- printVCFLine(vcf_writer,normalCall,tumorCall);
+ printVCFLine(vcf_writer,normalCall,tumorCall,discard_event);
- if ( bedWriter != null ) tumorCall.printBedLine(bedWriter);
+ if ( bedWriter != null ) tumorCall.printBedLine(bedWriter);
+
+ if ( verboseWriter != null ) printVerboseLine(verboseWriter, normalCall, tumorCall, discard_event );
+ lastGenotypedPosition = pos;
- if ( verboseWriter != null ) printVerboseLine(verboseWriter, normalCall, tumorCall );
- lastGenotypedPosition = pos;
- }
tumor_context.indelsAt(pos).clear();
normal_context.indelsAt(pos).clear();
// we dealt with this indel; don't want to see it again
// (we might otherwise in the case when 1) there is another indel that follows
// within MISMATCH_WIDTH bases and 2) we'd need to wait for more coverage for that next indel)
-
-// for ( IndelVariant var : variants ) {
-// System.out.print("\t"+var.getType()+"\t"+var.getBases()+"\t"+var.getCount());
-// }
}
if ( DEBUG ) System.out.println("DEBUG>> Actual shift to " + move_to + " ("+adjustedPosition+")");
@@ -947,14 +1036,14 @@ public class SomaticIndelDetectorWalker extends ReadWalker {
}
- public void printVerboseLine(Writer verboseWriter, IndelPrecall normalCall) {
+ public void printVerboseLine(Writer verboseWriter, IndelPrecall normalCall, boolean discard_event) {
RODRecordList annotationList = (refseqIterator == null ? null : refseqIterator.seekForward(location));
String annotationString = (refseqIterator == null ? "" : getAnnotationString(annotationList));
StringBuilder fullRecord = new StringBuilder();
fullRecord.append(makeFullRecord(normalCall));
fullRecord.append(annotationString);
- if ( ! normalCall.isCall() && normalCall.getVariant() != null ) fullRecord.append("\tFILTERED_NOCALL");
+ if ( discard_event && normalCall.getVariant() != null ) fullRecord.append("\tFILTERED_NOCALL");
try {
verboseWriter.write(fullRecord.toString());
verboseWriter.write('\n');
@@ -965,7 +1054,7 @@ public class SomaticIndelDetectorWalker extends ReadWalker {
}
- public void printVerboseLine(Writer verboseWriter, IndelPrecall normalCall, IndelPrecall tumorCall) {
+ public void printVerboseLine(Writer verboseWriter, IndelPrecall normalCall, IndelPrecall tumorCall, boolean discard_event) {
RODRecordList annotationList = (refseqIterator == null ? null : refseqIterator.seekForward(location));
String annotationString = (refseqIterator == null ? "" : getAnnotationString(annotationList));
@@ -1013,7 +1102,7 @@ public class SomaticIndelDetectorWalker extends ReadWalker {
fullRecord.append('\t');
fullRecord.append(annotationString);
- if ( ! tumorCall.isCall() && tumorCall.getVariant() != null ) fullRecord.append("\tFILTERED_NOCALL");
+ if ( discard_event && tumorCall.getVariant() != null ) fullRecord.append("\tFILTERED_NOCALL");
try {
verboseWriter.write(fullRecord.toString());
@@ -1023,7 +1112,7 @@ public class SomaticIndelDetectorWalker extends ReadWalker {
}
}
- public void printVCFLine(VCFWriter vcf, IndelPrecall call) {
+ public void printVCFLine(VCFWriter vcf, IndelPrecall call, boolean discard_event) {
long start = call.getPosition()-1;
// If the beginning of the chromosome is deleted (possible, however unlikely), it's unclear how to proceed.
@@ -1060,14 +1149,14 @@ public class SomaticIndelDetectorWalker extends ReadWalker {
Map attrs = call.makeStatsAttributes(null);
- if ( call.isCall() ) // we made a call - put actual het genotype here:
+ if ( ! discard_event ) // we made a call - put actual het genotype here:
genotypes.add(new Genotype(sample,alleles,Genotype.NO_LOG10_PERROR,null,attrs,false));
else // no call: genotype is ref/ref (but alleles still contain the alt if we observed anything at all)
genotypes.add(new Genotype(sample, homref_alleles,Genotype.NO_LOG10_PERROR,null,attrs,false));
}
Set filters = null;
- if ( call.getVariant() != null && ! call.isCall() ) {
+ if ( call.getVariant() != null && discard_event ) {
filters = new HashSet();
filters.add("NoCall");
}
@@ -1095,7 +1184,7 @@ public class SomaticIndelDetectorWalker extends ReadWalker {
}
}
- public void printVCFLine(VCFWriter vcf, IndelPrecall nCall, IndelPrecall tCall) {
+ public void printVCFLine(VCFWriter vcf, IndelPrecall nCall, IndelPrecall tCall, boolean discard_event) {
long start = tCall.getPosition()-1;
long stop = start;
@@ -1112,7 +1201,7 @@ public class SomaticIndelDetectorWalker extends ReadWalker {
Map attrs = new HashMap();
boolean isSomatic = false;
- if ( nCall.getCoverage() >= minNormalCoverage && nCall.getVariant() == null && tCall.getVariant() != null ) {
+ if ( nCall.getVariant() == null && tCall.getVariant() != null ) {
isSomatic = true;
attrs.put(VCFConstants.SOMATIC_KEY,true);
}
@@ -1155,7 +1244,7 @@ public class SomaticIndelDetectorWalker extends ReadWalker {
}
Set filters = null;
- if ( tCall.getVariant() != null && ! tCall.isCall() ) {
+ if ( tCall.getVariant() != null && discard_event ) {
filters = new HashSet();
filters.add("NoCall");
}
@@ -1602,6 +1691,13 @@ public class SomaticIndelDetectorWalker extends ReadWalker {
public IndelVariant getVariant() { return consensus_indel; }
+ public void fillContext(JexlContext context,String[] cassette) {
+ context.set(cassette[C_INDEL_F],((double)consensus_indel_count)/total_coverage);
+ context.set(cassette[C_INDEL_CF],((double)consensus_indel_count/all_indel_count));
+ context.set(cassette[C_COV],total_coverage);
+ context.set(cassette[C_CONS_CNT],consensus_indel_count);
+ }
+/*
public boolean isCall() {
boolean ret = ( consensus_indel_count >= minIndelCount &&
(double)consensus_indel_count > minFraction * total_coverage &&
@@ -1610,10 +1706,11 @@ public class SomaticIndelDetectorWalker extends ReadWalker {
" total_count="+all_indel_count+" cov="+total_coverage+
" minConsensusF="+((double)consensus_indel_count)/all_indel_count+
" minF="+((double)consensus_indel_count)/total_coverage);
+
return ret;
-
+// return true;
}
-
+*/
/** Utility method: finds the indel variant with the largest count (ie consensus) among all the observed
* variants, and sets the counts of consensus observations and all observations of any indels (including non-consensus)
* @param variants
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
index 74291e025..d18c7e10a 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
@@ -1,5 +1,6 @@
package org.broadinstitute.sting.gatk.walkers.varianteval;
+import com.google.java.contract.Requires;
import net.sf.picard.reference.IndexedFastaSequenceFile;
import net.sf.picard.util.IntervalTree;
import net.sf.samtools.SAMSequenceRecord;
@@ -19,11 +20,8 @@ import org.broadinstitute.sting.gatk.walkers.TreeReducible;
import org.broadinstitute.sting.gatk.walkers.Window;
import org.broadinstitute.sting.gatk.walkers.varianteval.evaluators.VariantEvaluator;
import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.IntervalStratification;
-import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.JexlExpression;
import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.VariantStratifier;
import org.broadinstitute.sting.gatk.walkers.varianteval.util.*;
-import org.broadinstitute.sting.gatk.walkers.variantrecalibration.Tranche;
-import org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibrator;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.SampleUtils;
@@ -32,7 +30,6 @@ import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.StingException;
import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.interval.IntervalUtils;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.sting.utils.variantcontext.VariantContextBuilder;
@@ -389,9 +386,9 @@ public class VariantEvalWalker extends RodWalker implements Tr
nec.apply(tracker, ref, context, comp, eval);
}
- // eval=null against all comps of different type
+ // eval=null against all comps of different type that aren't bound to another eval
for ( VariantContext otherComp : compSet ) {
- if ( otherComp != comp ) {
+ if ( otherComp != comp && ! compHasMatchingEval(otherComp, evalSetBySample) ) {
synchronized (nec) {
nec.apply(tracker, ref, context, otherComp, null);
}
@@ -409,6 +406,35 @@ public class VariantEvalWalker extends RodWalker implements Tr
return null;
}
+ @Requires({"comp != null", "evals != null"})
+ private boolean compHasMatchingEval(final VariantContext comp, final Collection evals) {
+ // find all of the matching comps
+ for ( final VariantContext eval : evals ) {
+ if ( eval != null && doEvalAndCompMatch(comp, eval, requireStrictAlleleMatch) != EvalCompMatchType.NO_MATCH )
+ return true;
+ }
+
+ // nothing matched
+ return false;
+ }
+
+ private enum EvalCompMatchType { NO_MATCH, STRICT, LENIENT }
+
+ @Requires({"eval != null", "comp != null"})
+ private EvalCompMatchType doEvalAndCompMatch(final VariantContext eval, final VariantContext comp, boolean requireStrictAlleleMatch) {
+ // find all of the matching comps
+ if ( comp.getType() != eval.getType() )
+ return EvalCompMatchType.NO_MATCH;
+
+ // find the comp which matches both the reference allele and alternate allele from eval
+ final Allele altEval = eval.getAlternateAlleles().size() == 0 ? null : eval.getAlternateAllele(0);
+ final Allele altComp = comp.getAlternateAlleles().size() == 0 ? null : comp.getAlternateAllele(0);
+ if ((altEval == null && altComp == null) || (altEval != null && altEval.equals(altComp) && eval.getReference().equals(comp.getReference())))
+ return EvalCompMatchType.STRICT;
+ else
+ return requireStrictAlleleMatch ? EvalCompMatchType.NO_MATCH : EvalCompMatchType.LENIENT;
+ }
+
private VariantContext findMatchingComp(final VariantContext eval, final Collection comps) {
// if no comps, return null
if ( comps == null || comps.isEmpty() )
@@ -419,26 +445,21 @@ public class VariantEvalWalker extends RodWalker implements Tr
return comps.iterator().next();
// find all of the matching comps
- List matchingComps = new ArrayList(comps.size());
- for ( VariantContext comp : comps ) {
- if ( comp.getType() == eval.getType() )
- matchingComps.add(comp);
+ VariantContext lenientMatch = null;
+ for ( final VariantContext comp : comps ) {
+ switch ( doEvalAndCompMatch(comp, eval, requireStrictAlleleMatch) ) {
+ case STRICT:
+ return comp;
+ case LENIENT:
+ if ( lenientMatch == null ) lenientMatch = comp;
+ break;
+ case NO_MATCH:
+ ;
+ }
}
- // if no matching comp, return null
- if ( matchingComps.size() == 0 )
- return null;
-
- // find the comp which matches both the reference allele and alternate allele from eval
- Allele altEval = eval.getAlternateAlleles().size() == 0 ? null : eval.getAlternateAllele(0);
- for ( VariantContext comp : matchingComps ) {
- Allele altComp = comp.getAlternateAlleles().size() == 0 ? null : comp.getAlternateAllele(0);
- if ( (altEval == null && altComp == null) || (altEval != null && altEval.equals(altComp) && eval.getReference().equals(comp.getReference())) )
- return comp;
- }
-
- // if none match, just return the first one unless we require a strict match
- return (requireStrictAlleleMatch ? null : matchingComps.get(0));
+ // nothing matched, just return lenientMatch, which might be null
+ return lenientMatch;
}
public Integer treeReduce(Integer lhs, Integer rhs) { return null; }
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java
index cb44ca522..fdeb6919d 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java
@@ -417,8 +417,6 @@ public class VariantEvalUtils {
}
} else {
stateKeys.add(stateKey);
-
- return stateKeys;
}
return stateKeys;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GaussianMixtureModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GaussianMixtureModel.java
index 82776ca2e..6f0ae7c25 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GaussianMixtureModel.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GaussianMixtureModel.java
@@ -140,15 +140,16 @@ public class GaussianMixtureModel {
}
for( final VariantDatum datum : data ) {
- final ArrayList pVarInGaussianLog10 = new ArrayList( gaussians.size() );
+ final double[] pVarInGaussianLog10 = new double[gaussians.size()];
+ int gaussianIndex = 0;
for( final MultivariateGaussian gaussian : gaussians ) {
final double pVarLog10 = gaussian.evaluateDatumLog10( datum );
- pVarInGaussianLog10.add( pVarLog10 );
+ pVarInGaussianLog10[gaussianIndex++] = pVarLog10;
}
- final double[] pVarInGaussianNormalized = MathUtils.normalizeFromLog10( pVarInGaussianLog10 );
- int iii = 0;
+ final double[] pVarInGaussianNormalized = MathUtils.normalizeFromLog10( pVarInGaussianLog10, false );
+ gaussianIndex = 0;
for( final MultivariateGaussian gaussian : gaussians ) {
- gaussian.assignPVarInGaussian( pVarInGaussianNormalized[iii++] ); //BUGBUG: to clean up
+ gaussian.assignPVarInGaussian( pVarInGaussianNormalized[gaussianIndex++] );
}
}
}
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
index 7cc5b1625..3cdcf4982 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
@@ -372,6 +372,8 @@ public class VariantRecalibrator extends RodWalker= 0", "hapStartInRefCoords >= 0"})
+ public byte[] insertAllele( final Allele refAllele, final Allele altAllele, int refInsertLocation, final int hapStartInRefCoords, final Cigar haplotypeCigar ) {
if( refAllele.length() != altAllele.length() ) { refInsertLocation++; }
- int haplotypeInsertLocation = getHaplotypeCoordinateForReferenceCoordinate(refStart + numBasesAddedToStartOfHaplotype, haplotypeCigar, refInsertLocation);
+ int haplotypeInsertLocation = getHaplotypeCoordinateForReferenceCoordinate(hapStartInRefCoords, haplotypeCigar, refInsertLocation);
if( haplotypeInsertLocation == -1 ) { // desired change falls inside deletion so don't bother creating a new haplotype
- return getBases().clone();
+ return bases.clone();
}
- haplotypeInsertLocation += numBasesAddedToStartOfHaplotype;
- final byte[] newHaplotype = getBases().clone();
+ byte[] newHaplotype;
try {
if( refAllele.length() == altAllele.length() ) { // SNP or MNP
+ newHaplotype = bases.clone();
for( int iii = 0; iii < altAllele.length(); iii++ ) {
newHaplotype[haplotypeInsertLocation+iii] = altAllele.getBases()[iii];
}
- } else if( refAllele.length() < altAllele.length() ) { // insertion
+ } else if( refAllele.length() < altAllele.length() ) { // insertion
final int altAlleleLength = altAllele.length();
+ newHaplotype = new byte[bases.length + altAlleleLength];
+ for( int iii = 0; iii < bases.length; iii++ ) {
+ newHaplotype[iii] = bases[iii];
+ }
for( int iii = newHaplotype.length - 1; iii > haplotypeInsertLocation + altAlleleLength - 1; iii-- ) {
newHaplotype[iii] = newHaplotype[iii-altAlleleLength];
}
@@ -138,24 +143,17 @@ public class Haplotype {
newHaplotype[haplotypeInsertLocation+iii] = altAllele.getBases()[iii];
}
} else { // deletion
- int refHaplotypeOffset = 0;
- for( final CigarElement ce : haplotypeCigar.getCigarElements()) {
- if(ce.getOperator() == CigarOperator.D) { refHaplotypeOffset += ce.getLength(); }
- else if(ce.getOperator() == CigarOperator.I) { refHaplotypeOffset -= ce.getLength(); }
- }
- for( int iii = 0; iii < altAllele.length(); iii++ ) {
- newHaplotype[haplotypeInsertLocation+iii] = altAllele.getBases()[iii];
- }
final int shift = refAllele.length() - altAllele.length();
- for( int iii = haplotypeInsertLocation + altAllele.length(); iii < newHaplotype.length - shift; iii++ ) {
- newHaplotype[iii] = newHaplotype[iii+shift];
+ newHaplotype = new byte[bases.length - shift];
+ for( int iii = 0; iii < haplotypeInsertLocation + altAllele.length(); iii++ ) {
+ newHaplotype[iii] = bases[iii];
}
- for( int iii = 0; iii < shift; iii++ ) {
- newHaplotype[iii+newHaplotype.length-shift] = paddedRef[refStart+refHaplotypeLength+refHaplotypeOffset+iii];
+ for( int iii = haplotypeInsertLocation + altAllele.length(); iii < newHaplotype.length; iii++ ) {
+ newHaplotype[iii] = bases[iii+shift];
}
}
} catch (Exception e) { // event already on haplotype is too large/complex to insert another allele, most likely because of not enough reference padding
- return getBases().clone();
+ return bases.clone();
}
return newHaplotype;
diff --git a/public/java/src/org/broadinstitute/sting/utils/MathUtils.java b/public/java/src/org/broadinstitute/sting/utils/MathUtils.java
index 6f2db67ee..a96cbffc5 100644
--- a/public/java/src/org/broadinstitute/sting/utils/MathUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/MathUtils.java
@@ -41,14 +41,6 @@ import java.util.*;
* @author Kiran Garimella
*/
public class MathUtils {
- /** Public constants - used for the Lanczos approximation to the factorial function
- * (for the calculation of the binomial/multinomial probability in logspace)
- * @param LANC_SEQ[] - an array holding the constants which correspond to the product
- * of Chebyshev Polynomial coefficients, and points on the Gamma function (for interpolation)
- * [see A Precision Approximation of the Gamma Function J. SIAM Numer. Anal. Ser. B, Vol. 1 1964. pp. 86-96]
- * @param LANC_G - a value for the Lanczos approximation to the gamma function that works to
- * high precision
- */
/**
* Private constructor. No instantiating this class!
@@ -56,6 +48,28 @@ public class MathUtils {
private MathUtils() {
}
+ public static final double[] log10Cache;
+ private static final double[] jacobianLogTable;
+ private static final double JACOBIAN_LOG_TABLE_STEP = 0.001;
+ private static final double MAX_JACOBIAN_TOLERANCE = 10.0;
+ private static final int JACOBIAN_LOG_TABLE_SIZE = (int) (MAX_JACOBIAN_TOLERANCE / JACOBIAN_LOG_TABLE_STEP) + 1;
+ private static final int MAXN = 11000;
+ private static final int LOG10_CACHE_SIZE = 4 * MAXN; // we need to be able to go up to 2*(2N) when calculating some of the coefficients
+
+ static {
+ log10Cache = new double[LOG10_CACHE_SIZE];
+ jacobianLogTable = new double[JACOBIAN_LOG_TABLE_SIZE];
+
+ log10Cache[0] = Double.NEGATIVE_INFINITY;
+ for (int k = 1; k < LOG10_CACHE_SIZE; k++)
+ log10Cache[k] = Math.log10(k);
+
+ for (int k = 0; k < JACOBIAN_LOG_TABLE_SIZE; k++) {
+ jacobianLogTable[k] = Math.log10(1.0 + Math.pow(10.0, -((double) k) * JACOBIAN_LOG_TABLE_STEP));
+
+ }
+ }
+
// A fast implementation of the Math.round() method. This method does not perform
// under/overflow checking, so this shouldn't be used in the general case (but is fine
// if one is already make those checks before calling in to the rounding).
@@ -536,7 +550,7 @@ public class MathUtils {
// all negative) the largest value; also, we need to convert to normal-space.
double maxValue = Utils.findMaxEntry(array);
- // we may decide to just normalize in log space with converting to linear space
+ // we may decide to just normalize in log space without converting to linear space
if (keepInLogSpace) {
for (int i = 0; i < array.length; i++)
array[i] -= maxValue;
@@ -563,29 +577,6 @@ public class MathUtils {
return normalized;
}
- public static double[] normalizeFromLog10(List array, boolean takeLog10OfOutput) {
- double[] normalized = new double[array.size()];
-
- // for precision purposes, we need to add (or really subtract, since they're
- // all negative) the largest value; also, we need to convert to normal-space.
- double maxValue = MathUtils.arrayMaxDouble(array);
- for (int i = 0; i < array.size(); i++)
- normalized[i] = Math.pow(10, array.get(i) - maxValue);
-
- // normalize
- double sum = 0.0;
- for (int i = 0; i < array.size(); i++)
- sum += normalized[i];
- for (int i = 0; i < array.size(); i++) {
- double x = normalized[i] / sum;
- if (takeLog10OfOutput)
- x = Math.log10(x);
- normalized[i] = x;
- }
-
- return normalized;
- }
-
/**
* normalizes the log10-based array. ASSUMES THAT ALL ARRAY ENTRIES ARE <= 0 (<= 1 IN REAL-SPACE).
*
@@ -596,10 +587,6 @@ public class MathUtils {
return normalizeFromLog10(array, false);
}
- public static double[] normalizeFromLog10(List array) {
- return normalizeFromLog10(array, false);
- }
-
public static int maxElementIndex(final double[] array) {
return maxElementIndex(array, array.length);
}
@@ -1207,78 +1194,11 @@ public class MathUtils {
return ((double) num) / (Math.max(denom, 1));
}
- public static final double[] log10Cache;
- public static final double[] jacobianLogTable;
- public static final int JACOBIAN_LOG_TABLE_SIZE = 101;
- public static final double JACOBIAN_LOG_TABLE_STEP = 0.1;
- public static final double INV_JACOBIAN_LOG_TABLE_STEP = 1.0 / JACOBIAN_LOG_TABLE_STEP;
- public static final double MAX_JACOBIAN_TOLERANCE = 10.0;
- private static final int MAXN = 11000;
- private static final int LOG10_CACHE_SIZE = 4 * MAXN; // we need to be able to go up to 2*(2N) when calculating some of the coefficients
-
- static {
- log10Cache = new double[LOG10_CACHE_SIZE];
- jacobianLogTable = new double[JACOBIAN_LOG_TABLE_SIZE];
-
- log10Cache[0] = Double.NEGATIVE_INFINITY;
- for (int k = 1; k < LOG10_CACHE_SIZE; k++)
- log10Cache[k] = Math.log10(k);
-
- for (int k = 0; k < JACOBIAN_LOG_TABLE_SIZE; k++) {
- jacobianLogTable[k] = Math.log10(1.0 + Math.pow(10.0, -((double) k) * JACOBIAN_LOG_TABLE_STEP));
-
- }
- }
-
- static public double softMax(final double[] vec) {
- double acc = vec[0];
- for (int k = 1; k < vec.length; k++)
- acc = softMax(acc, vec[k]);
-
- return acc;
-
- }
-
static public double max(double x0, double x1, double x2) {
double a = Math.max(x0, x1);
return Math.max(a, x2);
}
- static public double softMax(final double x0, final double x1, final double x2) {
- // compute naively log10(10^x[0] + 10^x[1]+...)
- // return Math.log10(MathUtils.sumLog10(vec));
-
- // better approximation: do Jacobian logarithm function on data pairs
- double a = softMax(x0, x1);
- return softMax(a, x2);
- }
-
- static public double softMax(final double x, final double y) {
- // we need to compute log10(10^x + 10^y)
- // By Jacobian logarithm identity, this is equal to
- // max(x,y) + log10(1+10^-abs(x-y))
- // we compute the second term as a table lookup
- // with integer quantization
-
- // slow exact version:
- // return Math.log10(Math.pow(10.0,x) + Math.pow(10.0,y));
-
- double diff = x - y;
-
- if (diff > MAX_JACOBIAN_TOLERANCE)
- return x;
- else if (diff < -MAX_JACOBIAN_TOLERANCE)
- return y;
- else if (diff >= 0) {
- int ind = (int) (diff * INV_JACOBIAN_LOG_TABLE_STEP + 0.5);
- return x + jacobianLogTable[ind];
- }
- else {
- int ind = (int) (-diff * INV_JACOBIAN_LOG_TABLE_STEP + 0.5);
- return y + jacobianLogTable[ind];
- }
- }
-
public static double phredScaleToProbability(byte q) {
return Math.pow(10, (-q) / 10.0);
}
@@ -1734,6 +1654,4 @@ public class MathUtils {
return bitSetFrom(baseTen+preContext); // the number representing this DNA string is the base_10 representation plus all combinations that preceded this string length.
}
-
-
}
diff --git a/public/java/src/org/broadinstitute/sting/utils/clipping/ClippingOp.java b/public/java/src/org/broadinstitute/sting/utils/clipping/ClippingOp.java
index fb133d902..62a67a1f2 100644
--- a/public/java/src/org/broadinstitute/sting/utils/clipping/ClippingOp.java
+++ b/public/java/src/org/broadinstitute/sting/utils/clipping/ClippingOp.java
@@ -4,6 +4,7 @@ import com.google.java.contract.Requires;
import net.sf.samtools.Cigar;
import net.sf.samtools.CigarElement;
import net.sf.samtools.CigarOperator;
+import org.broadinstitute.sting.gatk.walkers.bqsr.RecalDataManager;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
@@ -314,6 +315,15 @@ public class ClippingOp {
if (start == 0)
hardClippedRead.setAlignmentStart(read.getAlignmentStart() + calculateAlignmentStartShift(read.getCigar(), cigarShift.cigar));
+ if (read.hasBaseIndelQualities()) {
+ byte[] newBaseInsertionQuals = new byte[newLength];
+ byte[] newBaseDeletionQuals = new byte[newLength];
+ System.arraycopy(read.getBaseInsertionQualities(), copyStart, newBaseInsertionQuals, 0, newLength);
+ System.arraycopy(read.getBaseDeletionQualities(), copyStart, newBaseDeletionQuals, 0, newLength);
+ hardClippedRead.setBaseQualities(newBaseInsertionQuals, RecalDataManager.BaseRecalibrationType.BASE_INSERTION);
+ hardClippedRead.setBaseQualities(newBaseDeletionQuals, RecalDataManager.BaseRecalibrationType.BASE_DELETION);
+ }
+
return hardClippedRead;
}
diff --git a/public/java/src/org/broadinstitute/sting/utils/crypt/CryptUtils.java b/public/java/src/org/broadinstitute/sting/utils/crypt/CryptUtils.java
new file mode 100644
index 000000000..e84b1432e
--- /dev/null
+++ b/public/java/src/org/broadinstitute/sting/utils/crypt/CryptUtils.java
@@ -0,0 +1,390 @@
+/*
+ * Copyright (c) 2012, The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+package org.broadinstitute.sting.utils.crypt;
+
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.sting.utils.io.IOUtils;
+
+import javax.crypto.Cipher;
+import java.io.File;
+import java.io.InputStream;
+import java.security.*;
+import java.security.spec.InvalidKeySpecException;
+import java.security.spec.KeySpec;
+import java.security.spec.PKCS8EncodedKeySpec;
+import java.security.spec.X509EncodedKeySpec;
+import java.util.Arrays;
+
+/**
+ * A set of cryptographic utility methods and constants.
+ *
+ * Contains methods to:
+ *
+ * -Create a public/private key pair
+ * -Read and write public/private keys to/from files/streams
+ * -Load the GATK master private/public keys
+ * -Encrypt/decrypt data
+ *
+ * Also contains constants that control the cryptographic defaults
+ * throughout the GATK.
+ *
+ * @author David Roazen
+ */
+public class CryptUtils {
+
+ // ---------------------------------------------------------------------------------
+ // Constants (these control the default cryptographic settings throughout the GATK):
+ // ---------------------------------------------------------------------------------
+
+ /**
+ * Default key length in bits of newly-created keys. 2048 bits provides a good balance between
+ * security and speed.
+ */
+ public static final int DEFAULT_KEY_LENGTH = 2048;
+
+ /**
+ * Default encryption algorithm to use, when none is specified.
+ */
+ public static final String DEFAULT_ENCRYPTION_ALGORITHM = "RSA";
+
+ /**
+ * Default random-number generation algorithm to use, when none is specified.
+ */
+ public static final String DEFAULT_RANDOM_NUMBER_GENERATION_ALGORITHM = "SHA1PRNG";
+
+ /**
+ * Name of the public key file distributed with the GATK. This file is packaged
+ * into the GATK jar, and we use the system ClassLoader to find it.
+ */
+ public static final String GATK_DISTRIBUTED_PUBLIC_KEY_FILE_NAME = "GATK_public.key";
+
+ /**
+ * Location of the master copy of the GATK private key.
+ */
+ public static final String GATK_MASTER_PRIVATE_KEY_FILE = "/humgen/gsa-hpprojects/GATK/data/gatk_master_keys/GATK_private.key";
+
+ /**
+ * Location of the master copy of the GATK public key. This file should always be the same as
+ * the public key file distributed with the GATK (and there are automated tests to ensure that it is).
+ */
+ public static final String GATK_MASTER_PUBLIC_KEY_FILE = "/humgen/gsa-hpprojects/GATK/data/gatk_master_keys/GATK_public.key";
+
+ /**
+ * Directory where generated GATK user keys are stored. See the GATKKey class for more information.
+ */
+ public static final String GATK_USER_KEY_DIRECTORY = "/humgen/gsa-hpprojects/GATK/data/gatk_user_keys/";
+
+
+ // -----------------------
+ // Utility Methods:
+ // -----------------------
+
+ /**
+ * Generate a new public/private key pair using the default encryption settings defined above.
+ *
+ * @return A new public/private key pair created using the default settings
+ */
+ public static KeyPair generateKeyPair() {
+ return generateKeyPair(DEFAULT_KEY_LENGTH, DEFAULT_ENCRYPTION_ALGORITHM, DEFAULT_RANDOM_NUMBER_GENERATION_ALGORITHM);
+ }
+
+ /**
+ * Generate a new public/private key pair using custom encryption settings.
+ *
+ * @param keyLength Length of the key in bits
+ * @param encryptionAlgorithm Encryption algorithm to use
+ * @param randNumberAlgorithm Random-number generation algorithm to use
+ * @return A new public/private key pair, created according to the specified parameters
+ */
+ public static KeyPair generateKeyPair( int keyLength, String encryptionAlgorithm, String randNumberAlgorithm ) {
+ try {
+ KeyPairGenerator keyGen = KeyPairGenerator.getInstance(encryptionAlgorithm);
+ SecureRandom randomnessSource = createRandomnessSource(randNumberAlgorithm);
+
+ keyGen.initialize(keyLength, randomnessSource);
+ return keyGen.generateKeyPair();
+ }
+ catch ( NoSuchAlgorithmException e ) {
+ throw new ReviewedStingException(String.format("Could not find an implementation of the requested encryption algorithm %s", encryptionAlgorithm), e);
+ }
+ catch ( Exception e ) {
+ throw new ReviewedStingException("Error while generating key pair", e);
+ }
+ }
+
+ /**
+ * Create a source of randomness using the default random-number generation algorithm.
+ *
+ * @return A randomness source that uses the default algorithm
+ */
+ public static SecureRandom createRandomnessSource() {
+ return createRandomnessSource(DEFAULT_RANDOM_NUMBER_GENERATION_ALGORITHM);
+ }
+
+ /**
+ * Create a source of randomness using a custom random-number generation algorithm.
+ *
+ * @param randAlgorithm The random-number generation algorithm to use
+ * @return A randomness sources that uses the specified algorithm
+ */
+ public static SecureRandom createRandomnessSource ( String randAlgorithm ) {
+ try {
+ return SecureRandom.getInstance(randAlgorithm);
+ }
+ catch ( NoSuchAlgorithmException e ) {
+ throw new ReviewedStingException(String.format("Could not find an implementation of the requested random-number generation algorithm %s", randAlgorithm), e);
+ }
+ }
+
+ /**
+ * Writes a public/private key pair to disk
+ *
+ * @param keyPair The key pair we're writing to disk
+ * @param privateKeyFile Location to write the private key
+ * @param publicKeyFile Location to write the public key
+ */
+ public static void writeKeyPair ( KeyPair keyPair, File privateKeyFile, File publicKeyFile ) {
+ writeKey(keyPair.getPrivate(), privateKeyFile);
+ writeKey(keyPair.getPublic(), publicKeyFile);
+ }
+
+ /**
+ * Writes an arbitrary key to disk
+ *
+ * @param key The key to write
+ * @param destination Location to write the key to
+ */
+ public static void writeKey ( Key key, File destination ) {
+ IOUtils.writeByteArrayToFile(key.getEncoded(), destination);
+ }
+
+ /**
+ * Reads in a public key created using the default encryption algorithm from a file.
+ *
+ * @param source File containing the public key
+ * @return The public key read
+ */
+ public static PublicKey readPublicKey ( File source ) {
+ return decodePublicKey(IOUtils.readFileIntoByteArray(source), DEFAULT_ENCRYPTION_ALGORITHM);
+ }
+
+ /**
+ * Reads in a public key created using the default encryption algorithm from a stream.
+ *
+ * @param source Stream attached to the public key
+ * @return The public key read
+ */
+ public static PublicKey readPublicKey ( InputStream source ) {
+ return decodePublicKey(IOUtils.readStreamIntoByteArray(source), DEFAULT_ENCRYPTION_ALGORITHM);
+ }
+
+ /**
+ * Decodes the raw bytes of a public key into a usable object.
+ *
+ * @param rawKey The encoded bytes of a public key as read from, eg., a file. The
+ * key must be in the standard X.509 format for a public key.
+ * @param encryptionAlgorithm The encryption algorithm used to create the public key
+ * @return The public key as a usable object
+ */
+ public static PublicKey decodePublicKey ( byte[] rawKey, String encryptionAlgorithm ) {
+ try {
+ KeySpec keySpec = new X509EncodedKeySpec(rawKey);
+ KeyFactory keyFactory = KeyFactory.getInstance(encryptionAlgorithm);
+ return keyFactory.generatePublic(keySpec);
+ }
+ catch ( NoSuchAlgorithmException e ) {
+ throw new ReviewedStingException(String.format("Could not find an implementation of the requested encryption algorithm %s", encryptionAlgorithm), e);
+ }
+ catch ( InvalidKeySpecException e ) {
+ throw new ReviewedStingException("Unable to use X.509 key specification to decode the given key", e);
+ }
+ }
+
+ /**
+ * Reads in a private key created using the default encryption algorithm from a file.
+ *
+ * @param source File containing the private key
+ * @return The private key read
+ */
+ public static PrivateKey readPrivateKey ( File source ) {
+ return decodePrivateKey(IOUtils.readFileIntoByteArray(source), DEFAULT_ENCRYPTION_ALGORITHM);
+ }
+
+ /**
+ * Reads in a private key created using the default encryption algorithm from a stream.
+ *
+ * @param source Stream attached to the private key
+ * @return The private key read
+ */
+ public static PrivateKey readPrivateKey ( InputStream source ) {
+ return decodePrivateKey(IOUtils.readStreamIntoByteArray(source), DEFAULT_ENCRYPTION_ALGORITHM);
+ }
+
+ /**
+ * Decodes the raw bytes of a private key into a usable object.
+ *
+ * @param rawKey The encoded bytes of a private key as read from, eg., a file. The
+ * key must be in the standard PKCS #8 format for a private key.
+ * @param encryptionAlgorithm The encryption algorithm used to create the private key
+ * @return The private key as a usable object
+ */
+ public static PrivateKey decodePrivateKey ( byte[] rawKey, String encryptionAlgorithm ) {
+ try {
+ KeySpec keySpec = new PKCS8EncodedKeySpec(rawKey);
+ KeyFactory keyFactory = KeyFactory.getInstance(encryptionAlgorithm);
+ return keyFactory.generatePrivate(keySpec);
+ }
+ catch ( NoSuchAlgorithmException e ) {
+ throw new ReviewedStingException(String.format("Could not find an implementation of the requested encryption algorithm %s", encryptionAlgorithm), e);
+ }
+ catch ( InvalidKeySpecException e ) {
+ throw new ReviewedStingException("Unable to use the PKCS #8 key specification to decode the given key", e);
+ }
+ }
+
+ /**
+ * Loads the copy of the GATK public key that is distributed with the GATK. Uses the system
+ * ClassLoader to locate the public key file, which should be stored at the root of the GATK
+ * jar file.
+ *
+ * @return The GATK public key as a usable object
+ */
+ public static PublicKey loadGATKDistributedPublicKey() {
+ InputStream publicKeyInputStream = ClassLoader.getSystemResourceAsStream(GATK_DISTRIBUTED_PUBLIC_KEY_FILE_NAME);
+
+ if ( publicKeyInputStream == null ) {
+ throw new ReviewedStingException(String.format("Could not locate the GATK public key %s in the classpath",
+ GATK_DISTRIBUTED_PUBLIC_KEY_FILE_NAME));
+ }
+
+ return readPublicKey(publicKeyInputStream);
+ }
+
+ /**
+ * Loads the master copy of the GATK private key. You must have the appropriate UNIX permissions
+ * to do this!
+ *
+ * @return The GATK master private key as a usable object
+ */
+ public static PrivateKey loadGATKMasterPrivateKey() {
+ return readPrivateKey(new File(GATK_MASTER_PRIVATE_KEY_FILE));
+ }
+
+ /**
+ * Loads the master copy of the GATK public key. This should always be the same as the
+ * public key distributed with the GATK returned by loadGATKDistributedPublicKey().
+ *
+ * @return The GATK master public key as a usable object
+ */
+ public static PublicKey loadGATKMasterPublicKey() {
+ return readPublicKey(new File(GATK_MASTER_PUBLIC_KEY_FILE));
+ }
+
+ /**
+ * Encrypts the given data using the key provided.
+ *
+ * @param data The data to encrypt, as a byte array
+ * @param encryptKey The key with which to encrypt the data
+ * @return The encrypted version of the provided data
+ */
+ public static byte[] encryptData ( byte[] data, Key encryptKey ) {
+ return transformDataUsingCipher(data, encryptKey, Cipher.ENCRYPT_MODE);
+ }
+
+ /**
+ * Decrypts the given data using the key provided.
+ *
+ * @param encryptedData Data to decrypt, as a byte array
+ * @param decryptKey The key with which to decrypt the data
+ * @return The decrypted version of the provided data
+ */
+ public static byte[] decryptData ( byte[] encryptedData, Key decryptKey ) {
+ return transformDataUsingCipher(encryptedData, decryptKey, Cipher.DECRYPT_MODE);
+ }
+
+ /**
+ * Helper method for encryption/decryption that takes data and processes it using
+ * the given key
+ *
+ * @param data Data to encrypt/decrypt
+ * @param key Key to use to encrypt/decrypt the data
+ * @param cipherMode Specifies whether we are encrypting or decrypting
+ * @return The encrypted/decrypted data
+ */
+ private static byte[] transformDataUsingCipher ( byte[] data, Key key, int cipherMode ) {
+ try {
+ Cipher cipher = Cipher.getInstance(key.getAlgorithm());
+ cipher.init(cipherMode, key);
+ return cipher.doFinal(data);
+ }
+ catch ( NoSuchAlgorithmException e ) {
+ throw new ReviewedStingException(String.format("Could not find an implementation of the requested algorithm %s",
+ key.getAlgorithm()), e);
+ }
+ catch ( InvalidKeyException e ) {
+ throw new ReviewedStingException("Key is invalid", e);
+ }
+ catch ( GeneralSecurityException e ) {
+ throw new ReviewedStingException("Error during encryption", e);
+ }
+ }
+
+ /**
+ * Tests whether the public/private keys provided can each decrypt data encrypted by
+ * the other key -- ie., tests whether these two keys are part of the same public/private
+ * key pair.
+ *
+ * @param privateKey The private key to test
+ * @param publicKey The public key to test
+ * @return True if the keys are part of the same key pair and can decrypt each other's
+ * encrypted data, otherwise false.
+ */
+ public static boolean keysDecryptEachOther ( PrivateKey privateKey, PublicKey publicKey ) {
+ byte[] plainText = "Test PlainText".getBytes();
+
+ byte[] dataEncryptedUsingPrivateKey = CryptUtils.encryptData(plainText, privateKey);
+ byte[] dataEncryptedUsingPublicKey = CryptUtils.encryptData(plainText, publicKey);
+
+ byte[] privateKeyDataDecryptedWithPublicKey = CryptUtils.decryptData(dataEncryptedUsingPrivateKey, publicKey);
+ byte[] publicKeyDataDecryptedWithPrivateKey = CryptUtils.decryptData(dataEncryptedUsingPublicKey, privateKey);
+
+ // Make sure we actually transformed the data during encryption:
+ if ( Arrays.equals(plainText, dataEncryptedUsingPrivateKey) ||
+ Arrays.equals(plainText, dataEncryptedUsingPublicKey) ||
+ Arrays.equals(dataEncryptedUsingPrivateKey, dataEncryptedUsingPublicKey) ) {
+ return false;
+ }
+
+ // Make sure that we were able to recreate the original plaintext using
+ // both the public key on the private-key-encrypted data and the private
+ // key on the public-key-encrypted data:
+ if ( ! Arrays.equals(plainText, privateKeyDataDecryptedWithPublicKey) ||
+ ! Arrays.equals(plainText, publicKeyDataDecryptedWithPrivateKey) ) {
+ return false;
+ }
+
+ return true;
+ }
+}
diff --git a/public/java/src/org/broadinstitute/sting/utils/crypt/GATKKey.java b/public/java/src/org/broadinstitute/sting/utils/crypt/GATKKey.java
new file mode 100644
index 000000000..408cb56aa
--- /dev/null
+++ b/public/java/src/org/broadinstitute/sting/utils/crypt/GATKKey.java
@@ -0,0 +1,349 @@
+/*
+ * Copyright (c) 2012, The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+package org.broadinstitute.sting.utils.crypt;
+
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.io.IOUtils;
+
+import java.io.*;
+import java.security.*;
+import java.util.zip.GZIPInputStream;
+import java.util.zip.GZIPOutputStream;
+
+/**
+ * Class to represent a GATK user key.
+ *
+ * A GATK user key contains an email address and a cryptographic signature.
+ * The signature is the SHA-1 hash of the email address encrypted using
+ * the GATK master private key. The GATK master public key (distributed
+ * with the GATK) is used to decrypt the signature and validate the key
+ * at the start of each GATK run that requires a key.
+ *
+ * Keys are cryptographically secure in that valid keys definitely come
+ * from us and cannot be fabricated, however nothing prevents keys from
+ * being shared between users.
+ *
+ * GATK user keys have the following on-disk format:
+ *
+ * GZIP Container:
+ * Email address
+ * NUL byte (delimiter)
+ * Cryptographic Signature (encrypted SHA-1 hash of email address)
+ *
+ * The key data is wrapped within a GZIP container to placate over-zealous
+ * email filters (since keys must often be emailed) and also to provide an
+ * additional integrity check via the built-in GZIP CRC.
+ *
+ * @author David Roazen
+ */
+public class GATKKey {
+
+ /**
+ * Private key used to sign the GATK key. Required only when creating a new
+ * key from scratch, not when loading an existing key from disk.
+ */
+ private PrivateKey privateKey;
+
+ /**
+ * Public key used to validate the GATK key.
+ */
+ private PublicKey publicKey;
+
+ /**
+ * The user's email address, stored within the key and signed.
+ */
+ private String emailAddress;
+
+ /**
+ * The cryptographic signature of the email address. By default, this is
+ * the SHA-1 hash of the email address encrypted using the RSA algorithm.
+ */
+ private byte[] signature;
+
+ /**
+ * The combination of hash/encryption algorithms to use to generate the signature.
+ * By default this is "SHA1withRSA"
+ */
+ private String signingAlgorithm;
+
+ /**
+ * Default hash/encryption algorithms to use to sign the key.
+ */
+ public static final String DEFAULT_SIGNING_ALGORITHM = "SHA1withRSA";
+
+ /**
+ * Byte value used to separate the email address from its signature in the key file.
+ */
+ public static final byte GATK_KEY_SECTIONAL_DELIMITER = 0;
+
+
+ // -----------------------
+ // Constructors:
+ // -----------------------
+
+ /**
+ * Constructor to create a new GATK key from scratch using an email address
+ * and public/private key pair. The private key is used for signing, and the
+ * public key is used to validate the newly-created key.
+ *
+ * @param privateKey Private key used to sign the new GATK key
+ * @param publicKey Public key used to validate the new GATK key
+ * @param emailAddress The user's email address, which we will store in the key and sign
+ */
+ public GATKKey ( PrivateKey privateKey, PublicKey publicKey, String emailAddress ) {
+ this(privateKey, publicKey, emailAddress, DEFAULT_SIGNING_ALGORITHM);
+ }
+
+ /**
+ * Constructor to create a new GATK key from scratch using an email address
+ * and public/private key pair, and additionally specify the signing algorithm
+ * to use. The private key is used for signing, and the public key is used to
+ * validate the newly-created key.
+ *
+ * @param privateKey Private key used to sign the new GATK key
+ * @param publicKey Public key used to validate the new GATK key
+ * @param emailAddress The user's email address, which we will store in the key and sign
+ * @param signingAlgorithm The combination of hash and encryption algorithms to use to sign the key
+ */
+ public GATKKey ( PrivateKey privateKey, PublicKey publicKey, String emailAddress, String signingAlgorithm ) {
+ if ( privateKey == null || publicKey == null || emailAddress == null || emailAddress.length() == 0 || signingAlgorithm == null ) {
+ throw new ReviewedStingException("Cannot construct GATKKey using null/empty arguments");
+ }
+
+ this.privateKey = privateKey;
+ this.publicKey = publicKey;
+ this.emailAddress = emailAddress;
+ this.signingAlgorithm = signingAlgorithm;
+
+ validateEmailAddress();
+ generateSignature();
+
+ if ( ! isValid() ) {
+ throw new ReviewedStingException("Newly-generated GATK key fails validation -- this should never happen!");
+ }
+ }
+
+ /**
+ * Constructor to load an existing GATK key from a file.
+ *
+ * During loading, the key file is checked for integrity, but not cryptographic
+ * validity (which must be done through a subsequent call to isValid()).
+ *
+ * @param publicKey Public key that will be used to validate the loaded GATK key
+ * in subsequent calls to isValid()
+ * @param keyFile File containing the GATK key to load
+ */
+ public GATKKey ( PublicKey publicKey, File keyFile ) {
+ this(publicKey, keyFile, DEFAULT_SIGNING_ALGORITHM);
+ }
+
+ /**
+ * Constructor to load an existing GATK key from a file, and additionally specify
+ * the signing algorithm used to sign the key being loaded.
+ *
+ * During loading, the key file is checked for integrity, but not cryptographic
+ * validity (which must be done through a subsequent call to isValid()).
+ *
+ * @param publicKey Public key that will be used to validate the loaded GATK key
+ * in subsequent calls to isValid()
+ * @param keyFile File containing the GATK key to load
+ * @param signingAlgorithm The combination of hash and encryption algorithms used to sign the key
+ */
+ public GATKKey ( PublicKey publicKey, File keyFile, String signingAlgorithm ) {
+ if ( publicKey == null || keyFile == null || signingAlgorithm == null ) {
+ throw new ReviewedStingException("Cannot construct GATKKey using null arguments");
+ }
+
+ this.publicKey = publicKey;
+ this.signingAlgorithm = signingAlgorithm;
+
+ readKey(keyFile);
+ }
+
+ // -----------------------
+ // Public API Methods:
+ // -----------------------
+
+ /**
+ * Writes out this key to a file in the format described at the top of this class,
+ * encapsulating the key within a GZIP container.
+ *
+ * @param destination File to write the key to
+ */
+ public void writeKey ( File destination ) {
+ try {
+ byte[] keyBytes = marshalKeyData();
+ IOUtils.writeByteArrayToStream(keyBytes, new GZIPOutputStream(new FileOutputStream(destination)));
+ }
+ catch ( IOException e ) {
+ throw new UserException.CouldNotCreateOutputFile(destination, e);
+ }
+ }
+
+ /**
+ * Checks whether the signature of this key is cryptographically valid (ie., can be
+ * decrypted by the public key to produce a valid SHA-1 hash of the email address
+ * in the key).
+ *
+ * @return True if the key's signature passes validation, otherwise false
+ */
+ public boolean isValid() {
+ try {
+ Signature sig = Signature.getInstance(signingAlgorithm);
+ sig.initVerify(publicKey);
+ sig.update(emailAddress.getBytes());
+ return sig.verify(signature);
+ }
+ catch ( NoSuchAlgorithmException e ) {
+ throw new ReviewedStingException(String.format("Signing algorithm %s not found", signingAlgorithm), e);
+ }
+ catch ( InvalidKeyException e ) {
+ // If the GATK public key is invalid, it's likely our problem, not the user's:
+ throw new ReviewedStingException(String.format("Public key %s is invalid", publicKey), e);
+ }
+ catch ( SignatureException e ) {
+ throw new UserException.UnreadableKeyException("Signature is invalid or signing algorithm was unable to process the input data", e);
+ }
+ }
+
+ // -----------------------
+ // Private Helper Methods:
+ // -----------------------
+
+ /**
+ * Helper method that creates a signature for this key using the combination of
+ * hash/encryption algorithms specified at construction time.
+ */
+ private void generateSignature() {
+ try {
+ Signature sig = Signature.getInstance(signingAlgorithm);
+ sig.initSign(privateKey, CryptUtils.createRandomnessSource());
+ sig.update(emailAddress.getBytes());
+ signature = sig.sign();
+ }
+ catch ( NoSuchAlgorithmException e ) {
+ throw new ReviewedStingException(String.format("Signing algorithm %s not found", signingAlgorithm), e);
+ }
+ catch ( InvalidKeyException e ) {
+ throw new ReviewedStingException(String.format("Private key %s is invalid", privateKey), e);
+ }
+ catch ( SignatureException e ) {
+ throw new ReviewedStingException(String.format("Error creating signature for email address %s", emailAddress), e);
+ }
+ }
+
+ /**
+ * Helper method that reads in a GATK key from a file. Should not be called directly --
+ * use the appropriate constructor above.
+ *
+ * @param source File to read the key from
+ */
+ private void readKey ( File source ) {
+ try {
+ byte[] keyBytes = IOUtils.readStreamIntoByteArray(new GZIPInputStream(new FileInputStream(source)));
+
+ // As a sanity check, compare the number of bytes read to the uncompressed file size
+ // stored in the GZIP ISIZE field. If they don't match, the key must be corrupt:
+ if ( keyBytes.length != IOUtils.getGZIPFileUncompressedSize(source) ) {
+ throw new UserException.UnreadableKeyException("Number of bytes read does not match the uncompressed size specified in the GZIP ISIZE field");
+ }
+
+ unmarshalKeyData(keyBytes);
+ }
+ catch ( FileNotFoundException e ) {
+ throw new UserException.CouldNotReadInputFile(source, e);
+ }
+ catch ( IOException e ) {
+ throw new UserException.UnreadableKeyException(source, e);
+ }
+ catch ( UserException.CouldNotReadInputFile e ) {
+ throw new UserException.UnreadableKeyException(source, e);
+ }
+ }
+
+ /**
+ * Helper method that assembles the email address and signature into a format
+ * suitable for writing to disk.
+ *
+ * @return The aggregated key data, ready to be written to disk
+ */
+ private byte[] marshalKeyData() {
+ byte[] emailAddressBytes = emailAddress.getBytes();
+ byte[] assembledKey = new byte[emailAddressBytes.length + 1 + signature.length];
+
+ System.arraycopy(emailAddressBytes, 0, assembledKey, 0, emailAddressBytes.length);
+ assembledKey[emailAddressBytes.length] = GATK_KEY_SECTIONAL_DELIMITER;
+ System.arraycopy(signature, 0, assembledKey, emailAddressBytes.length + 1, signature.length);
+
+ return assembledKey;
+ }
+
+ /**
+ * Helper method that parses the raw key data from disk into its component
+ * email address and signature. Performs some basic validation in the process.
+ *
+ * @param keyBytes The raw, uncompressed key data read from disk
+ */
+ private void unmarshalKeyData ( byte[] keyBytes ) {
+ int delimiterPosition = -1;
+
+ for ( int i = 0; i < keyBytes.length; i++ ) {
+ if ( keyBytes[i] == GATK_KEY_SECTIONAL_DELIMITER ) {
+ delimiterPosition = i;
+ break;
+ }
+ }
+
+ if ( delimiterPosition == -1 ) {
+ throw new UserException.UnreadableKeyException("Malformed GATK key contains no sectional delimiter");
+ }
+ else if ( delimiterPosition == 0 ) {
+ throw new UserException.UnreadableKeyException("Malformed GATK key contains no email address");
+ }
+ else if ( delimiterPosition == keyBytes.length - 1 ) {
+ throw new UserException.UnreadableKeyException("Malformed GATK key contains no signature");
+ }
+
+ byte[] emailAddressBytes = new byte[delimiterPosition];
+ System.arraycopy(keyBytes, 0, emailAddressBytes, 0, delimiterPosition);
+ emailAddress = new String(emailAddressBytes);
+
+ signature = new byte[keyBytes.length - delimiterPosition - 1];
+ System.arraycopy(keyBytes, delimiterPosition + 1, signature, 0, keyBytes.length - delimiterPosition - 1);
+ }
+
+ /**
+ * Helper method that ensures that the user's email address does not contain the NUL byte, which we
+ * reserve as a delimiter within each key file.
+ */
+ private void validateEmailAddress() {
+ for ( byte b : emailAddress.getBytes() ) {
+ if ( b == GATK_KEY_SECTIONAL_DELIMITER ) {
+ throw new UserException(String.format("Email address must not contain a byte with value %d", GATK_KEY_SECTIONAL_DELIMITER));
+ }
+ }
+ }
+}
diff --git a/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java b/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java
index 2ece3b077..6cc8008d2 100755
--- a/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java
+++ b/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java
@@ -132,6 +132,10 @@ public class UserException extends ReviewedStingException {
public CouldNotReadInputFile(File file, Exception e) {
this(file, e.getMessage());
}
+
+ public CouldNotReadInputFile(String message) {
+ super(message);
+ }
}
@@ -151,6 +155,10 @@ public class UserException extends ReviewedStingException {
public CouldNotCreateOutputFile(File file, Exception e) {
super(String.format("Couldn't write file %s because exception %s", file.getAbsolutePath(), e.getMessage()));
}
+
+ public CouldNotCreateOutputFile(String message, Exception e) {
+ super(message, e);
+ }
}
public static class MissortedBAM extends UserException {
@@ -319,4 +327,32 @@ public class UserException extends ReviewedStingException {
"and try again.", null);
}
}
+
+ public static class UnreadableKeyException extends UserException {
+ public UnreadableKeyException ( File f, Exception e ) {
+ super(String.format("Key file %s cannot be read (possibly the key file is corrupt?). Error was: %s. " +
+ "Please see http://www.broadinstitute.org/gsa/wiki/index.php/Phone_home for help.",
+ f.getAbsolutePath(), e.getMessage()));
+ }
+
+ public UnreadableKeyException ( String message, Exception e ) {
+ this(String.format("%s. Error was: %s", message, e.getMessage()));
+ }
+
+ public UnreadableKeyException ( String message ) {
+ super(String.format("Key file cannot be read (possibly the key file is corrupt?): %s. " +
+ "Please see http://www.broadinstitute.org/gsa/wiki/index.php/Phone_home for help.",
+ message));
+ }
+ }
+
+ public static class KeySignatureVerificationException extends UserException {
+ public KeySignatureVerificationException ( File f ) {
+ super(String.format("The signature in key file %s failed cryptographic verification. " +
+ "If this key was valid in the past, it's likely been revoked. " +
+ "Please see http://www.broadinstitute.org/gsa/wiki/index.php/Phone_home " +
+ "for help.",
+ f.getAbsolutePath()));
+ }
+ }
}
diff --git a/public/java/src/org/broadinstitute/sting/utils/fragments/FragmentUtils.java b/public/java/src/org/broadinstitute/sting/utils/fragments/FragmentUtils.java
index 7104b1edd..eea45567f 100644
--- a/public/java/src/org/broadinstitute/sting/utils/fragments/FragmentUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/fragments/FragmentUtils.java
@@ -151,23 +151,16 @@ public class FragmentUtils {
final int numBases = firstReadStop + secondRead.getReadLength();
final byte[] bases = new byte[numBases];
final byte[] quals = new byte[numBases];
- // BUGBUG: too verbose, clean this up.
final byte[] insertionQuals = new byte[numBases];
final byte[] deletionQuals = new byte[numBases];
final byte[] firstReadBases = firstRead.getReadBases();
final byte[] firstReadQuals = firstRead.getBaseQualities();
- final byte[] firstReadInsertionQuals = firstRead.getBaseInsertionQualities();
- final byte[] firstReadDeletionQuals = firstRead.getBaseDeletionQualities();
final byte[] secondReadBases = secondRead.getReadBases();
final byte[] secondReadQuals = secondRead.getBaseQualities();
- final byte[] secondReadInsertionQuals = secondRead.getBaseInsertionQualities();
- final byte[] secondReadDeletionQuals = secondRead.getBaseDeletionQualities();
for(int iii = 0; iii < firstReadStop; iii++) {
bases[iii] = firstReadBases[iii];
quals[iii] = firstReadQuals[iii];
- insertionQuals[iii] = firstReadInsertionQuals[iii];
- deletionQuals[iii] = firstReadDeletionQuals[iii];
}
for(int iii = firstReadStop; iii < firstRead.getReadLength(); iii++) {
if( firstReadQuals[iii] > MIN_QUAL_BAD_OVERLAP && secondReadQuals[iii-firstReadStop] > MIN_QUAL_BAD_OVERLAP && firstReadBases[iii] != secondReadBases[iii-firstReadStop] ) {
@@ -175,22 +168,16 @@ public class FragmentUtils {
}
bases[iii] = ( firstReadQuals[iii] > secondReadQuals[iii-firstReadStop] ? firstReadBases[iii] : secondReadBases[iii-firstReadStop] );
quals[iii] = ( firstReadQuals[iii] > secondReadQuals[iii-firstReadStop] ? firstReadQuals[iii] : secondReadQuals[iii-firstReadStop] );
- insertionQuals[iii] = ( firstReadQuals[iii] > secondReadQuals[iii-firstReadStop] ? firstReadInsertionQuals[iii] : secondReadInsertionQuals[iii-firstReadStop] ); // Purposefully checking the highest base quality score
- deletionQuals[iii] = ( firstReadQuals[iii] > secondReadQuals[iii-firstReadStop] ? firstReadDeletionQuals[iii] : secondReadDeletionQuals[iii-firstReadStop] ); // Purposefully checking the highest base quality score
}
for(int iii = firstRead.getReadLength(); iii < numBases; iii++) {
bases[iii] = secondReadBases[iii-firstReadStop];
quals[iii] = secondReadQuals[iii-firstReadStop];
- insertionQuals[iii] = secondReadInsertionQuals[iii-firstReadStop];
- deletionQuals[iii] = secondReadDeletionQuals[iii-firstReadStop];
}
final GATKSAMRecord returnRead = new GATKSAMRecord(firstRead.getHeader());
returnRead.setAlignmentStart(firstRead.getUnclippedStart());
returnRead.setReadBases( bases );
- returnRead.setBaseQualities( quals, RecalDataManager.BaseRecalibrationType.BASE_SUBSTITUTION );
- returnRead.setBaseQualities( insertionQuals, RecalDataManager.BaseRecalibrationType.BASE_INSERTION );
- returnRead.setBaseQualities( deletionQuals, RecalDataManager.BaseRecalibrationType.BASE_DELETION );
+ returnRead.setBaseQualities( quals );
returnRead.setReadGroup( firstRead.getReadGroup() );
returnRead.setReferenceName( firstRead.getReferenceName() );
final CigarElement c = new CigarElement(bases.length, CigarOperator.M);
@@ -199,6 +186,27 @@ public class FragmentUtils {
returnRead.setCigar( new Cigar( cList ));
returnRead.setMappingQuality( firstRead.getMappingQuality() );
+ if( firstRead.hasBaseIndelQualities() || secondRead.hasBaseIndelQualities() ) {
+ final byte[] firstReadInsertionQuals = firstRead.getBaseInsertionQualities();
+ final byte[] firstReadDeletionQuals = firstRead.getBaseDeletionQualities();
+ final byte[] secondReadInsertionQuals = secondRead.getBaseInsertionQualities();
+ final byte[] secondReadDeletionQuals = secondRead.getBaseDeletionQualities();
+ for(int iii = 0; iii < firstReadStop; iii++) {
+ insertionQuals[iii] = firstReadInsertionQuals[iii];
+ deletionQuals[iii] = firstReadDeletionQuals[iii];
+ }
+ for(int iii = firstReadStop; iii < firstRead.getReadLength(); iii++) {
+ insertionQuals[iii] = ( firstReadQuals[iii] > secondReadQuals[iii-firstReadStop] ? firstReadInsertionQuals[iii] : secondReadInsertionQuals[iii-firstReadStop] ); // Purposefully checking the highest *base* quality score
+ deletionQuals[iii] = ( firstReadQuals[iii] > secondReadQuals[iii-firstReadStop] ? firstReadDeletionQuals[iii] : secondReadDeletionQuals[iii-firstReadStop] ); // Purposefully checking the highest *base* quality score
+ }
+ for(int iii = firstRead.getReadLength(); iii < numBases; iii++) {
+ insertionQuals[iii] = secondReadInsertionQuals[iii-firstReadStop];
+ deletionQuals[iii] = secondReadDeletionQuals[iii-firstReadStop];
+ }
+ returnRead.setBaseQualities( insertionQuals, RecalDataManager.BaseRecalibrationType.BASE_INSERTION );
+ returnRead.setBaseQualities( deletionQuals, RecalDataManager.BaseRecalibrationType.BASE_DELETION );
+ }
+
final ArrayList returnList = new ArrayList();
returnList.add(returnRead);
return returnList;
diff --git a/public/java/src/org/broadinstitute/sting/utils/io/IOUtils.java b/public/java/src/org/broadinstitute/sting/utils/io/IOUtils.java
index a5ba857ef..160df0e51 100644
--- a/public/java/src/org/broadinstitute/sting/utils/io/IOUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/io/IOUtils.java
@@ -29,10 +29,13 @@ import org.apache.commons.io.FilenameUtils;
import org.apache.commons.io.LineIterator;
import org.apache.commons.lang.StringUtils;
import org.apache.log4j.Logger;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.StingException;
import org.broadinstitute.sting.utils.exceptions.UserException;
import java.io.*;
+import java.nio.ByteBuffer;
+import java.nio.ByteOrder;
import java.util.*;
public class IOUtils {
@@ -400,4 +403,173 @@ public class IOUtils {
public static boolean isSpecialFile(File file) {
return file != null && (file.getAbsolutePath().startsWith("/dev/") || file.equals(DEV_DIR));
}
+
+ /**
+ * Reads the entirety of the given file into a byte array. Uses a read buffer size of 4096 bytes.
+ *
+ * @param source File to read
+ * @return The contents of the file as a byte array
+ */
+ public static byte[] readFileIntoByteArray ( File source ) {
+ return readFileIntoByteArray(source, 4096);
+ }
+
+ /**
+ * Reads the entirety of the given file into a byte array using the requested read buffer size.
+ *
+ * @param source File to read
+ * @param readBufferSize Number of bytes to read in at one time
+ * @return The contents of the file as a byte array
+ */
+ public static byte[] readFileIntoByteArray ( File source, int readBufferSize ) {
+ if ( source == null ) {
+ throw new ReviewedStingException("Source file was null");
+ }
+
+ byte[] fileContents;
+
+ try {
+ fileContents = readStreamIntoByteArray(new FileInputStream(source), readBufferSize);
+ }
+ catch ( FileNotFoundException e ) {
+ throw new UserException.CouldNotReadInputFile(source, e);
+ }
+
+ if ( fileContents.length != source.length() ) {
+ throw new UserException.CouldNotReadInputFile(String.format("Unable to completely read file %s: read only %d/%d bytes",
+ source.getAbsolutePath(), fileContents.length, source.length()));
+ }
+
+ return fileContents;
+ }
+
+ /**
+ * Reads all data from the given stream into a byte array. Uses a read buffer size of 4096 bytes.
+ *
+ * @param in Stream to read data from
+ * @return The contents of the stream as a byte array
+ */
+ public static byte[] readStreamIntoByteArray ( InputStream in ) {
+ return readStreamIntoByteArray(in, 4096);
+ }
+
+ /**
+ * Reads all data from the given stream into a byte array using the requested read buffer size.
+ *
+ * @param in Stream to read data from
+ * @param readBufferSize Number of bytes to read in at one time
+ * @return The contents of the stream as a byte array
+ */
+ public static byte[] readStreamIntoByteArray ( InputStream in, int readBufferSize ) {
+ if ( in == null ) {
+ throw new ReviewedStingException("Input stream was null");
+ }
+ else if ( readBufferSize <= 0 ) {
+ throw new ReviewedStingException("Read buffer size must be > 0");
+ }
+
+ // Use a fixed-size buffer for each read, but a dynamically-growing buffer
+ // to hold the accumulated contents of the file/stream:
+ byte[] readBuffer = new byte[readBufferSize];
+ ByteArrayOutputStream fileBuffer = new ByteArrayOutputStream(readBufferSize * 4);
+
+ try {
+ try {
+ int currentBytesRead;
+
+ while ( (currentBytesRead = in.read(readBuffer, 0, readBuffer.length)) >= 0 ) {
+ fileBuffer.write(readBuffer, 0, currentBytesRead);
+ }
+ }
+ finally {
+ in.close();
+ }
+ }
+ catch ( IOException e ) {
+ throw new UserException.CouldNotReadInputFile("I/O error reading from input stream", e);
+ }
+
+ return fileBuffer.toByteArray();
+ }
+
+ /**
+ * Writes the given array of bytes to a file
+ *
+ * @param bytes Data to write
+ * @param destination File to write the data to
+ */
+ public static void writeByteArrayToFile ( byte[] bytes, File destination ) {
+ if ( destination == null ) {
+ throw new ReviewedStingException("Destination file was null");
+ }
+
+ try {
+ writeByteArrayToStream(bytes, new FileOutputStream(destination));
+ }
+ catch ( FileNotFoundException e ) {
+ throw new UserException.CouldNotCreateOutputFile(destination, e);
+ }
+ }
+
+ /**
+ * Writes the given array of bytes to a stream
+ *
+ * @param bytes Data to write
+ * @param out Stream to write the data to
+ */
+ public static void writeByteArrayToStream ( byte[] bytes, OutputStream out ) {
+ if ( bytes == null || out == null ) {
+ throw new ReviewedStingException("Data to write or output stream was null");
+ }
+
+ try {
+ try {
+ out.write(bytes);
+ }
+ finally {
+ out.close();
+ }
+ }
+ catch ( IOException e ) {
+ throw new UserException.CouldNotCreateOutputFile("I/O error writing to output stream", e);
+ }
+ }
+
+ /**
+ * Determines the uncompressed size of a GZIP file. Uses the GZIP ISIZE field in the last
+ * 4 bytes of the file to get this information.
+ *
+ * @param gzipFile GZIP-format file whose uncompressed size to determine
+ * @return The uncompressed size (in bytes) of the GZIP file
+ */
+ public static int getGZIPFileUncompressedSize ( File gzipFile ) {
+ if ( gzipFile == null ) {
+ throw new ReviewedStingException("GZIP file to examine was null");
+ }
+
+ try {
+ // The GZIP ISIZE field holds the uncompressed size of the compressed data.
+ // It occupies the last 4 bytes of any GZIP file:
+ RandomAccessFile in = new RandomAccessFile(gzipFile, "r");
+ in.seek(gzipFile.length() - 4);
+ byte[] sizeBytes = new byte[4];
+ in.read(sizeBytes, 0, 4);
+
+ ByteBuffer byteBuf = ByteBuffer.wrap(sizeBytes);
+ byteBuf.order(ByteOrder.LITTLE_ENDIAN); // The GZIP spec mandates little-endian byte order
+ int uncompressedSize = byteBuf.getInt();
+
+ // If the size read in is negative, we've overflowed our signed integer:
+ if ( uncompressedSize < 0 ) {
+ throw new UserException.CouldNotReadInputFile(String.format("Cannot accurately determine the uncompressed size of file %s " +
+ "because it's either larger than %d bytes or the GZIP ISIZE field is corrupt",
+ gzipFile.getAbsolutePath(), Integer.MAX_VALUE));
+ }
+
+ return uncompressedSize;
+ }
+ catch ( IOException e ) {
+ throw new UserException.CouldNotReadInputFile(gzipFile, e);
+ }
+ }
}
diff --git a/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java b/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java
index f5a9b2f45..648dafb81 100755
--- a/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java
+++ b/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java
@@ -194,6 +194,10 @@ public class GATKSAMRecord extends BAMRecord {
}
}
+ public boolean hasBaseIndelQualities() {
+ return getAttribute( BQSR_BASE_INSERTION_QUALITIES ) != null || getAttribute( BQSR_BASE_DELETION_QUALITIES ) != null;
+ }
+
public byte[] getBaseInsertionQualities() {
byte[] quals = SAMUtils.fastqToPhred( getStringAttribute( BQSR_BASE_INSERTION_QUALITIES ) );
if( quals == null ) {
diff --git a/public/java/test/org/broadinstitute/sting/BaseTest.java b/public/java/test/org/broadinstitute/sting/BaseTest.java
index ac3a970f9..bc4ce098b 100755
--- a/public/java/test/org/broadinstitute/sting/BaseTest.java
+++ b/public/java/test/org/broadinstitute/sting/BaseTest.java
@@ -6,6 +6,7 @@ import org.apache.log4j.Logger;
import org.apache.log4j.PatternLayout;
import org.apache.log4j.spi.LoggingEvent;
import org.broadinstitute.sting.commandline.CommandLineUtils;
+import org.broadinstitute.sting.utils.crypt.CryptUtils;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.io.IOUtils;
@@ -87,6 +88,9 @@ public abstract class BaseTest {
public static final File testDirFile = new File("public/testdata/");
public static final String testDir = testDirFile.getAbsolutePath() + "/";
+ public static final String keysDataLocation = validationDataLocation + "keys/";
+ public static final String gatkKeyFile = CryptUtils.GATK_USER_KEY_DIRECTORY + "gsamembers_broadinstitute.org.key";
+
/** before the class starts up */
static {
// setup a basic log configuration
diff --git a/public/java/test/org/broadinstitute/sting/MedianUnitTest.java b/public/java/test/org/broadinstitute/sting/MedianUnitTest.java
index c12db9b77..db89aee78 100644
--- a/public/java/test/org/broadinstitute/sting/MedianUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/MedianUnitTest.java
@@ -29,7 +29,6 @@ package org.broadinstitute.sting;
// the imports for unit testing.
-import org.broadinstitute.sting.gatk.walkers.haplotypecaller.LikelihoodCalculationEngine;
import org.broadinstitute.sting.utils.Median;
import org.testng.Assert;
import org.testng.annotations.BeforeSuite;
@@ -42,12 +41,6 @@ import java.util.List;
public class MedianUnitTest extends BaseTest {
- LikelihoodCalculationEngine engine;
-
- @BeforeSuite
- public void before() {
- engine = new LikelihoodCalculationEngine(0, 0, false);
- }
// --------------------------------------------------------------------------------
//
diff --git a/public/java/test/org/broadinstitute/sting/WalkerTest.java b/public/java/test/org/broadinstitute/sting/WalkerTest.java
index ca7653b58..c9e3b6b1b 100755
--- a/public/java/test/org/broadinstitute/sting/WalkerTest.java
+++ b/public/java/test/org/broadinstitute/sting/WalkerTest.java
@@ -30,6 +30,7 @@ import org.broad.tribble.FeatureCodec;
import org.broad.tribble.Tribble;
import org.broad.tribble.index.Index;
import org.broad.tribble.index.IndexFactory;
+import org.broadinstitute.sting.gatk.phonehome.GATKRunReport;
import org.broadinstitute.sting.utils.codecs.vcf.VCFCodec;
import org.broadinstitute.sting.gatk.CommandLineExecutable;
import org.broadinstitute.sting.gatk.CommandLineGATK;
@@ -45,7 +46,7 @@ import java.io.File;
import java.util.*;
public class WalkerTest extends BaseTest {
- private static final boolean ENABLE_REPORTING = false;
+ private static final boolean ENABLE_PHONE_HOME_FOR_TESTS = false;
@BeforeMethod
public void initializeRandomGenerator() {
@@ -121,11 +122,19 @@ public class WalkerTest extends BaseTest {
}
public class WalkerTestSpec {
+
+ // Arguments implicitly included in all Walker command lines, unless explicitly
+ // disabled using the disableImplicitArgs() method below.
+ final String IMPLICIT_ARGS = ENABLE_PHONE_HOME_FOR_TESTS ?
+ String.format("-et %s", GATKRunReport.PhoneHomeOption.STANDARD) :
+ String.format("-et %s -K %s", GATKRunReport.PhoneHomeOption.NO_ET, gatkKeyFile);
+
String args = "";
int nOutputFiles = -1;
List md5s = null;
List exts = null;
Class expectedException = null;
+ boolean includeImplicitArgs = true;
// the default output path for the integration test
private File outputFileLocation = null;
@@ -159,6 +168,10 @@ public class WalkerTest extends BaseTest {
this.expectedException = expectedException;
}
+ public String getArgsWithImplicitArgs() {
+ return args + (includeImplicitArgs ? " " + IMPLICIT_ARGS : "");
+ }
+
public void setOutputFileLocation(File outputFileLocation) {
this.outputFileLocation = outputFileLocation;
}
@@ -180,6 +193,9 @@ public class WalkerTest extends BaseTest {
auxillaryFiles.put(expectededMD5sum, outputfile);
}
+ public void disableImplicitArgs() {
+ includeImplicitArgs = false;
+ }
}
protected boolean parameterize() {
@@ -213,7 +229,7 @@ public class WalkerTest extends BaseTest {
tmpFiles.add(fl);
}
- final String args = String.format(spec.args, tmpFiles.toArray());
+ final String args = String.format(spec.getArgsWithImplicitArgs(), tmpFiles.toArray());
System.out.println(Utils.dupString('-', 80));
if ( spec.expectsException() ) {
@@ -277,13 +293,10 @@ public class WalkerTest extends BaseTest {
* @param args the argument list
* @param expectedException the expected exception or null
*/
- public static void executeTest(String name, String args, Class expectedException) {
+ private void executeTest(String name, String args, Class expectedException) {
CommandLineGATK instance = new CommandLineGATK();
String[] command = Utils.escapeExpressions(args);
- // add the logging level to each of the integration test commands
- command = Utils.appendArray(command, "-et", ENABLE_REPORTING ? "STANDARD" : "NO_ET");
-
// run the executable
boolean gotAnException = false;
try {
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/ErrorRatePerCycleIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/ErrorRatePerCycleIntegrationTest.java
new file mode 100644
index 000000000..accb9c0cf
--- /dev/null
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/ErrorRatePerCycleIntegrationTest.java
@@ -0,0 +1,41 @@
+/*
+ * Copyright (c) 2012, The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+package org.broadinstitute.sting.gatk.walkers.diagnostics;
+
+import org.broadinstitute.sting.WalkerTest;
+import org.testng.annotations.Test;
+
+import java.util.Arrays;
+
+public class ErrorRatePerCycleIntegrationTest extends WalkerTest {
+ @Test
+ public void basicTest() {
+ WalkerTestSpec spec = new WalkerTestSpec(
+ "-T ErrorRatePerCycle -R " + b37KGReference + " -I " + b37GoodBAM + " -L 20:10,000,000-10,100,000 -o %s",
+ 1,
+ Arrays.asList("0cc212ecb6df300e321784039ff29f13"));
+ executeTest("ErrorRatePerCycle:", spec);
+ }
+}
\ No newline at end of file
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
index 823eeeeb9..cfb0d11a1 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
@@ -28,7 +28,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testMultiSamplePilot1() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
baseCommand + " -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -o %s -L 1:10,022,000-10,025,000", 1,
- Arrays.asList("202b337ebbea3def1be8495eb363dfa8"));
+ Arrays.asList("8f81a14fffc1a59b4b066f8595dc1232"));
executeTest("test MultiSample Pilot1", spec);
}
@@ -52,7 +52,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testSingleSamplePilot2() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,100,000", 1,
- Arrays.asList("ae29b9c9aacce8046dc780430540cd62"));
+ Arrays.asList("c5b53231f4f6d9524bc4ec8115f44f5c"));
executeTest("test SingleSample Pilot2", spec);
}
@@ -60,7 +60,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testMultipleSNPAlleles() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper -R " + b37KGReference + " -nosl -NO_HEADER -glm BOTH --dbsnp " + b37dbSNP129 + " -I " + validationDataLocation + "multiallelic.snps.bam -o %s -L " + validationDataLocation + "multiallelic.snps.intervals", 1,
- Arrays.asList("10027d13befaa07b7900a7af0ae0791c"));
+ Arrays.asList("5af005255240a2186f04cb50851b8b6f"));
executeTest("test Multiple SNP alleles", spec);
}
@@ -70,7 +70,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
//
// --------------------------------------------------------------------------------------------------------------
- private final static String COMPRESSED_OUTPUT_MD5 = "fda341de80b3f6fd42a83352b18b1d65";
+ private final static String COMPRESSED_OUTPUT_MD5 = "a08df9aea2b3df09cf90ff8e6e3be3ea";
@Test
public void testCompressedOutput() {
@@ -91,7 +91,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
// Note that we need to turn off any randomization for this to work, so no downsampling and no annotations
- String md5 = "32a34362dff51d8b73a3335048516d82";
+ String md5 = "6358934c1c26345013a38261b8c45aa4";
WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
baseCommand + " -dt NONE -G none -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,075,000", 1,
@@ -179,8 +179,8 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
@Test
public void testHeterozyosity() {
HashMap e = new HashMap();
- e.put( 0.01, "2cb2544739e01f6c08fd820112914317" );
- e.put( 1.0 / 1850, "730b2b83a4b1f6d46fc3b5cd7d90756c" );
+ e.put( 0.01, "926b58038dd4989bf7eda697a847eea9" );
+ e.put( 1.0 / 1850, "93f44105b43b65730a3b821e27b0fa16" );
for ( Map.Entry entry : e.entrySet() ) {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
@@ -204,7 +204,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
" -o %s" +
" -L 1:10,000,000-10,100,000",
1,
- Arrays.asList("f0fbe472f155baf594b1eeb58166edef"));
+ Arrays.asList("a1b75a7e12b160b0be823228c958573f"));
executeTest(String.format("test multiple technologies"), spec);
}
@@ -223,7 +223,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
" -L 1:10,000,000-10,100,000" +
" -baq CALCULATE_AS_NECESSARY",
1,
- Arrays.asList("8c87c749a7bb5a76ed8504d4ec254272"));
+ Arrays.asList("3bda1279cd6dcb47885f3e19466f11b9"));
executeTest(String.format("test calling with BAQ"), spec);
}
@@ -242,7 +242,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
" -o %s" +
" -L 1:10,000,000-10,500,000",
1,
- Arrays.asList("bd9d3d50a1f49605d7cd592a0f446899"));
+ Arrays.asList("d9fc3ba94a0d46029778c7b457e7292a"));
executeTest(String.format("test indel caller in SLX"), spec);
}
@@ -257,7 +257,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
" -minIndelCnt 1" +
" -L 1:10,000,000-10,100,000",
1,
- Arrays.asList("2ad52c2e75b3ffbfd8f03237c444e8e6"));
+ Arrays.asList("b2e30ae3e5ffa6108f9f6178b1d2e679"));
executeTest(String.format("test indel caller in SLX with low min allele count"), spec);
}
@@ -270,7 +270,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
" -o %s" +
" -L 1:10,000,000-10,500,000",
1,
- Arrays.asList("91cd6d2e3972b0b8e4064bb35a33241f"));
+ Arrays.asList("2cd182a84613fa91a6020466d2d327e2"));
executeTest(String.format("test indel calling, multiple technologies"), spec);
}
@@ -280,7 +280,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "indelAllelesForUG.vcf -I " + validationDataLocation +
"pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1,
- Arrays.asList("c60a44ba94a80a0cb1fba8b6f90a13cd"));
+ Arrays.asList("9cd08dc412a007933381e9c76c073899"));
executeTest("test MultiSample Pilot2 indels with alleles passed in", spec1);
}
@@ -290,7 +290,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
baseCommandIndels + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles "
+ validationDataLocation + "indelAllelesForUG.vcf -I " + validationDataLocation +
"pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1,
- Arrays.asList("320f61c87253aba77d6dc782242cba8b"));
+ Arrays.asList("5ef1f007d3ef77c1b8f31e5e036eff53"));
executeTest("test MultiSample Pilot2 indels with alleles passed in and emitting all sites", spec2);
}
@@ -300,7 +300,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
WalkerTest.WalkerTestSpec spec3 = new WalkerTest.WalkerTestSpec(
baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "ALL.wgs.union_v2.20101123.indels.sites.vcf -I " + validationDataLocation +
"pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,080,000", 1,
- Arrays.asList("c9897b80615c53a4ea10a4b193d56d9c"));
+ Arrays.asList("2609675a356f2dfc86f8a1d911210978"));
executeTest("test MultiSample Pilot2 indels with complicated records", spec3);
}
@@ -309,7 +309,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
WalkerTest.WalkerTestSpec spec4 = new WalkerTest.WalkerTestSpec(
baseCommandIndelsb37 + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "ALL.wgs.union_v2_chr20_100_110K.20101123.indels.sites.vcf -I " + validationDataLocation +
"phase1_GBR_realigned.chr20.100K-110K.bam -o %s -L 20:100,000-110,000", 1,
- Arrays.asList("5282fdb1711a532d726c13507bf80a21"));
+ Arrays.asList("4fdd8da77167881b71b3547da5c13f94"));
executeTest("test MultiSample Phase1 indels with complicated records", spec4);
}
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
index 5c3a43c96..36c093e8f 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
@@ -30,7 +30,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
"-o %s"
),
1,
- Arrays.asList("f909fd8374f663e983b9b3fda4cf5cf1")
+ Arrays.asList("c8d8bffa5c572df9dec7364f71a1b943")
);
executeTest("testFunctionClassWithSnpeff", spec);
}
@@ -277,7 +277,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
" --eval " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf" +
" --comp:comp_genotypes,VCF3 " + validationDataLocation + "yri.trio.gatk.ug.head.vcf";
WalkerTestSpec spec = new WalkerTestSpec(withSelect(tests, "DP < 50", "DP50") + " " + extraArgs + " -ST CpG -o %s",
- 1, Arrays.asList("4f60acc8a4b21c4b4ccb51ad9071449c"));
+ 1, Arrays.asList("c49e239292704447a36e01ee9a71e729"));
executeTestParallel("testSelect1", spec);
}
@@ -335,7 +335,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
" --dbsnp " + b37dbSNP132 +
" --eval:evalBI " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bi.sites.vcf" +
" -noST -ST Novelty -o %s";
- WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("190e1a171132832bf92fbca56a9c40bb"));
+ WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("e42cda858649a35eaa9d14ea2d70a956"));
executeTestParallel("testEvalTrackWithoutGenotypes",spec);
}
@@ -347,7 +347,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
" --eval:evalBI " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bi.sites.vcf" +
" --eval:evalBC " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bc.sites.vcf" +
" -noST -ST Novelty -o %s";
- WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("08586d443fdcf3b7f63b8f9e3a943c62"));
+ WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("9561cb4c7aa36dcf30ba253385299859"));
executeTestParallel("testMultipleEvalTracksWithoutGenotypes",spec);
}
@@ -463,7 +463,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
"-o %s"
),
1,
- Arrays.asList("a6f8b32fa732632da13dfe3ddcc73cef")
+ Arrays.asList("397b0e77459b9b69d2e0dd1dac320c3c")
);
executeTest("testModernVCFWithLargeIndels", spec);
}
diff --git a/public/java/test/org/broadinstitute/sting/utils/HaplotypeUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/HaplotypeUnitTest.java
new file mode 100644
index 000000000..25bd7a2eb
--- /dev/null
+++ b/public/java/test/org/broadinstitute/sting/utils/HaplotypeUnitTest.java
@@ -0,0 +1,163 @@
+/*
+ * Copyright (c) 2010 The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
+ * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+package org.broadinstitute.sting.utils;
+
+
+import net.sf.samtools.Cigar;
+import net.sf.samtools.CigarElement;
+import net.sf.samtools.CigarOperator;
+import org.broadinstitute.sting.BaseTest;
+import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.testng.Assert;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
+import java.util.*;
+
+/**
+ * Basic unit test for Haplotype Class
+ */
+public class HaplotypeUnitTest extends BaseTest {
+ @BeforeClass
+ public void init() {
+ }
+
+ @Test
+ public void testSimpleInsertionAllele() {
+ final String bases = "ACTGGTCAACTGGTCAACTGGTCAACTGGTCA";
+
+ final ArrayList h1CigarList = new ArrayList();
+ h1CigarList.add(new CigarElement(bases.length(), CigarOperator.M));
+ final Cigar h1Cigar = new Cigar(h1CigarList);
+ String h1bases = "AACTTCTGGTCAACTGGTCAACTGGTCAACTGGTCA";
+ basicInsertTest("-", "ACTT", 1, h1Cigar, bases, h1bases);
+ h1bases = "ACTGGTCACTTAACTGGTCAACTGGTCAACTGGTCA";
+ basicInsertTest("-", "ACTT", 7, h1Cigar, bases, h1bases);
+ h1bases = "ACTGGTCAACTGGTCAAACTTCTGGTCAACTGGTCA";
+ basicInsertTest("-", "ACTT", 17, h1Cigar, bases, h1bases);
+ }
+
+ @Test
+ public void testSimpleDeletionAllele() {
+ final String bases = "ACTGGTCAACTGGTCAACTGGTCAACTGGTCA";
+
+ final ArrayList h1CigarList = new ArrayList();
+ h1CigarList.add(new CigarElement(bases.length(), CigarOperator.M));
+ final Cigar h1Cigar = new Cigar(h1CigarList);
+ String h1bases = "ATCAACTGGTCAACTGGTCAACTGGTCA";
+ basicInsertTest("ACTT", "-", 1, h1Cigar, bases, h1bases);
+ h1bases = "ACTGGTCGGTCAACTGGTCAACTGGTCA";
+ basicInsertTest("ACTT", "-", 7, h1Cigar, bases, h1bases);
+ h1bases = "ACTGGTCAACTGGTCAATCAACTGGTCA";
+ basicInsertTest("ACTT", "-", 17, h1Cigar, bases, h1bases);
+ }
+
+ @Test
+ public void testSimpleSNPAllele() {
+ final String bases = "ACTGGTCAACTGGTCAACTGGTCAACTGGTCA";
+
+ final ArrayList h1CigarList = new ArrayList();
+ h1CigarList.add(new CigarElement(bases.length(), CigarOperator.M));
+ final Cigar h1Cigar = new Cigar(h1CigarList);
+ String h1bases = "AGTGGTCAACTGGTCAACTGGTCAACTGGTCA";
+ basicInsertTest("C", "G", 1, h1Cigar, bases, h1bases);
+ h1bases = "ACTGGTCTACTGGTCAACTGGTCAACTGGTCA";
+ basicInsertTest("A", "T", 7, h1Cigar, bases, h1bases);
+ h1bases = "ACTGGTCAACTGGTCAAATGGTCAACTGGTCA";
+ basicInsertTest("C", "A", 17, h1Cigar, bases, h1bases);
+ }
+
+ @Test
+ public void testComplexInsertionAllele() {
+ final String bases = "ATCG" + "CCGGCCGGCC" + "ATCGATCG" + "AGGGGGA" + "AGGC";
+
+ final ArrayList h1CigarList = new ArrayList();
+ h1CigarList.add(new CigarElement(4, CigarOperator.M));
+ h1CigarList.add(new CigarElement(10, CigarOperator.I));
+ h1CigarList.add(new CigarElement(8, CigarOperator.M));
+ h1CigarList.add(new CigarElement(3, CigarOperator.D));
+ h1CigarList.add(new CigarElement(7, CigarOperator.M));
+ h1CigarList.add(new CigarElement(4, CigarOperator.M));
+ final Cigar h1Cigar = new Cigar(h1CigarList);
+ String h1bases = "AACTTTCG" + "CCGGCCGGCC" + "ATCGATCG" + "AGGGGGA" + "AGGC";
+ basicInsertTest("-", "ACTT", 1, h1Cigar, bases, h1bases);
+ h1bases = "ATCG" + "CCGGCCGGCC" + "ATCACTTGATCG" + "AGGGGGA" + "AGGC";
+ basicInsertTest("-", "ACTT", 7, h1Cigar, bases, h1bases);
+ h1bases = "ATCG" + "CCGGCCGGCC" + "ATCGATCG" + "AGACTTGGGGA" + "AGGC";
+ basicInsertTest("-", "ACTT", 17, h1Cigar, bases, h1bases);
+ }
+
+ @Test
+ public void testComplexDeletionAllele() {
+ final String bases = "ATCG" + "CCGGCCGGCC" + "ATCGATCG" + "AGGGGGA" + "AGGC";
+
+ final ArrayList h1CigarList = new ArrayList();
+ h1CigarList.add(new CigarElement(4, CigarOperator.M));
+ h1CigarList.add(new CigarElement(10, CigarOperator.I));
+ h1CigarList.add(new CigarElement(8, CigarOperator.M));
+ h1CigarList.add(new CigarElement(3, CigarOperator.D));
+ h1CigarList.add(new CigarElement(7, CigarOperator.M));
+ h1CigarList.add(new CigarElement(4, CigarOperator.M));
+ final Cigar h1Cigar = new Cigar(h1CigarList);
+ String h1bases = "A" + "CGGCCGGCC" + "ATCGATCG" + "AGGGGGA" + "AGGC";
+ basicInsertTest("ACTT", "-", 1, h1Cigar, bases, h1bases);
+ h1bases = "ATCG" + "CCGGCCGGCC" + "ATCG" + "AGGGGGA" + "AGGC";
+ basicInsertTest("ACTT", "-", 7, h1Cigar, bases, h1bases);
+ h1bases = "ATCG" + "CCGGCCGGCC" + "ATCGATCG" + "AGA" + "AGGC";
+ basicInsertTest("ACTT", "-", 17, h1Cigar, bases, h1bases);
+ }
+
+ @Test
+ public void testComplexSNPAllele() {
+ final String bases = "ATCG" + "CCGGCCGGCC" + "ATCGATCG" + "AGGGGGA" + "AGGC";
+
+ final ArrayList h1CigarList = new ArrayList();
+ h1CigarList.add(new CigarElement(4, CigarOperator.M));
+ h1CigarList.add(new CigarElement(10, CigarOperator.I));
+ h1CigarList.add(new CigarElement(8, CigarOperator.M));
+ h1CigarList.add(new CigarElement(3, CigarOperator.D));
+ h1CigarList.add(new CigarElement(7, CigarOperator.M));
+ h1CigarList.add(new CigarElement(4, CigarOperator.M));
+ final Cigar h1Cigar = new Cigar(h1CigarList);
+ String h1bases = "AGCG" + "CCGGCCGGCC" + "ATCGATCG" + "AGGGGGA" + "AGGC";
+ basicInsertTest("T", "G", 1, h1Cigar, bases, h1bases);
+ h1bases = "ATCG" + "CCGGCCGGCC" + "ATCTATCG" + "AGGGGGA" + "AGGC";
+ basicInsertTest("G", "T", 7, h1Cigar, bases, h1bases);
+ h1bases = "ATCG" + "CCGGCCGGCC" + "ATCGATCG" + "AGCGGGA" + "AGGC";
+ basicInsertTest("G", "C", 17, h1Cigar, bases, h1bases);
+ }
+
+ private void basicInsertTest(String ref, String alt, int loc, Cigar cigar, String hap, String newHap) {
+ final int INDEL_PADDING_BASE = (ref.length() == alt.length() ? 0 : 1);
+ final Haplotype h = new Haplotype(hap.getBytes());
+ final Allele h1refAllele = Allele.create(ref, true);
+ final Allele h1altAllele = Allele.create(alt, false);
+ final Haplotype h1 = new Haplotype( h.insertAllele(h1refAllele, h1altAllele, loc - INDEL_PADDING_BASE, 0, cigar) );
+ final Haplotype h1expected = new Haplotype(newHap.getBytes());
+ Assert.assertEquals(h1, h1expected);
+
+ }
+}
diff --git a/public/java/test/org/broadinstitute/sting/utils/MathUtilsUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/MathUtilsUnitTest.java
index 75fc44873..1ba6c74d4 100755
--- a/public/java/test/org/broadinstitute/sting/utils/MathUtilsUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/utils/MathUtilsUnitTest.java
@@ -205,6 +205,24 @@ public class MathUtilsUnitTest extends BaseTest {
}
}
+ /**
+ * Private functions used by testArrayShuffle()
+ */
+ private boolean hasUniqueElements(Object[] x) {
+ for (int i = 0; i < x.length; i++)
+ for (int j = i + 1; j < x.length; j++)
+ if (x[i].equals(x[j]) || x[i] == x[j])
+ return false;
+ return true;
+ }
+
+ private boolean hasAllElements(final Object[] expected, final Object[] actual) {
+ HashSet set = new HashSet();
+ set.addAll(Arrays.asList(expected));
+ set.removeAll(Arrays.asList(actual));
+ return set.isEmpty();
+ }
+
@Test(enabled = true)
public void testIntAndBitSetConversion() {
Assert.assertEquals(MathUtils.intFrom(MathUtils.bitSetFrom(428)), 428);
@@ -234,26 +252,71 @@ public class MathUtilsUnitTest extends BaseTest {
Assert.assertEquals(MathUtils.dnaFrom(MathUtils.bitSetFrom("AACGTCAATGCAGTCAAGTCAGACGTGGGTT")), "AACGTCAATGCAGTCAAGTCAGACGTGGGTT"); // testing max precision (length == 31)
}
+ @Test
+ public void testApproximateLog10SumLog10() {
+ Assert.assertEquals(MathUtils.approximateLog10SumLog10(0.0, 0.0), Math.log10(Math.pow(10.0, 0.0) + Math.pow(10.0, 0.0)), 1e-3);
+ Assert.assertEquals(MathUtils.approximateLog10SumLog10(-1.0, 0.0), Math.log10(Math.pow(10.0, -1.0) + Math.pow(10.0, 0.0)), 1e-3);
+ Assert.assertEquals(MathUtils.approximateLog10SumLog10(0.0, -1.0), Math.log10(Math.pow(10.0, 0.0) + Math.pow(10.0, -1.0)), 1e-3);
+ Assert.assertEquals(MathUtils.approximateLog10SumLog10(-2.2, -3.5), Math.log10(Math.pow(10.0, -2.2) + Math.pow(10.0, -3.5)), 1e-3);
+ Assert.assertEquals(MathUtils.approximateLog10SumLog10(-1.0, -7.1), Math.log10(Math.pow(10.0, -1.0) + Math.pow(10.0, -7.1)), 1e-3);
+ Assert.assertEquals(MathUtils.approximateLog10SumLog10(5.0, 6.2), Math.log10(Math.pow(10.0, 5.0) + Math.pow(10.0, 6.2)), 1e-3);
+ Assert.assertEquals(MathUtils.approximateLog10SumLog10(38.1, 16.2), Math.log10(Math.pow(10.0, 38.1) + Math.pow(10.0, 16.2)), 1e-3);
+ Assert.assertEquals(MathUtils.approximateLog10SumLog10(-38.1, 6.2), Math.log10(Math.pow(10.0, -38.1) + Math.pow(10.0, 6.2)), 1e-3);
+ Assert.assertEquals(MathUtils.approximateLog10SumLog10(-19.1, -37.1), Math.log10(Math.pow(10.0, -19.1) + Math.pow(10.0, -37.1)), 1e-3);
+ Assert.assertEquals(MathUtils.approximateLog10SumLog10(-29.1, -27.6), Math.log10(Math.pow(10.0, -29.1) + Math.pow(10.0, -27.6)), 1e-3);
+ Assert.assertEquals(MathUtils.approximateLog10SumLog10(-0.12345, -0.23456), Math.log10(Math.pow(10.0, -0.12345) + Math.pow(10.0, -0.23456)), 1e-3);
+ Assert.assertEquals(MathUtils.approximateLog10SumLog10(-15.7654, -17.0101), Math.log10(Math.pow(10.0, -15.7654) + Math.pow(10.0, -17.0101)), 1e-3);
- private boolean hasUniqueElements(Object[] x) {
- for (int i = 0; i < x.length; i++)
- for (int j = i + 1; j < x.length; j++)
- if (x[i].equals(x[j]) || x[i] == x[j])
- return false;
+ Assert.assertEquals(MathUtils.approximateLog10SumLog10(new double[]{0.0, 0.0}), Math.log10(Math.pow(10.0, 0.0) + Math.pow(10.0, 0.0)), 1e-3);
+ Assert.assertEquals(MathUtils.approximateLog10SumLog10(new double[]{-1.0, 0.0}), Math.log10(Math.pow(10.0, -1.0) + Math.pow(10.0, 0.0)), 1e-3);
+ Assert.assertEquals(MathUtils.approximateLog10SumLog10(new double[]{0.0, -1.0}), Math.log10(Math.pow(10.0, 0.0) + Math.pow(10.0, -1.0)), 1e-3);
+ Assert.assertEquals(MathUtils.approximateLog10SumLog10(new double[]{-2.2, -3.5}), Math.log10(Math.pow(10.0, -2.2) + Math.pow(10.0, -3.5)), 1e-3);
+ Assert.assertEquals(MathUtils.approximateLog10SumLog10(new double[]{-1.0, -7.1}), Math.log10(Math.pow(10.0, -1.0) + Math.pow(10.0, -7.1)), 1e-3);
+ Assert.assertEquals(MathUtils.approximateLog10SumLog10(new double[]{5.0, 6.2}), Math.log10(Math.pow(10.0, 5.0) + Math.pow(10.0, 6.2)), 1e-3);
+ Assert.assertEquals(MathUtils.approximateLog10SumLog10(new double[]{38.1, 16.2}), Math.log10(Math.pow(10.0, 38.1) + Math.pow(10.0, 16.2)), 1e-3);
+ Assert.assertEquals(MathUtils.approximateLog10SumLog10(new double[]{-38.1, 6.2}), Math.log10(Math.pow(10.0, -38.1) + Math.pow(10.0, 6.2)), 1e-3);
+ Assert.assertEquals(MathUtils.approximateLog10SumLog10(new double[]{-19.1, -37.1}), Math.log10(Math.pow(10.0, -19.1) + Math.pow(10.0, -37.1)), 1e-3);
+ Assert.assertEquals(MathUtils.approximateLog10SumLog10(new double[]{-29.1, -27.6}), Math.log10(Math.pow(10.0, -29.1) + Math.pow(10.0, -27.6)), 1e-3);
+ Assert.assertEquals(MathUtils.approximateLog10SumLog10(new double[]{-0.12345, -0.23456}), Math.log10(Math.pow(10.0, -0.12345) + Math.pow(10.0, -0.23456)), 1e-3);
+ Assert.assertEquals(MathUtils.approximateLog10SumLog10(new double[]{-15.7654, -17.0101}), Math.log10(Math.pow(10.0, -15.7654) + Math.pow(10.0, -17.0101)), 1e-3);
+
+ Assert.assertEquals(MathUtils.approximateLog10SumLog10(new double[]{0.0, 0.0, 0.0}), Math.log10(Math.pow(10.0, 0.0) + Math.pow(10.0, 0.0) + Math.pow(10.0, 0.0)), 1e-3);
+ Assert.assertEquals(MathUtils.approximateLog10SumLog10(new double[]{-1.0, 0.0, 0.0}), Math.log10(Math.pow(10.0, -1.0) + Math.pow(10.0, 0.0) + Math.pow(10.0, 0.0)), 1e-3);
+ Assert.assertEquals(MathUtils.approximateLog10SumLog10(new double[]{0.0, -1.0, -2.5}), Math.log10(Math.pow(10.0, 0.0) + Math.pow(10.0, -1.0) + Math.pow(10.0, -2.5)), 1e-3);
+ Assert.assertEquals(MathUtils.approximateLog10SumLog10(new double[]{-2.2, -3.5, -1.1}), Math.log10(Math.pow(10.0, -2.2) + Math.pow(10.0, -3.5) + Math.pow(10.0, -1.1)), 1e-3);
+ Assert.assertEquals(MathUtils.approximateLog10SumLog10(new double[]{-1.0, -7.1, 0.5}), Math.log10(Math.pow(10.0, -1.0) + Math.pow(10.0, -7.1) + Math.pow(10.0, 0.5)), 1e-3);
+ Assert.assertEquals(MathUtils.approximateLog10SumLog10(new double[]{5.0, 6.2, 1.3}), Math.log10(Math.pow(10.0, 5.0) + Math.pow(10.0, 6.2) + Math.pow(10.0, 1.3)), 1e-3);
+ Assert.assertEquals(MathUtils.approximateLog10SumLog10(new double[]{38.1, 16.2, 18.1}), Math.log10(Math.pow(10.0, 38.1) + Math.pow(10.0, 16.2) + Math.pow(10.0, 18.1)), 1e-3);
+ Assert.assertEquals(MathUtils.approximateLog10SumLog10(new double[]{-38.1, 6.2, 26.6}), Math.log10(Math.pow(10.0, -38.1) + Math.pow(10.0, 6.2) + Math.pow(10.0, 26.6)), 1e-3);
+ Assert.assertEquals(MathUtils.approximateLog10SumLog10(new double[]{-19.1, -37.1, -45.1}), Math.log10(Math.pow(10.0, -19.1) + Math.pow(10.0, -37.1) + Math.pow(10.0, -45.1)), 1e-3);
+ Assert.assertEquals(MathUtils.approximateLog10SumLog10(new double[]{-29.1, -27.6, -26.2}), Math.log10(Math.pow(10.0, -29.1) + Math.pow(10.0, -27.6) + Math.pow(10.0, -26.2)), 1e-3);
+ Assert.assertEquals(MathUtils.approximateLog10SumLog10(new double[]{-0.12345, -0.23456, -0.34567}), Math.log10(Math.pow(10.0, -0.12345) + Math.pow(10.0, -0.23456) + Math.pow(10.0, -0.34567)), 1e-3);
+ Assert.assertEquals(MathUtils.approximateLog10SumLog10(new double[]{-15.7654, -17.0101, -17.9341}), Math.log10(Math.pow(10.0, -15.7654) + Math.pow(10.0, -17.0101) + Math.pow(10.0, -17.9341)), 1e-3);
+ }
+
+ @Test
+ public void testNormalizeFromLog10() {
+ Assert.assertTrue(compareDoubleArrays(MathUtils.normalizeFromLog10(new double[]{0.0, 0.0, -1.0, -1.1, -7.8}, false, true), new double[]{0.0, 0.0, -1.0, -1.1, -7.8}));
+ Assert.assertTrue(compareDoubleArrays(MathUtils.normalizeFromLog10(new double[]{-1.0, -1.0, -1.0, -1.1, -7.8}, false, true), new double[]{0.0, 0.0, 0.0, -0.1, -6.8}));
+ Assert.assertTrue(compareDoubleArrays(MathUtils.normalizeFromLog10(new double[]{-10.0, -7.8, -10.5, -1.1, -10.0}, false, true), new double[]{-8.9, -6.7, -9.4, 0.0, -8.9}));
+
+ Assert.assertTrue(compareDoubleArrays(MathUtils.normalizeFromLog10(new double[]{-1.0, -1.0, -1.0, -1.0}), new double[]{0.25, 0.25, 0.25, 0.25}));
+ Assert.assertTrue(compareDoubleArrays(MathUtils.normalizeFromLog10(new double[]{-1.0, -3.0, -1.0, -1.0}), new double[]{0.1 * 1.0 / 0.301, 0.001 * 1.0 / 0.301, 0.1 * 1.0 / 0.301, 0.1 * 1.0 / 0.301}));
+ Assert.assertTrue(compareDoubleArrays(MathUtils.normalizeFromLog10(new double[]{-1.0, -3.0, -1.0, -2.0}), new double[]{0.1 * 1.0 / 0.211, 0.001 * 1.0 / 0.211, 0.1 * 1.0 / 0.211, 0.01 * 1.0 / 0.211}));
+ }
+
+ /**
+ * Private function used by testNormalizeFromLog10()
+ */
+ private boolean compareDoubleArrays(double[] b1, double[] b2) {
+ if( b1.length != b2.length ) {
+ return false; // sanity check
+ }
+
+ for( int i=0; i < b1.length; i++ ){
+ if ( MathUtils.compareDoubles(b1[i], b2[i]) != 0 )
+ return false;
+ }
return true;
}
-
- private boolean hasAllElements(final Object[] expected, final Object[] actual) {
- HashSet set = new HashSet();
- set.addAll(Arrays.asList(expected));
- set.removeAll(Arrays.asList(actual));
- return set.isEmpty();
- }
-
- private void p (Object []x) {
- for (Object v: x)
- System.out.print((Integer) v + " ");
- System.out.println();
- }
-
}
diff --git a/public/java/test/org/broadinstitute/sting/utils/crypt/CryptUtilsUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/crypt/CryptUtilsUnitTest.java
new file mode 100644
index 000000000..f5cfea148
--- /dev/null
+++ b/public/java/test/org/broadinstitute/sting/utils/crypt/CryptUtilsUnitTest.java
@@ -0,0 +1,198 @@
+/*
+ * Copyright (c) 2012, The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+package org.broadinstitute.sting.utils.crypt;
+
+import org.broadinstitute.sting.BaseTest;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.testng.SkipException;
+import org.testng.annotations.DataProvider;
+import org.testng.annotations.Test;
+import org.testng.Assert;
+
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.IOException;
+import java.security.Key;
+import java.security.KeyPair;
+import java.security.PrivateKey;
+import java.security.PublicKey;
+import java.util.Arrays;
+
+public class CryptUtilsUnitTest extends BaseTest {
+
+ @Test
+ public void testGenerateValidKeyPairWithDefaultSettings() {
+ KeyPair keyPair = CryptUtils.generateKeyPair();
+ Assert.assertTrue(CryptUtils.keysDecryptEachOther(keyPair.getPrivate(), keyPair.getPublic()));
+ }
+
+ @DataProvider( name = "InvalidKeyPairSettings" )
+ public Object[][] invalidKeyPairSettingsDataProvider() {
+ return new Object[][] {
+ { -1, CryptUtils.DEFAULT_ENCRYPTION_ALGORITHM, CryptUtils.DEFAULT_RANDOM_NUMBER_GENERATION_ALGORITHM},
+ { CryptUtils.DEFAULT_KEY_LENGTH, "Made-up algorithm", CryptUtils.DEFAULT_RANDOM_NUMBER_GENERATION_ALGORITHM},
+ { CryptUtils.DEFAULT_KEY_LENGTH, CryptUtils.DEFAULT_ENCRYPTION_ALGORITHM, "Made-up algorithm"}
+ };
+ }
+
+ @Test( dataProvider = "InvalidKeyPairSettings", expectedExceptions = ReviewedStingException.class )
+ public void testGenerateKeyPairWithInvalidSettings( int keyLength, String encryptionAlgorithm, String randomNumberGenerationAlgorithm ) {
+ KeyPair keyPair = CryptUtils.generateKeyPair(keyLength, encryptionAlgorithm, randomNumberGenerationAlgorithm);
+ }
+
+ @Test
+ public void testGATKMasterKeyPairMutualDecryption() {
+ if ( gatkPrivateKeyExistsButReadPermissionDenied() ) {
+ throw new SkipException(String.format("Skipping test %s because we do not have permission to read the GATK private key",
+ "testGATKMasterKeyPairMutualDecryption"));
+ }
+
+ Assert.assertTrue(CryptUtils.keysDecryptEachOther(CryptUtils.loadGATKMasterPrivateKey(), CryptUtils.loadGATKMasterPublicKey()));
+ }
+
+ @Test
+ public void testGATKMasterPrivateKeyWithDistributedPublicKeyMutualDecryption() {
+ if ( gatkPrivateKeyExistsButReadPermissionDenied() ) {
+ throw new SkipException(String.format("Skipping test %s because we do not have permission to read the GATK private key",
+ "testGATKMasterPrivateKeyWithDistributedPublicKeyMutualDecryption"));
+ }
+
+ Assert.assertTrue(CryptUtils.keysDecryptEachOther(CryptUtils.loadGATKMasterPrivateKey(), CryptUtils.loadGATKDistributedPublicKey()));
+ }
+
+ @Test
+ public void testKeyPairWriteThenRead() {
+ KeyPair keyPair = CryptUtils.generateKeyPair();
+ File privateKeyFile = createTempFile("testKeyPairWriteThenRead_private", "key");
+ File publicKeyFile = createTempFile("testKeyPairWriteThenRead_public", "key");
+
+ CryptUtils.writeKeyPair(keyPair, privateKeyFile, publicKeyFile);
+
+ assertKeysAreEqual(keyPair.getPrivate(), CryptUtils.readPrivateKey(privateKeyFile));
+ assertKeysAreEqual(keyPair.getPublic(), CryptUtils.readPublicKey(publicKeyFile));
+ }
+
+ @Test
+ public void testPublicKeyWriteThenReadFromFile() {
+ File keyFile = createTempFile("testPublicKeyWriteThenReadFromFile", "key");
+ PublicKey publicKey = CryptUtils.generateKeyPair().getPublic();
+
+ CryptUtils.writeKey(publicKey, keyFile);
+
+ assertKeysAreEqual(publicKey, CryptUtils.readPublicKey(keyFile));
+ }
+
+ @Test
+ public void testPublicKeyWriteThenReadFromStream() throws IOException {
+ File keyFile = createTempFile("testPublicKeyWriteThenReadFromStream", "key");
+ PublicKey publicKey = CryptUtils.generateKeyPair().getPublic();
+
+ CryptUtils.writeKey(publicKey, keyFile);
+
+ assertKeysAreEqual(publicKey, CryptUtils.readPublicKey(new FileInputStream(keyFile)));
+ }
+
+ @Test
+ public void testPrivateKeyWriteThenReadFromFile() {
+ File keyFile = createTempFile("testPrivateKeyWriteThenReadFromFile", "key");
+ PrivateKey privateKey = CryptUtils.generateKeyPair().getPrivate();
+
+ CryptUtils.writeKey(privateKey, keyFile);
+
+ assertKeysAreEqual(privateKey, CryptUtils.readPrivateKey(keyFile));
+ }
+
+ @Test
+ public void testPrivateKeyWriteThenReadFromStream() throws IOException {
+ File keyFile = createTempFile("testPrivateKeyWriteThenReadFromStream", "key");
+ PrivateKey privateKey = CryptUtils.generateKeyPair().getPrivate();
+
+ CryptUtils.writeKey(privateKey, keyFile);
+
+ assertKeysAreEqual(privateKey, CryptUtils.readPrivateKey(new FileInputStream(keyFile)));
+ }
+
+ @Test( expectedExceptions = UserException.CouldNotReadInputFile.class )
+ public void testReadNonExistentPublicKey() {
+ File nonExistentFile = new File("jdshgkdfhg.key");
+ Assert.assertFalse(nonExistentFile.exists());
+
+ CryptUtils.readPublicKey(nonExistentFile);
+ }
+
+ @Test( expectedExceptions = UserException.CouldNotReadInputFile.class )
+ public void testReadNonExistentPrivateKey() {
+ File nonExistentFile = new File("jdshgkdfhg.key");
+ Assert.assertFalse(nonExistentFile.exists());
+
+ CryptUtils.readPrivateKey(nonExistentFile);
+ }
+
+ @Test
+ public void testDecodePublicKey() {
+ PublicKey originalKey = CryptUtils.generateKeyPair().getPublic();
+ PublicKey decodedKey = CryptUtils.decodePublicKey(originalKey.getEncoded(), CryptUtils.DEFAULT_ENCRYPTION_ALGORITHM);
+ assertKeysAreEqual(originalKey, decodedKey);
+ }
+
+ @Test
+ public void testDecodePrivateKey() {
+ PrivateKey originalKey = CryptUtils.generateKeyPair().getPrivate();
+ PrivateKey decodedKey = CryptUtils.decodePrivateKey(originalKey.getEncoded(), CryptUtils.DEFAULT_ENCRYPTION_ALGORITHM);
+ assertKeysAreEqual(originalKey, decodedKey);
+ }
+
+ @Test
+ public void testLoadGATKMasterPrivateKey() {
+ if ( gatkPrivateKeyExistsButReadPermissionDenied() ) {
+ throw new SkipException(String.format("Skipping test %s because we do not have permission to read the GATK private key",
+ "testLoadGATKMasterPrivateKey"));
+ }
+
+ PrivateKey gatkMasterPrivateKey = CryptUtils.loadGATKMasterPrivateKey();
+ }
+
+ @Test
+ public void testLoadGATKMasterPublicKey() {
+ PublicKey gatkMasterPublicKey = CryptUtils.loadGATKMasterPublicKey();
+ }
+
+ @Test
+ public void testLoadGATKDistributedPublicKey() {
+ PublicKey gatkDistributedPublicKey = CryptUtils.loadGATKDistributedPublicKey();
+ }
+
+ private void assertKeysAreEqual( Key originalKey, Key keyFromDisk ) {
+ Assert.assertTrue(Arrays.equals(originalKey.getEncoded(), keyFromDisk.getEncoded()));
+ Assert.assertEquals(originalKey.getAlgorithm(), keyFromDisk.getAlgorithm());
+ Assert.assertEquals(originalKey.getFormat(), keyFromDisk.getFormat());
+ }
+
+ private boolean gatkPrivateKeyExistsButReadPermissionDenied() {
+ File gatkPrivateKey = new File(CryptUtils.GATK_MASTER_PRIVATE_KEY_FILE);
+ return gatkPrivateKey.exists() && ! gatkPrivateKey.canRead();
+ }
+}
diff --git a/public/java/test/org/broadinstitute/sting/utils/crypt/GATKKeyIntegrationTest.java b/public/java/test/org/broadinstitute/sting/utils/crypt/GATKKeyIntegrationTest.java
new file mode 100644
index 000000000..8fb75ef38
--- /dev/null
+++ b/public/java/test/org/broadinstitute/sting/utils/crypt/GATKKeyIntegrationTest.java
@@ -0,0 +1,156 @@
+/*
+ * Copyright (c) 2012, The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+package org.broadinstitute.sting.utils.crypt;
+
+import org.broadinstitute.sting.WalkerTest;
+import org.broadinstitute.sting.gatk.phonehome.GATKRunReport;
+import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.testng.annotations.DataProvider;
+import org.testng.annotations.Test;
+
+import java.util.Arrays;
+
+public class GATKKeyIntegrationTest extends WalkerTest {
+
+ public static final String BASE_COMMAND = String.format("-T PrintReads -R %s -I %s -o %%s",
+ testDir + "exampleFASTA.fasta",
+ testDir + "exampleBAM.bam");
+ public static final String MD5_UPON_SUCCESSFUL_RUN = "b9dc5bf6753ca2819e70b056eaf61258";
+
+
+ private void runGATKKeyTest ( String testName, String etArg, String keyArg, Class expectedException, String md5 ) {
+ String command = BASE_COMMAND + String.format(" %s %s", etArg, keyArg);
+
+ WalkerTestSpec spec = expectedException != null ?
+ new WalkerTestSpec(command, 1, expectedException) :
+ new WalkerTestSpec(command, 1, Arrays.asList(md5));
+
+ spec.disableImplicitArgs(); // Turn off automatic inclusion of -et/-K args by WalkerTest
+ executeTest(testName, spec);
+ }
+
+ @Test
+ public void testValidKeyNoET() {
+ runGATKKeyTest("testValidKeyNoET",
+ "-et " + GATKRunReport.PhoneHomeOption.NO_ET,
+ "-K " + keysDataLocation + "valid.key",
+ null,
+ MD5_UPON_SUCCESSFUL_RUN);
+ }
+
+ @Test
+ public void testValidKeyETStdout() {
+ runGATKKeyTest("testValidKeyETStdout",
+ "-et " + GATKRunReport.PhoneHomeOption.STDOUT,
+ "-K " + keysDataLocation + "valid.key",
+ null,
+ MD5_UPON_SUCCESSFUL_RUN);
+ }
+
+ @Test
+ public void testValidKeyETStandard() {
+ runGATKKeyTest("testValidKeyETStandard",
+ "",
+ "-K " + keysDataLocation + "valid.key",
+ null,
+ MD5_UPON_SUCCESSFUL_RUN);
+ }
+
+ @Test
+ public void testNoKeyNoET() {
+ runGATKKeyTest("testNoKeyNoET",
+ "-et " + GATKRunReport.PhoneHomeOption.NO_ET,
+ "",
+ UserException.class,
+ null);
+ }
+
+ @Test
+ public void testNoKeyETStdout() {
+ runGATKKeyTest("testNoKeyETStdout",
+ "-et " + GATKRunReport.PhoneHomeOption.STDOUT,
+ "",
+ UserException.class,
+ null);
+ }
+
+ @Test
+ public void testNoKeyETStandard() {
+ runGATKKeyTest("testNoKeyETStandard",
+ "",
+ "",
+ null,
+ MD5_UPON_SUCCESSFUL_RUN);
+ }
+
+ @Test
+ public void testRevokedKey() {
+ runGATKKeyTest("testRevokedKey",
+ "-et " + GATKRunReport.PhoneHomeOption.NO_ET,
+ "-K " + keysDataLocation + "revoked.key",
+ UserException.KeySignatureVerificationException.class,
+ null);
+ }
+
+ @DataProvider(name = "CorruptKeyTestData")
+ public Object[][] corruptKeyDataProvider() {
+ return new Object[][] {
+ { "corrupt_empty.key", UserException.UnreadableKeyException.class },
+ { "corrupt_single_byte_file.key", UserException.UnreadableKeyException.class },
+ { "corrupt_random_contents.key", UserException.UnreadableKeyException.class },
+ { "corrupt_single_byte_deletion.key", UserException.UnreadableKeyException.class },
+ { "corrupt_single_byte_insertion.key", UserException.UnreadableKeyException.class },
+ { "corrupt_single_byte_change.key", UserException.UnreadableKeyException.class },
+ { "corrupt_multi_byte_deletion.key", UserException.UnreadableKeyException.class },
+ { "corrupt_multi_byte_insertion.key", UserException.UnreadableKeyException.class },
+ { "corrupt_multi_byte_change.key", UserException.UnreadableKeyException.class },
+ { "corrupt_bad_isize_field.key", UserException.UnreadableKeyException.class },
+ { "corrupt_bad_crc.key", UserException.UnreadableKeyException.class },
+ { "corrupt_no_email_address.key", UserException.UnreadableKeyException.class },
+ { "corrupt_no_sectional_delimiter.key", UserException.KeySignatureVerificationException.class },
+ { "corrupt_no_signature.key", UserException.UnreadableKeyException.class },
+ { "corrupt_bad_signature.key", UserException.KeySignatureVerificationException.class },
+ { "corrupt_non_gzipped_valid_key.key", UserException.UnreadableKeyException.class }
+ };
+ }
+
+ @Test(dataProvider = "CorruptKeyTestData")
+ public void testCorruptKey ( String corruptKeyName, Class expectedException ) {
+ runGATKKeyTest(String.format("testCorruptKey (%s)", corruptKeyName),
+ "-et " + GATKRunReport.PhoneHomeOption.NO_ET,
+ "-K " + keysDataLocation + corruptKeyName,
+ expectedException,
+ null);
+ }
+
+ @Test
+ public void testCorruptButNonRequiredKey() {
+ runGATKKeyTest("testCorruptButNonRequiredKey",
+ "",
+ "-K " + keysDataLocation + "corrupt_random_contents.key",
+ null,
+ MD5_UPON_SUCCESSFUL_RUN);
+ }
+}
diff --git a/public/java/test/org/broadinstitute/sting/utils/crypt/GATKKeyUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/crypt/GATKKeyUnitTest.java
new file mode 100644
index 000000000..660f95796
--- /dev/null
+++ b/public/java/test/org/broadinstitute/sting/utils/crypt/GATKKeyUnitTest.java
@@ -0,0 +1,128 @@
+/*
+ * Copyright (c) 2012, The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+package org.broadinstitute.sting.utils.crypt;
+
+import org.broadinstitute.sting.BaseTest;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.testng.SkipException;
+import org.testng.annotations.Test;
+import org.testng.Assert;
+
+import java.io.File;
+import java.security.KeyPair;
+import java.security.PrivateKey;
+import java.security.PublicKey;
+
+public class GATKKeyUnitTest extends BaseTest {
+
+ @Test
+ public void testCreateGATKKeyUsingMasterKeyPair() {
+ if ( gatkPrivateKeyExistsButReadPermissionDenied() ) {
+ throw new SkipException(String.format("Skipping test %s because we do not have permission to read the GATK private key",
+ "testCreateGATKKeyUsingMasterKeyPair"));
+ }
+
+ PrivateKey masterPrivateKey = CryptUtils.loadGATKMasterPrivateKey();
+ PublicKey masterPublicKey = CryptUtils.loadGATKMasterPublicKey();
+
+ // We should be able to create a valid GATKKey using our master key pair:
+ GATKKey key = new GATKKey(masterPrivateKey, masterPublicKey, "foo@bar.com");
+ Assert.assertTrue(key.isValid());
+ }
+
+ @Test
+ public void testCreateGATKKeyUsingMasterPrivateKeyAndDistributedPublicKey() {
+ if ( gatkPrivateKeyExistsButReadPermissionDenied() ) {
+ throw new SkipException(String.format("Skipping test %s because we do not have permission to read the GATK private key",
+ "testCreateGATKKeyUsingMasterPrivateKeyAndDistributedPublicKey"));
+ }
+
+ PrivateKey masterPrivateKey = CryptUtils.loadGATKMasterPrivateKey();
+ PublicKey distributedPublicKey = CryptUtils.loadGATKDistributedPublicKey();
+
+ // We should also be able to create a valid GATKKey using our master private
+ // key and the public key we distribute with the GATK:
+ GATKKey key = new GATKKey(masterPrivateKey, distributedPublicKey, "foo@bar.com");
+ Assert.assertTrue(key.isValid());
+ }
+
+ @Test( expectedExceptions = ReviewedStingException.class )
+ public void testKeyPairMismatch() {
+ KeyPair firstKeyPair = CryptUtils.generateKeyPair();
+ KeyPair secondKeyPair = CryptUtils.generateKeyPair();
+
+ // Attempting to create a GATK Key with private and public keys that aren't part of the
+ // same key pair should immediately trigger a validation failure:
+ GATKKey key = new GATKKey(firstKeyPair.getPrivate(), secondKeyPair.getPublic(), "foo@bar.com");
+ }
+
+ @Test( expectedExceptions = ReviewedStingException.class )
+ public void testEncryptionAlgorithmMismatch() {
+ KeyPair keyPair = CryptUtils.generateKeyPair(CryptUtils.DEFAULT_KEY_LENGTH, "DSA", CryptUtils.DEFAULT_RANDOM_NUMBER_GENERATION_ALGORITHM);
+
+ // Attempting to use a DSA private key to create an RSA signature should throw an error:
+ GATKKey key = new GATKKey(keyPair.getPrivate(), keyPair.getPublic(), "foo@bar.com", "SHA1withRSA");
+ }
+
+ @Test( expectedExceptions = UserException.class )
+ public void testInvalidEmailAddress() {
+ String emailAddressWithNulByte = new String(new byte[] { 0 });
+ KeyPair keyPair = CryptUtils.generateKeyPair();
+
+ // Email addresses cannot contain the NUL byte, since it's used as a sectional delimiter in the key file:
+ GATKKey key = new GATKKey(keyPair.getPrivate(), keyPair.getPublic(), emailAddressWithNulByte);
+ }
+
+ @Test
+ public void testCreateGATKKeyFromValidKeyFile() {
+ GATKKey key = new GATKKey(CryptUtils.loadGATKDistributedPublicKey(), new File(keysDataLocation + "valid.key"));
+ Assert.assertTrue(key.isValid());
+ }
+
+ @Test( expectedExceptions = UserException.UnreadableKeyException.class )
+ public void testCreateGATKKeyFromCorruptKeyFile() {
+ GATKKey key = new GATKKey(CryptUtils.loadGATKDistributedPublicKey(), new File(keysDataLocation + "corrupt_random_contents.key"));
+ }
+
+ @Test
+ public void testCreateGATKKeyFromRevokedKeyFile() {
+ GATKKey key = new GATKKey(CryptUtils.loadGATKDistributedPublicKey(), new File(keysDataLocation + "revoked.key"));
+ Assert.assertFalse(key.isValid());
+ }
+
+ @Test( expectedExceptions = UserException.CouldNotReadInputFile.class )
+ public void testCreateGATKKeyFromNonExistentFile() {
+ File nonExistentFile = new File("ghfdkgsdhg.key");
+ Assert.assertFalse(nonExistentFile.exists());
+
+ GATKKey key = new GATKKey(CryptUtils.loadGATKDistributedPublicKey(), nonExistentFile);
+ }
+
+ private boolean gatkPrivateKeyExistsButReadPermissionDenied() {
+ File gatkPrivateKey = new File(CryptUtils.GATK_MASTER_PRIVATE_KEY_FILE);
+ return gatkPrivateKey.exists() && ! gatkPrivateKey.canRead();
+ }
+}
diff --git a/public/java/test/org/broadinstitute/sting/utils/io/IOUtilsUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/io/IOUtilsUnitTest.java
index 757e6efdf..941d2b14c 100644
--- a/public/java/test/org/broadinstitute/sting/utils/io/IOUtilsUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/utils/io/IOUtilsUnitTest.java
@@ -27,12 +27,18 @@ package org.broadinstitute.sting.utils.io;
import org.apache.commons.io.FileUtils;
import org.broadinstitute.sting.BaseTest;
import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileOutputStream;
import java.io.IOException;
import java.util.Arrays;
import java.util.List;
+import java.util.Random;
+import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.testng.Assert;
+import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;
public class IOUtilsUnitTest extends BaseTest {
@@ -230,4 +236,90 @@ public class IOUtilsUnitTest extends BaseTest {
Assert.assertFalse(IOUtils.isSpecialFile(new File("/home/user/my.file")));
Assert.assertFalse(IOUtils.isSpecialFile(new File("/devfake/null")));
}
+
+ @DataProvider( name = "ByteArrayIOTestData")
+ public Object[][] byteArrayIOTestDataProvider() {
+ return new Object[][] {
+ // file size, read buffer size
+ { 0, 4096 },
+ { 1, 4096 },
+ { 2000, 4096 },
+ { 4095, 4096 },
+ { 4096, 4096 },
+ { 4097, 4096 },
+ { 6000, 4096 },
+ { 8191, 4096 },
+ { 8192, 4096 },
+ { 8193, 4096 },
+ { 10000, 4096 }
+ };
+ }
+
+ @Test( dataProvider = "ByteArrayIOTestData" )
+ public void testWriteThenReadFileIntoByteArray ( int fileSize, int readBufferSize ) throws Exception {
+ File tempFile = createTempFile(String.format("testWriteThenReadFileIntoByteArray_%d_%d", fileSize, readBufferSize), "tmp");
+
+ byte[] dataWritten = getDeterministicRandomData(fileSize);
+ IOUtils.writeByteArrayToFile(dataWritten, tempFile);
+ byte[] dataRead = IOUtils.readFileIntoByteArray(tempFile, readBufferSize);
+
+ Assert.assertEquals(dataRead.length, dataWritten.length);
+ Assert.assertTrue(Arrays.equals(dataRead, dataWritten));
+ }
+
+ @Test( dataProvider = "ByteArrayIOTestData" )
+ public void testWriteThenReadStreamIntoByteArray ( int fileSize, int readBufferSize ) throws Exception {
+ File tempFile = createTempFile(String.format("testWriteThenReadStreamIntoByteArray_%d_%d", fileSize, readBufferSize), "tmp");
+
+ byte[] dataWritten = getDeterministicRandomData(fileSize);
+ IOUtils.writeByteArrayToStream(dataWritten, new FileOutputStream(tempFile));
+ byte[] dataRead = IOUtils.readStreamIntoByteArray(new FileInputStream(tempFile), readBufferSize);
+
+ Assert.assertEquals(dataRead.length, dataWritten.length);
+ Assert.assertTrue(Arrays.equals(dataRead, dataWritten));
+ }
+
+ @Test( expectedExceptions = UserException.CouldNotReadInputFile.class )
+ public void testReadNonExistentFileIntoByteArray() {
+ File nonExistentFile = new File("djfhsdkjghdfk");
+ Assert.assertFalse(nonExistentFile.exists());
+
+ IOUtils.readFileIntoByteArray(nonExistentFile);
+ }
+
+ @Test( expectedExceptions = ReviewedStingException.class )
+ public void testReadNullStreamIntoByteArray() {
+ IOUtils.readStreamIntoByteArray(null);
+ }
+
+ @Test( expectedExceptions = ReviewedStingException.class )
+ public void testReadStreamIntoByteArrayInvalidBufferSize() throws Exception {
+ IOUtils.readStreamIntoByteArray(new FileInputStream(createTempFile("testReadStreamIntoByteArrayInvalidBufferSize", "tmp")),
+ -1);
+ }
+
+ @Test( expectedExceptions = UserException.CouldNotCreateOutputFile.class )
+ public void testWriteByteArrayToUncreatableFile() {
+ IOUtils.writeByteArrayToFile(new byte[]{0}, new File("/dev/foo/bar"));
+ }
+
+ @Test( expectedExceptions = ReviewedStingException.class )
+ public void testWriteNullByteArrayToFile() {
+ IOUtils.writeByteArrayToFile(null, createTempFile("testWriteNullByteArrayToFile", "tmp"));
+ }
+
+ @Test( expectedExceptions = ReviewedStingException.class )
+ public void testWriteByteArrayToNullStream() {
+ IOUtils.writeByteArrayToStream(new byte[]{0}, null);
+ }
+
+ private byte[] getDeterministicRandomData ( int size ) {
+ GenomeAnalysisEngine.resetRandomGenerator();
+ Random rand = GenomeAnalysisEngine.getRandomGenerator();
+
+ byte[] randomData = new byte[size];
+ rand.nextBytes(randomData);
+
+ return randomData;
+ }
}
diff --git a/public/keys/GATK_public.key b/public/keys/GATK_public.key
new file mode 100644
index 000000000..05cdde1c2
Binary files /dev/null and b/public/keys/GATK_public.key differ
diff --git a/public/packages/GATKEngine.xml b/public/packages/GATKEngine.xml
index 283b5eabf..68459f6d2 100644
--- a/public/packages/GATKEngine.xml
+++ b/public/packages/GATKEngine.xml
@@ -36,6 +36,8 @@