bugfix and nio access in Fingerprinting code (no need to panic) (#1694)

* - Convert CalculateFingerprintMetrics, ExtractFingerprint, and ExtractContamination to use NIO and thus be able to to their work on a non-localized input file.
- Fixed a bug in the AD output of extractFingerprint and CalculateContamination (Ref and Alt were swapped...)
- Renamed PL variable to be GL since that's what is actually was.

* -removed unneeded mathUtil method.

src/main/java/picard/fingerprint/CalculateFingerprintMetrics.java

@@ -33,6 +33,7 @@
 import org.apache.commons.math3.stat.inference.ChiSquareTest;
 import org.broadinstitute.barclay.argparser.Argument;
 import org.broadinstitute.barclay.argparser.CommandLineProgramProperties;
+import org.broadinstitute.barclay.argparser.Hidden;
 import org.broadinstitute.barclay.help.DocumentedFeature;
 import picard.cmdline.CommandLineProgram;
 import picard.cmdline.StandardOptionDefinitions;
@@ -70,7 +71,7 @@ public class CalculateFingerprintMetrics extends CommandLineProgram {
 
     static final String USAGE_DETAILS =
             "This tools collects various statistics that pertain to a single fingerprint (<b>not</b> the comparison, or " +
-                    "\'fingerprinting\' of two distinct samples) and reports the results in a metrics file. " +
+                    "'fingerprinting' of two distinct samples) and reports the results in a metrics file. " +
                     "<p>" +
                     "The statistics collected are p-values, where the null-hypothesis is that the fingerprint is collected from " +
                     "a non-contaminated, diploid human, whose genotypes are modelled by the probabilities given in the " +
@@ -112,6 +113,10 @@ public class CalculateFingerprintMetrics extends CommandLineProgram {
     @Argument(doc="Number of randomization trials for calculating the DISCRIMINATORY_POWER metric.")
     public final int NUMBER_OF_SAMPLING = 100;
 
+    @Hidden
+    @Argument(doc = "When true code will check for readability on input files (this can be slow on cloud access)")
+    public boolean TEST_INPUT_READABILITY = true;
+
     // a fixed random seed for reproducibility;
     private static final int RANDOM_SEED = 42;
     private static final ChiSquareTest chiSquareTest = new ChiSquareTest();
@@ -120,7 +125,9 @@ public class CalculateFingerprintMetrics extends CommandLineProgram {
     protected int doWork() {
 
         final List<Path> inputPaths = IOUtil.getPaths(INPUT);
-        IOUtil.assertPathsAreReadable(inputPaths);
+        if (TEST_INPUT_READABILITY) {
+            IOUtil.assertPathsAreReadable(inputPaths);
+        }
         IOUtil.assertFileIsReadable(HAPLOTYPE_MAP);
         IOUtil.assertFileIsWritable(OUTPUT);
 
@@ -197,7 +204,7 @@ public FingerprintMetrics getFingerprintMetrics(final Fingerprint fingerprint) {
         fingerprintMetrics.LOG10_HOM_CHI_SQUARED_PVALUE = Math.log10(homsChiSquaredTest);
 
         // calculate LOD (cross-entropy)
-        fingerprintMetrics.HOM_CROSS_ENTROPY_LOD = MathUtil.klDivergance(homAllele1VsAllele2Counts, homAllele1VsAllele2Expect);;
+        fingerprintMetrics.HOM_CROSS_ENTROPY_LOD = MathUtil.klDivergance(homAllele1VsAllele2Counts, homAllele1VsAllele2Expect);
 
         final MathUtils.RunningStat randomTrials = new MathUtils.RunningStat();
 

src/main/java/picard/fingerprint/ExtractFingerprint.java

@@ -28,11 +28,14 @@
 import htsjdk.samtools.util.Log;
 import org.broadinstitute.barclay.argparser.Argument;
 import org.broadinstitute.barclay.argparser.CommandLineProgramProperties;
+import org.broadinstitute.barclay.argparser.Hidden;
 import picard.cmdline.CommandLineProgram;
 import picard.cmdline.StandardOptionDefinitions;
 import picard.cmdline.programgroups.DiagnosticsAndQCProgramGroup;
 
 import java.io.File;
+import java.io.IOException;
+import java.nio.file.Path;
 import java.util.Map;
 
 /**
@@ -50,7 +53,7 @@
 public class ExtractFingerprint extends CommandLineProgram {
 
     @Argument(shortName = StandardOptionDefinitions.INPUT_SHORT_NAME, doc = "Input SAM/BAM/CRAM file.")
-    public File INPUT;
+    public String INPUT;
 
     @Argument(shortName = StandardOptionDefinitions.OUTPUT_SHORT_NAME, doc = "Output fingerprint file (VCF).")
     public File OUTPUT;
@@ -75,6 +78,10 @@ public class ExtractFingerprint extends CommandLineProgram {
             "It names the sample in the VCF <SAMPLE>-contaminant, using the SM value from the SAM header.")
     public boolean EXTRACT_CONTAMINATION = false;
 
+    @Hidden
+    @Argument(doc = "When true code will check for readability on input files (this can be slow on cloud access)")
+    public boolean TEST_INPUT_READABILITY = true;
+
     @Override
     protected boolean requiresReference() {
         return true;
@@ -84,7 +91,17 @@ protected boolean requiresReference() {
 
     @Override
     protected int doWork() {
-        IOUtil.assertFileIsReadable(INPUT);
+//        IOUtil.assertFileIsReadable(INPUT);
+        final Path inputPath;
+        try {
+            inputPath = IOUtil.getPath(INPUT);
+        } catch (IOException e) {
+            throw new RuntimeException(e);
+        }
+        if (TEST_INPUT_READABILITY) {
+            IOUtil.assertFileIsReadable(inputPath);
+        }
+
         IOUtil.assertFileIsReadable(HAPLOTYPE_MAP);
         IOUtil.assertFileIsWritable(OUTPUT);
         IOUtil.assertFileIsReadable(referenceSequence.getReferenceFile());
@@ -104,7 +121,7 @@ protected int doWork() {
             checker.setDefaultSampleID(SAMPLE_ALIAS);
         }
 
-        final Map<String, Fingerprint> fingerprintMap = checker.identifyContaminant(INPUT.toPath(), CONTAMINATION);
+        final Map<String, Fingerprint> fingerprintMap = checker.identifyContaminant(inputPath, CONTAMINATION);
 
         if (fingerprintMap.size() != 1) {
             log.error("Expected exactly 1 fingerprint, found " + fingerprintMap.size());

src/main/java/picard/fingerprint/FingerprintChecker.java

@@ -481,9 +481,9 @@ public Map<FingerprintIdDetails, Fingerprint> fingerprintSamFile(final Path samF
         checkDictionaryGoodForFingerprinting(in.getFileHeader().getSequenceDictionary());
 
         if (!in.hasIndex()) {
-            log.warn(String.format("Operating without an index! We could be here for a while. (%s)", samFile));
+            log.warn(String.format("Operating without an index! We could be here for a while. (%s)", samFile.toUri().toString()));
         } else {
-            log.info(String.format("Reading an indexed file (%s)", samFile));
+            log.info(String.format("Reading an indexed file (%s)", samFile.toUri().toString()));
         }
 
         final SamLocusIterator iterator = new SamLocusIterator(in, this.haplotypes.getIntervalList(), in.hasIndex());

src/main/java/picard/fingerprint/FingerprintUtils.java

@@ -173,18 +173,19 @@ private static VariantContext getVariantContext(final ReferenceSequenceFile refe
             obsAlt = haplotypeProbabilities.getObsAllele2();
         }
 
-        final double[] origPLs = haplotypeProbabilities.getLogLikelihoods();
-        final double[] PLs =  Arrays.copyOf(origPLs,origPLs.length);
+        final double[] origGLs = haplotypeProbabilities.getLogLikelihoods();
+        final double[] GLs =  Arrays.copyOf(origGLs, origGLs.length);
+
         if (swap12) {
-            ArrayUtils.reverse(PLs);
+            ArrayUtils.reverse(GLs);
         }
         final List<Allele> alleles = Arrays.asList(alleleRef, alleleAlt);
 
         final Genotype gt = new GenotypeBuilder()
                 .DP(haplotypeProbabilities.getTotalObs())
                 .noAttributes()
-                .PL(PLs)
-                .AD(new int[]{obsAlt, obsRef})
+                .PL(GLs)
+                .AD(new int[]{obsRef, obsAlt})
                 .name(sample)
                 .make();
         try {

src/main/java/picard/fingerprint/HaplotypeProbabilitiesFromContaminatorSequence.java

@@ -90,10 +90,11 @@ public void addToProbs(final Snp snp, final byte base, final byte qual) {
 
         for (final Genotype contGeno : Genotype.values()) {
             for (final Genotype mainGeno : Genotype.values()) {
-                //theta is the expected frequency of the alternate allele
+                // theta is the expected frequency of the alternate allele
                 final double theta = 0.5 * ((1 - contamination) * mainGeno.v + contamination * contGeno.v);
-                likelihoodMap[contGeno.v][mainGeno.v] *= ((altAllele ? theta : (1 - theta)) * (1 - pErr) +
-                        (!altAllele ? theta : (1 - theta)) * pErr);
+                likelihoodMap[contGeno.v][mainGeno.v] *=
+                        (( altAllele ? theta : (1 - theta)) * (1 - pErr) +
+                         (!altAllele ? theta : (1 - theta)) * pErr         );
             }
         }
     }

src/main/java/picard/fingerprint/IdentifyContaminant.java

@@ -26,6 +26,7 @@
 
 import org.broadinstitute.barclay.argparser.Argument;
 import org.broadinstitute.barclay.argparser.CommandLineProgramProperties;
+import org.broadinstitute.barclay.argparser.Hidden;
 import picard.cmdline.CommandLineProgram;
 import picard.cmdline.StandardOptionDefinitions;
 import picard.cmdline.programgroups.DiagnosticsAndQCProgramGroup;
@@ -48,7 +49,7 @@
 public class IdentifyContaminant extends CommandLineProgram {
 
     @Argument(shortName = StandardOptionDefinitions.INPUT_SHORT_NAME, doc = "Input SAM or BAM file.")
-    public File INPUT;
+    public String INPUT;
 
     @Argument(shortName = StandardOptionDefinitions.OUTPUT_SHORT_NAME, doc = "Output fingerprint file (VCF).")
     public File OUTPUT;
@@ -71,6 +72,10 @@ public class IdentifyContaminant extends CommandLineProgram {
             "It names the sample in the VCF <SAMPLE>, using the SM value from the SAM header.")
     public boolean EXTRACT_CONTAMINATED = false;
 
+    @Hidden
+    @Argument(doc = "When true code will check for readability on input files (this can be slow on cloud access)")
+    public boolean TEST_INPUT_READABILITY = true;
+
     @Override
     protected boolean requiresReference() {
         return true;
@@ -90,6 +95,7 @@ protected int doWork() {
         extractFingerprint.SAMPLE_ALIAS = SAMPLE_ALIAS;
         extractFingerprint.VALIDATION_STRINGENCY = VALIDATION_STRINGENCY;
         extractFingerprint.VERBOSITY = VERBOSITY;
+        extractFingerprint.TEST_INPUT_READABILITY = TEST_INPUT_READABILITY;
         extractFingerprint.referenceSequence = referenceSequence;
 
         extractFingerprint.doWork();