org.broadinstitute.hellbender.tools.funcotator.TranscriptSelectionMode Maven / Gradle / Ivy
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package org.broadinstitute.hellbender.tools.funcotator;
import org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation;
import org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGTFFieldConstants;
import org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature;
import java.util.Comparator;
import java.util.Set;
/**
* The manner to select a single transcript from a set of transcripts to report as the "best" or main transcript.
* That is, the transcript that has the most information on it in the output.
*/
public enum TranscriptSelectionMode {
/**
* BEST_EFFECT
*
* Select a transcript to be reported with details with priority on effect according to the folowing list of selection criteria:
*
* Choose the transcript that is on the custom list specified by the user. If no list was specified, treat as if no transcripts were on the list (tie).
* In case of tie, choose the transcript that yields the variant classification highest on the variant classification rank list (see below).
* If still a tie, choose the transcript with highest level of curation. Note that this means lower number is better for level (see below).
* If still a tie, choose the transcript with the best appris annotation (see below).
* If still a tie, choose the transcript with the longest transcript sequence length.
* If still a tie, choose the first transcript, alphabetically.
*
* Levels of Curation:
* 1 (verified loci)
* 2 manually annotated loci
* 3 automatically annotated loci
*
* Variant Classification Scores (See {@link org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation.VariantClassification} as well):
* De_novo_Start_OutOfFrame 0
* Nonsense_Mutation 0
* Nonstop_Mutation 0
* Missense_Mutation 1
* De_novo_Start_InFrame 1
* In_Frame_Del 1
* In_Frame_Ins 1
* Frame_Shift_Del 2
* Frame_Shift_Ins 2
* Frame_Shift_Sub 2
* Start_Codon_SNP 3
* Start_Codon_Del 3
* Start_Codon_Ins 3
* Start_Codon_DNP 3
* Start_Codon_TNP 3
* Start_Codon_ONP 3
* Stop_Codon_SNP 3
* Stop_Codon_Del 3
* Stop_Codon_Ins 3
* Stop_Codon_DNP 3
* Stop_Codon_TNP 3
* Stop_Codon_ONP 3
* Splice_Site 4
* Splice_Site_SNP 4
* Splice_Site_Del 4
* Splice_Site_Ins 4
* Splice_Site_DNP 4
* Splice_Site_TNP 4
* Splice_Site_ONP 4
* Splice_Site 4
* miRNA 4
* Silent 5
* 3UTR 6
* 5UTR 6
* Intron 7
* 5Flank 8
* 3Flank 8
* Non-coding_Transcript 9
* IGR 20
* TX-REF-MISMATCH 100
*
* APPRIS Ranks (http://appris.bioinfo.cnio.es/):
*
* appris_principal
* appris_candidate_highest_score
* appris_candidate_longest_ccds
* appris_candidate_ccds
* appris_candidate_longest_seq
* appris_candidate_longest
* appris_candidate
* no appris tag present
*/
BEST_EFFECT {
public Comparator getComparator(final Set userRequestedTranscripts) {
return new BestEffectGencodeFuncotationComparator(userRequestedTranscripts);
}
},
/**
* CANONICAL
*
* Select a transcript to be reported with details with priority on canonical order according to the folowing list of selection criteria:
*
* Choose the transcript that is on the custom list specified by the user. If no list was specified, treat as if all transcripts were on the list (tie).
* In case of tie, choose the transcript with highest level of curation. Note that this means lower number is better for level (see below).
* If still a tie, choose the transcript that yields the variant classification highest on the variant classification rank list (see below).
* If still a tie, choose the transcript with the best appris annotation (see below).
* If still a tie, choose the transcript with the longest transcript sequence length.
* If still a tie, choose the first transcript, alphabetically.
*
* Levels of Curation:
* 1 (verified loci)
* 2 manually annotated loci
* 3 automatically annotated loci
*
* Variant Classification Scores (See {@link GencodeFuncotation.VariantClassification} as well):
* De_novo_Start_OutOfFrame 0
* Nonsense_Mutation 0
* Nonstop_Mutation 0
* Missense_Mutation 1
* De_novo_Start_InFrame 1
* In_Frame_Del 1
* In_Frame_Ins 1
* Frame_Shift_Del 2
* Frame_Shift_Ins 2
* Frame_Shift_Sub 2
* Start_Codon_SNP 3
* Start_Codon_Del 3
* Start_Codon_Ins 3
* Start_Codon_DNP 3
* Start_Codon_TNP 3
* Start_Codon_ONP 3
* Stop_Codon_SNP 3
* Stop_Codon_Del 3
* Stop_Codon_Ins 3
* Stop_Codon_DNP 3
* Stop_Codon_TNP 3
* Stop_Codon_ONP 3
* Splice_Site 4
* Splice_Site_SNP 4
* Splice_Site_Del 4
* Splice_Site_Ins 4
* Splice_Site_DNP 4
* Splice_Site_TNP 4
* Splice_Site_ONP 4
* Splice_Site 4
* miRNA 4
* Silent 5
* 3UTR 6
* 5UTR 6
* Intron 7
* 5Flank 8
* 3Flank 8
* Non-coding_Transcript 9
* IGR 20
* TX-REF-MISMATCH 100
*
* APPRIS Ranks (http://appris.bioinfo.cnio.es/):
*
* appris_principal
* appris_candidate_highest_score
* appris_candidate_longest_ccds
* appris_candidate_ccds
* appris_candidate_longest_seq
* appris_candidate_longest
* appris_candidate
* no appris tag present
*/
CANONICAL {
public Comparator getComparator(final Set userRequestedTranscripts) {
return new CanonicalGencodeFuncotationComparator(userRequestedTranscripts);
}
},
/**
* Same as CANONICAL, but indicates that no transcripts should be dropped. Render all overlapping transcripts.
*/
ALL {
public Comparator getComparator(final Set userRequestedTranscripts) {
return new CanonicalGencodeFuncotationComparator(userRequestedTranscripts);
}
};
public abstract Comparator getComparator(final Set userRequestedTranscripts);
private static class ComparatorByUserTranscript implements Comparator {
private final Set userRequestedTranscripts;
public ComparatorByUserTranscript( final Set userRequestedTranscripts ) {
this.userRequestedTranscripts = userRequestedTranscripts;
}
@Override
public int compare( final GencodeFuncotation a, final GencodeFuncotation b ) {
// Choose the transcript that is on the custom list specified by the user:
if ( FuncotatorUtils.isFuncotationInTranscriptList(a, userRequestedTranscripts) && (!FuncotatorUtils.isFuncotationInTranscriptList(b, userRequestedTranscripts)) ) {
return -1;
}
else if ( (!FuncotatorUtils.isFuncotationInTranscriptList(a, userRequestedTranscripts)) && FuncotatorUtils.isFuncotationInTranscriptList(b, userRequestedTranscripts) ) {
return 1;
}
else {
return 0;
}
}
}
private static class ComparatorByIgrStatus implements Comparator {
public ComparatorByIgrStatus(){}
@Override
public int compare( final GencodeFuncotation a, final GencodeFuncotation b ) {
// Check to see if one is an IGR. IGR's have only a subset of the information in them, so it's easier to
// order them if they're IGRs:
if ( (b.getVariantClassification().equals(GencodeFuncotation.VariantClassification.IGR)) &&
(!a.getVariantClassification().equals(GencodeFuncotation.VariantClassification.IGR)) ) {
return -1;
}
else if ( (a.getVariantClassification().equals(GencodeFuncotation.VariantClassification.IGR)) &&
(!b.getVariantClassification().equals(GencodeFuncotation.VariantClassification.IGR)) ) {
return 1;
}
else {
return 0;
}
}
}
private static class ComparatorByVariantClassification implements Comparator {
public ComparatorByVariantClassification(){}
@Override
public int compare( final GencodeFuncotation a, final GencodeFuncotation b ) {
// Check highest variant classification:
if ( a.getVariantClassification().getSeverity() < b.getVariantClassification().getSeverity() ) {
return -1;
}
else if ( a.getVariantClassification().getSeverity() > b.getVariantClassification().getSeverity() ) {
return 1;
}
else {
return 0;
}
}
}
private static class ComparatorByProteinCodingStatus implements Comparator {
public ComparatorByProteinCodingStatus(){}
@Override
public int compare( final GencodeFuncotation a, final GencodeFuncotation b ) {
// Is it protein coding?
final boolean isAProteinCoding = GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString().equals(a.getGeneTranscriptType());
final boolean isBProteinCoding = GencodeGTFFieldConstants.KnownGeneBiotype.PROTEIN_CODING.toString().equals(b.getGeneTranscriptType());
if ( isAProteinCoding != isBProteinCoding ) {
if ( isAProteinCoding ) {
return -1;
}
else {
return 1;
}
}
else {
return 0;
}
}
}
private static class ComparatorByLocusLevel implements Comparator {
public ComparatorByLocusLevel(){}
@Override
public int compare( final GencodeFuncotation a, final GencodeFuncotation b ) {
// Check locus/curation levels:
if ( (a.getLocusLevel() != null) && (b.getLocusLevel() == null) ) {
return -1;
}
else if ( (a.getLocusLevel() == null ) && (b.getLocusLevel() != null) ) {
return 1;
}
else if ( (a.getLocusLevel() == null ) && (b.getLocusLevel() == null) ) {
return 0;
}
else {
return a.getLocusLevel().compareTo( b.getLocusLevel() );
}
}
}
private static class ComparatorByApprisRank implements Comparator {
public ComparatorByApprisRank(){}
@Override
public int compare( final GencodeFuncotation a, final GencodeFuncotation b ) {
// Check the appris annotation:
if ( (a.getApprisRank() != null) && (b.getApprisRank() == null) ) {
return -1;
}
else if ( (a.getApprisRank() == null ) && (b.getApprisRank() != null) ) {
return 1;
}
else if ( (a.getApprisRank() != null) && (b.getApprisRank() != null) && (!a.getApprisRank().equals(b.getApprisRank())) ) {
return a.getApprisRank().compareTo( b.getApprisRank() );
}
else {
return 0;
}
}
}
private static class ComparatorByTranscriptSequenceLength implements Comparator {
public ComparatorByTranscriptSequenceLength(){}
@Override
public int compare( final GencodeFuncotation a, final GencodeFuncotation b ) {
// Check transcript sequence length:
// Note that since we want longer transcripts to be sorted earlier in the list, we reverse b and a in the last check.
if ( (a.getTranscriptLength() != null) && (b.getTranscriptLength() == null) ) {
return -1;
}
else if ( (a.getTranscriptLength() == null ) && (b.getTranscriptLength() != null) ) {
return 1;
}
else if ( (a.getTranscriptLength() != null) && (b.getTranscriptLength() != null) && (!a.getTranscriptLength().equals(b.getTranscriptLength())) ) {
return b.getTranscriptLength().compareTo( a.getTranscriptLength() );
}
else {
return 0;
}
}
}
private static class ComparatorByTranscriptName implements Comparator {
public ComparatorByTranscriptName(){}
@Override
public int compare( final GencodeFuncotation a, final GencodeFuncotation b ) {
// Compare ABC order by transcript name:
if ( (a.getAnnotationTranscript() != null) && (b.getAnnotationTranscript() == null) ) {
return -1;
}
else if ( (a.getAnnotationTranscript() == null ) && (b.getAnnotationTranscript() != null) ) {
return 1;
}
// Need a default case in case all the comparison criteria are the same:
else if ( (a.getAnnotationTranscript() == null ) && (b.getAnnotationTranscript() == null) ) {
return -1;
}
else {
return a.getAnnotationTranscript().compareTo(b.getAnnotationTranscript());
}
}
}
/**
* Comparator class for Best Effect order.
* Complex enough that a Lambda would be utter madness.
*/
static class BestEffectGencodeFuncotationComparator implements Comparator {
private final Comparator byUserTranscript;
private final Comparator byIgrStatus;
private final Comparator byVariantClassification;
private final Comparator byProteinCodingStatus;
private final Comparator byLocusLevel;
private final Comparator byApprisRank;
private final Comparator byTranscriptLength;
private final Comparator byTranscriptName;
private final Comparator chainedComparator;
public BestEffectGencodeFuncotationComparator( final Set userRequestedTranscripts ) {
byUserTranscript = new ComparatorByUserTranscript(userRequestedTranscripts);
byIgrStatus = new ComparatorByIgrStatus();
byVariantClassification = new ComparatorByVariantClassification();
byProteinCodingStatus = new ComparatorByProteinCodingStatus();
byLocusLevel = new ComparatorByLocusLevel();
byApprisRank = new ComparatorByApprisRank();
byTranscriptLength = new ComparatorByTranscriptSequenceLength();
byTranscriptName = new ComparatorByTranscriptName();
chainedComparator = byUserTranscript
.thenComparing(byIgrStatus)
.thenComparing(byVariantClassification)
.thenComparing(byProteinCodingStatus)
.thenComparing(byLocusLevel)
.thenComparing(byApprisRank)
.thenComparing(byTranscriptLength)
.thenComparing(byTranscriptName);
}
@Override
public int compare( final GencodeFuncotation a, final GencodeFuncotation b ) {
// 0 - Choose the transcript that is on the custom list specified by the user
// 1a) - Check to see if one is an IGR.
// 1b) - Check highest variant classification.
// 2a) - Is it protein coding?
// 2b) - Check locus/curation levels.
// 3) - Check the appris annotation.
// 4) - Check transcript sequence length.
// 5) - Default to ABC order by transcript name.
return chainedComparator.compare(a, b);
}
}
/**
* Comparator class for Canonical order.
* Complex enough that a Lambda would be utter madness.
*/
static class CanonicalGencodeFuncotationComparator implements Comparator {
private final Comparator byUserTranscript;
private final Comparator byIgrStatus;
private final Comparator byVariantClassification;
private final Comparator byProteinCodingStatus;
private final Comparator byLocusLevel;
private final Comparator byApprisRank;
private final Comparator byTranscriptLength;
private final Comparator byTranscriptName;
private final Comparator chainedComparator;
public CanonicalGencodeFuncotationComparator(final Set userRequestedTranscripts ) {
byUserTranscript = new ComparatorByUserTranscript(userRequestedTranscripts);
byIgrStatus = new ComparatorByIgrStatus();
byVariantClassification = new ComparatorByVariantClassification();
byProteinCodingStatus = new ComparatorByProteinCodingStatus();
byLocusLevel = new ComparatorByLocusLevel();
byApprisRank = new ComparatorByApprisRank();
byTranscriptLength = new ComparatorByTranscriptSequenceLength();
byTranscriptName = new ComparatorByTranscriptName();
chainedComparator = byUserTranscript
.thenComparing(byProteinCodingStatus)
.thenComparing(byLocusLevel)
.thenComparing(byApprisRank)
.thenComparing(byIgrStatus)
.thenComparing(byVariantClassification)
.thenComparing(byTranscriptLength)
.thenComparing(byTranscriptName);
}
@Override
public int compare( final GencodeFuncotation a, final GencodeFuncotation b ) {
// 0) - Choose the transcript that is on the custom list specified by the user:
// 1a) - Is it protein coding?
// 1b) - Check locus/curation levels.
// 2) - Check the appris annotation:
// 3a) - Check to see if one is an IGR.
// 3b) - Check highest variant classification:
// 4) - Check transcript sequence length:
// 5) - Default to ABC order by transcript name:
return chainedComparator.compare(a, b);
}
}
}
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