zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable

This commit is contained in:
Matt Hanna 2011-07-18 14:56:41 -04:00
parent e5e7523f8b 6d5e87da10
commit 15b44ac2c3
4 changed files with 71 additions and 28 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

10
public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/BAMDiffableReader.java
View File

@ -29,9 +29,7 @@ import net.sf.samtools.SAMRecord;
import net.sf.samtools.SAMRecordIterator;
import net.sf.samtools.util.BlockCompressedInputStream;
import java.io.File;
import java.io.FileInputStream;
import java.io.IOException;
import java.io.*;
import java.util.Arrays;
@ -102,8 +100,10 @@ public class BAMDiffableReader implements DiffableReader {
final byte[] BAM_MAGIC = "BAM\1".getBytes();
final byte[] buffer = new byte[BAM_MAGIC.length];
try {
FileInputStream fstream = new FileInputStream(file);
new BlockCompressedInputStream(fstream).read(buffer,0,BAM_MAGIC.length);
InputStream fstream = new BufferedInputStream(new FileInputStream(file));
if ( !BlockCompressedInputStream.isValidFile(fstream) )
return false;
new BlockCompressedInputStream(fstream).read(buffer, 0, BAM_MAGIC.length);
return Arrays.equals(buffer, BAM_MAGIC);
} catch ( IOException e ) {
return false;

23
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java
View File

@ -25,6 +25,7 @@
package org.broadinstitute.sting.gatk.walkers.variantutils;
import org.apache.poi.hpsf.Variant;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Hidden;
import org.broadinstitute.sting.commandline.Output;
@ -149,7 +150,7 @@ public class CombineVariants extends RodWalker<Integer, Integer> {
// get all of the vcf rods at this locus
// Need to provide reference bases to simpleMerge starting at current locus
Collection<VariantContext> vcs = tracker.getAllVariantContexts(ref, null,context.getLocation(), true, false);
Collection<VariantContext> vcs = tracker.getAllVariantContexts(ref, null, context.getLocation(), true, false);
if ( sitesOnlyVCF ) {
vcs = VariantContextUtils.sitesOnlyVariantContexts(vcs);
@ -172,17 +173,25 @@ public class CombineVariants extends RodWalker<Integer, Integer> {
if (minimumN > 1 && (vcs.size() - numFilteredRecords < minimumN))
return 0;
VariantContext mergedVC;
List<VariantContext> mergedVCs = new ArrayList<VariantContext>();
if ( master ) {
mergedVC = VariantContextUtils.masterMerge(vcs, "master");
mergedVCs.add(VariantContextUtils.masterMerge(vcs, "master"));
} else {
mergedVC = VariantContextUtils.simpleMerge(getToolkit().getGenomeLocParser(),vcs, priority, filteredRecordsMergeType,
genotypeMergeOption, true, printComplexMerges, ref.getBase(), SET_KEY, filteredAreUncalled, MERGE_INFO_WITH_MAX_AC);
Map<VariantContext.Type, List<VariantContext>> VCsByType = VariantContextUtils.separateVariantContextsByType(vcs);
// iterate over the types so that it's deterministic
for ( VariantContext.Type type : VariantContext.Type.values() ) {
if ( VCsByType.containsKey(type) )
mergedVCs.add(VariantContextUtils.simpleMerge(getToolkit().getGenomeLocParser(), VCsByType.get(type),
priority, filteredRecordsMergeType, genotypeMergeOption, true, printComplexMerges,
ref.getBase(), SET_KEY, filteredAreUncalled, MERGE_INFO_WITH_MAX_AC));
}
}
//out.printf(" merged => %s%nannotated => %s%n", mergedVC, annotatedMergedVC);
for ( VariantContext mergedVC : mergedVCs ) {
// only operate at the start of events
if ( mergedVC == null )
continue;
if ( mergedVC != null ) { // only operate at the start of events
HashMap<String, Object> attributes = new HashMap<String, Object>(mergedVC.getAttributes());
// re-compute chromosome counts
VariantContextUtils.calculateChromosomeCounts(mergedVC, attributes, false);

60
public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java
View File

@ -289,8 +289,8 @@ public class VariantContextUtils {
/**
* Returns a newly allocated VC that is the same as VC, but without genotypes
* @param vc
* @return
* @param vc variant context
* @return new VC without genotypes
*/
@Requires("vc != null")
@Ensures("result != null")
@ -303,8 +303,8 @@ public class VariantContextUtils {
/**
* Returns a newly allocated list of VC, where each VC is the same as the input VCs, but without genotypes
* @param vcs
* @return
* @param vcs collection of VCs
* @return new VCs without genotypes
*/
@Requires("vcs != null")
@Ensures("result != null")
@ -362,9 +362,9 @@ public class VariantContextUtils {
* information per genotype. The master merge will add the PQ information from each genotype record, where
* appropriate, to the master VC.
*
* @param unsortedVCs
* @param masterName
* @return
* @param unsortedVCs collection of VCs
* @param masterName name of master VC
* @return master-merged VC
*/
public static VariantContext masterMerge(Collection<VariantContext> unsortedVCs, String masterName) {
VariantContext master = findMaster(unsortedVCs, masterName);
@ -435,11 +435,15 @@ public class VariantContextUtils {
* If uniqifySamples is true, the priority order is ignored and names are created by concatenating the VC name with
* the sample name
*
* @param unsortedVCs
* @param priorityListOfVCs
* @param filteredRecordMergeType
* @param genotypeMergeOptions
* @return
* @param genomeLocParser loc parser
* @param unsortedVCs collection of unsorted VCs
* @param priorityListOfVCs priority list detailing the order in which we should grab the VCs
* @param filteredRecordMergeType merge type for filtered records
* @param genotypeMergeOptions merge option for genotypes
* @param annotateOrigin should we annotate the set it came from?
* @param printMessages should we print messages?
* @param inputRefBase the ref base
* @return new VariantContext
*/
public static VariantContext simpleMerge(GenomeLocParser genomeLocParser, Collection<VariantContext> unsortedVCs, List<String> priorityListOfVCs,
FilteredRecordMergeType filteredRecordMergeType, GenotypeMergeType genotypeMergeOptions,
@ -448,6 +452,24 @@ public class VariantContextUtils {
return simpleMerge(genomeLocParser, unsortedVCs, priorityListOfVCs, filteredRecordMergeType, genotypeMergeOptions, annotateOrigin, printMessages, inputRefBase, "set", false, false);
}
/**
* Merges VariantContexts into a single hybrid. Takes genotypes for common samples in priority order, if provided.
* If uniqifySamples is true, the priority order is ignored and names are created by concatenating the VC name with
* the sample name
*
* @param genomeLocParser loc parser
* @param unsortedVCs collection of unsorted VCs
* @param priorityListOfVCs priority list detailing the order in which we should grab the VCs
* @param filteredRecordMergeType merge type for filtered records
* @param genotypeMergeOptions merge option for genotypes
* @param annotateOrigin should we annotate the set it came from?
* @param printMessages should we print messages?
* @param inputRefBase the ref base
* @param setKey the key name of the set
* @param filteredAreUncalled are filtered records uncalled?
* @param mergeInfoWithMaxAC should we merge in info from the VC with maximum allele count?
* @return new VariantContext
*/
public static VariantContext simpleMerge(GenomeLocParser genomeLocParser, Collection<VariantContext> unsortedVCs, List<String> priorityListOfVCs,
FilteredRecordMergeType filteredRecordMergeType, GenotypeMergeType genotypeMergeOptions,
boolean annotateOrigin, boolean printMessages, byte inputRefBase, String setKey,
@ -470,7 +492,7 @@ public class VariantContextUtils {
if ( ! filteredAreUncalled || vc.isNotFiltered() )
VCs.add(VariantContext.createVariantContextWithPaddedAlleles(vc,inputRefBase,false));
}
if ( VCs.size() == 0 ) // everything is filtered out and we're filteredareUncalled
if ( VCs.size() == 0 ) // everything is filtered out and we're filteredAreUncalled
return null;
// establish the baseline info from the first VC
@ -615,6 +637,17 @@ public class VariantContextUtils {
return merged;
}
public static Map<VariantContext.Type, List<VariantContext>> separateVariantContextsByType(Collection<VariantContext> VCs) {
HashMap<VariantContext.Type, List<VariantContext>> mappedVCs = new HashMap<VariantContext.Type, List<VariantContext>>();
for ( VariantContext vc : VCs ) {
if ( !mappedVCs.containsKey(vc.getType()) )
mappedVCs.put(vc.getType(), new ArrayList<VariantContext>());
mappedVCs.get(vc.getType()).add(vc);
}
return mappedVCs;
}
private static class AlleleMapper {
private VariantContext vc = null;
private Map<Allele, Allele> map = null;
@ -834,6 +867,7 @@ public class VariantContextUtils {
/**
* create a genome location, given a variant context
* @param genomeLocParser parser
* @param vc the variant context
* @return the genomeLoc
*/

6
public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java
View File

@ -80,9 +80,9 @@ public class CombineVariantsIntegrationTest extends WalkerTest {
@Test public void combineTrioCalls() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "YRI.trio.2010_03.genotypes.vcf.gz", "", "1d5a021387a8a86554db45a29f66140f", false); } // official project VCF files in tabix format
@Test public void combineTrioCallsMin() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "YRI.trio.2010_03.genotypes.vcf.gz", " -minimalVCF", "20163d60f18a46496f6da744ab5cc0f9", false); } // official project VCF files in tabix format
@Test public void combine2Indels() { combine2("CEU.dindel.vcf4.trio.2010_06.indel.genotypes.vcf", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "", "5b82f37df1f5ba40f0474d71c94142ec", false); }
@Test public void combine2Indels() { combine2("CEU.dindel.vcf4.trio.2010_06.indel.genotypes.vcf", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "", "f1cf095c2fe9641b7ca1f8ee2c46fd4a", false); }
@Test public void combineSNPsAndIndels() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "", "c58dca482bf97069eac6d9f1a07a2cba", false); }
@Test public void combineSNPsAndIndels() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "", "e144b6283765494bfe8189ac59965083", false); }
@Test public void uniqueSNPs() { combine2("pilot2.snps.vcf4.genotypes.vcf", "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf", "", "89f55abea8f59e39d1effb908440548c", true); }
@ -100,7 +100,7 @@ public class CombineVariantsIntegrationTest extends WalkerTest {
" -priority NA19240_BGI,NA19240_ILLUMINA,NA19240_WUGSC,denovoInfo" +
" -genotypeMergeOptions UNIQUIFY -L 1"),
1,
Arrays.asList("8b78339ccf7a5a5a837f79e88a3a38e5"));
Arrays.asList("1de95f91ca15d2a8856de35dee0ce33e"));
executeTest("threeWayWithRefs", spec);
}