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un-break accidental rebase breaking
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@jamesemery
jamesemery committed Jan 11, 2022
1 parent ce3a00c commit 601a8f3
Showing 1 changed file with 151 additions and 1 deletion.
152 changes: 151 additions & 1 deletion ...itute/hellbender/tools/walkers/haplotypecaller/AssemblyBasedCallerArgumentCollection.java
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Expand Up @@ -4,10 +4,12 @@
import org.broadinstitute.barclay.argparser.Advanced;
import org.broadinstitute.barclay.argparser.Argument;
import org.broadinstitute.barclay.argparser.ArgumentCollection;
import org.broadinstitute.gatk.nativebindings.smithwaterman.SWParameters;
import org.broadinstitute.hellbender.engine.FeatureInput;
import org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.ReadThreadingAssembler;
import org.broadinstitute.hellbender.utils.haplotype.HaplotypeBAMWriter;
import org.broadinstitute.hellbender.utils.smithwaterman.SmithWatermanAligner;
import org.broadinstitute.hellbender.utils.smithwaterman.SmithWatermanAlignmentConstants;

/**
* Set of arguments for Assembly Based Callers
Expand All @@ -34,6 +36,26 @@ public abstract class AssemblyBasedCallerArgumentCollection {

public static final String PILEUP_DETECTION_LONG_NAME = "pileup-detection";

public static final String SMITH_WATERMAN_DANGLING_END_MATCH_VALUE_LONG_NAME = "smith-waterman-dangling-end-match-value";
public static final String SMITH_WATERMAN_DANGLING_END_MISMATCH_PENALTY_LONG_NAME = "smith-waterman-dangling-end-mismatch-penalty";
public static final String SMITH_WATERMAN_DANGLING_END_GAP_OPEN_PENALTY_LONG_NAME = "smith-waterman-dangling-end-gap-open-penalty";
public static final String SMITH_WATERMAN_DANGLING_END_GAP_EXTEND_PENALTY_LONG_NAME = "smith-waterman-dangling-end-gap-extend-penalty";
public static final String SMITH_WATERMAN_HAPLOTYPE_TO_REFERENCE_MATCH_VALUE_LONG_NAME = "smith-waterman-haplotype-to-reference-match-value";
public static final String SMITH_WATERMAN_HAPLOTYPE_TO_REFERENCE_MISMATCH_PENALTY_LONG_NAME = "smith-waterman-haplotype-to-reference-mismatch-penalty";
public static final String SMITH_WATERMAN_HAPLOTYPE_TO_REFERENCE_GAP_OPEN_PENALTY_LONG_NAME = "smith-waterman-haplotype-to-reference-gap-open-penalty";
public static final String SMITH_WATERMAN_HAPLOTYPE_TO_REFERENCE_GAP_EXTEND_PENALTY_LONG_NAME = "smith-waterman-haplotype-to-reference-gap-extend-penalty";
public static final String SMITH_WATERMAN_READ_TO_HAPLOTYPE_MATCH_VALUE_LONG_NAME = "smith-waterman-read-to-haplotype-match-value";
public static final String SMITH_WATERMAN_READ_TO_HAPLOTYPE_MISMATCH_PENALTY_LONG_NAME = "smith-waterman-read-to-haplotype-mismatch-penalty";
public static final String SMITH_WATERMAN_READ_TO_HAPLOTYPE_GAP_OPEN_PENALTY_LONG_NAME = "smith-waterman-read-to-haplotype-gap-open-penalty";
public static final String SMITH_WATERMAN_READ_TO_HAPLOTYPE_GAP_EXTEND_PENALTY_LONG_NAME = "smith-waterman-read-to-haplotype-gap-extend-penalty";

/** See documentation at {@link SmithWatermanAlignmentConstants#STANDARD_NGS}. */
private static final SWParameters DEFAULT_DANGLING_END_SMITH_WATERMAN_PARAMETERS = SmithWatermanAlignmentConstants.STANDARD_NGS;
/** See documentation at {@link SmithWatermanAlignmentConstants#NEW_SW_PARAMETERS}. */
private static final SWParameters DEFAULT_HAPLOTYPE_TO_REFERENCE_SMITH_WATERMAN_PARAMETERS = SmithWatermanAlignmentConstants.NEW_SW_PARAMETERS;
/** See documentation at {@link SmithWatermanAlignmentConstants#ALIGNMENT_TO_BEST_HAPLOTYPE_SW_PARAMETERS}. */
private static final SWParameters DEFAULT_READ_TO_HAPLOTYPE_SMITH_WATERMAN_PARAMETERS = SmithWatermanAlignmentConstants.ALIGNMENT_TO_BEST_HAPLOTYPE_SW_PARAMETERS;

public ReadThreadingAssembler createReadThreadingAssembler() {
final ReadThreadingAssembler assemblyEngine = assemblerArgs.makeReadThreadingAssembler();
assemblyEngine.setDebug(assemblerArgs.debugAssembly);
Expand Down Expand Up @@ -153,4 +175,132 @@ public ReadThreadingAssembler createReadThreadingAssembler() {
"that overlap the variant or any base no further than this distance expressed in base pairs",
optional = true)
public int informativeReadOverlapMargin = 2;
}

/**
* Enables pileup-based haplotype creation and variant detection
*
* NOTE: --pileup-detection is a beta feature. Use this mode at your own risk.
*/
@Argument(fullName= PILEUP_DETECTION_LONG_NAME, doc = "If enabled, the variant caller will create pileup-based haplotypes in addition to the assembly-based haplotype generation.", optional = true)
public boolean usePileupDetection = false;


// -----------------------------------------------------------------------------------------------
// Smith-Waterman parameters for dangling-end recovery
// -----------------------------------------------------------------------------------------------

@Advanced
@Argument(fullName = SMITH_WATERMAN_DANGLING_END_MATCH_VALUE_LONG_NAME,
doc = "Smith-Waterman match value for dangling-end recovery.",
minValue = 0,
optional = true)
public int smithWatermanDanglingEndMatchValue = DEFAULT_DANGLING_END_SMITH_WATERMAN_PARAMETERS.getMatchValue();

@Advanced
@Argument(fullName = SMITH_WATERMAN_DANGLING_END_MISMATCH_PENALTY_LONG_NAME,
doc = "Smith-Waterman mismatch penalty for dangling-end recovery.",
maxValue = 0,
optional = true)
public int smithWatermanDanglingEndMismatchPenalty = DEFAULT_DANGLING_END_SMITH_WATERMAN_PARAMETERS.getMismatchPenalty();

@Advanced
@Argument(fullName = SMITH_WATERMAN_DANGLING_END_GAP_OPEN_PENALTY_LONG_NAME,
doc = "Smith-Waterman gap-open penalty for dangling-end recovery.",
maxValue = 0,
optional = true)
public int smithWatermanDanglingEndGapOpenPenalty = DEFAULT_DANGLING_END_SMITH_WATERMAN_PARAMETERS.getGapOpenPenalty();

@Advanced
@Argument(fullName = SMITH_WATERMAN_DANGLING_END_GAP_EXTEND_PENALTY_LONG_NAME,
doc = "Smith-Waterman gap-extend penalty for dangling-end recovery.",
maxValue = 0,
optional = true)
public int smithWatermanDanglingEndGapExtendPenalty = DEFAULT_DANGLING_END_SMITH_WATERMAN_PARAMETERS.getGapExtendPenalty();

// -----------------------------------------------------------------------------------------------
// Smith-Waterman parameters for haplotype-to-reference alignment
// -----------------------------------------------------------------------------------------------

@Advanced
@Argument(fullName = SMITH_WATERMAN_HAPLOTYPE_TO_REFERENCE_MATCH_VALUE_LONG_NAME,
doc = "Smith-Waterman match value for haplotype-to-reference alignment.",
minValue = 0,
optional = true)
public int smithWatermanHaplotypeToReferenceMatchValue = DEFAULT_HAPLOTYPE_TO_REFERENCE_SMITH_WATERMAN_PARAMETERS.getMatchValue();

@Advanced
@Argument(fullName = SMITH_WATERMAN_HAPLOTYPE_TO_REFERENCE_MISMATCH_PENALTY_LONG_NAME,
doc = "Smith-Waterman mismatch penalty for haplotype-to-reference alignment.",
maxValue = 0,
optional = true)
public int smithWatermanHaplotypeToReferenceMismatchPenalty = DEFAULT_HAPLOTYPE_TO_REFERENCE_SMITH_WATERMAN_PARAMETERS.getMismatchPenalty();

@Advanced
@Argument(fullName = SMITH_WATERMAN_HAPLOTYPE_TO_REFERENCE_GAP_OPEN_PENALTY_LONG_NAME,
doc = "Smith-Waterman gap-open penalty for haplotype-to-reference alignment.",
maxValue = 0,
optional = true)
public int smithWatermanHaplotypeToReferenceGapOpenPenalty = DEFAULT_HAPLOTYPE_TO_REFERENCE_SMITH_WATERMAN_PARAMETERS.getGapOpenPenalty();

@Advanced
@Argument(fullName = SMITH_WATERMAN_HAPLOTYPE_TO_REFERENCE_GAP_EXTEND_PENALTY_LONG_NAME,
doc = "Smith-Waterman gap-extend penalty for haplotype-to-reference alignment.",
maxValue = 0,
optional = true)
public int smithWatermanHaplotypeToReferenceGapExtendPenalty = DEFAULT_HAPLOTYPE_TO_REFERENCE_SMITH_WATERMAN_PARAMETERS.getGapExtendPenalty();

// -----------------------------------------------------------------------------------------------
// Smith-Waterman parameters for read-to-haplotype alignment
// -----------------------------------------------------------------------------------------------

@Advanced
@Argument(fullName = SMITH_WATERMAN_READ_TO_HAPLOTYPE_MATCH_VALUE_LONG_NAME,
doc = "Smith-Waterman match value for read-to-haplotype alignment.",
minValue = 0,
optional = true)
public int smithWatermanReadToHaplotypeMatchValue = DEFAULT_READ_TO_HAPLOTYPE_SMITH_WATERMAN_PARAMETERS.getMatchValue();

@Advanced
@Argument(fullName = SMITH_WATERMAN_READ_TO_HAPLOTYPE_MISMATCH_PENALTY_LONG_NAME,
doc = "Smith-Waterman mismatch penalty for read-to-haplotype alignment.",
maxValue = 0,
optional = true)
public int smithWatermanReadToHaplotypeMismatchPenalty = DEFAULT_READ_TO_HAPLOTYPE_SMITH_WATERMAN_PARAMETERS.getMismatchPenalty();

@Advanced
@Argument(fullName = SMITH_WATERMAN_READ_TO_HAPLOTYPE_GAP_OPEN_PENALTY_LONG_NAME,
doc = "Smith-Waterman gap-open penalty for read-to-haplotype alignment.",
maxValue = 0,
optional = true)
public int smithWatermanReadToHaplotypeGapOpenPenalty = DEFAULT_READ_TO_HAPLOTYPE_SMITH_WATERMAN_PARAMETERS.getGapOpenPenalty();

@Advanced
@Argument(fullName = SMITH_WATERMAN_READ_TO_HAPLOTYPE_GAP_EXTEND_PENALTY_LONG_NAME,
doc = "Smith-Waterman gap-extend penalty for read-to-haplotype alignment.",
maxValue = 0,
optional = true)
public int smithWatermanReadToHaplotypeGapExtendPenalty = DEFAULT_READ_TO_HAPLOTYPE_SMITH_WATERMAN_PARAMETERS.getGapExtendPenalty();

public SWParameters getDanglingEndSWParameters() {
return new SWParameters(
smithWatermanDanglingEndMatchValue,
smithWatermanDanglingEndMismatchPenalty,
smithWatermanDanglingEndGapOpenPenalty,
smithWatermanDanglingEndGapExtendPenalty);
}

public SWParameters getHaplotypeToReferenceSWParameters() {
return new SWParameters(
smithWatermanHaplotypeToReferenceMatchValue,
smithWatermanHaplotypeToReferenceMismatchPenalty,
smithWatermanHaplotypeToReferenceGapOpenPenalty,
smithWatermanHaplotypeToReferenceGapExtendPenalty);
}

public SWParameters getReadToHaplotypeSWParameters() {
return new SWParameters(
smithWatermanReadToHaplotypeMatchValue,
smithWatermanReadToHaplotypeMismatchPenalty,
smithWatermanReadToHaplotypeGapOpenPenalty,
smithWatermanReadToHaplotypeGapExtendPenalty);
}

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