java.lang.StringIndexOutOfBoundsException

[visze]

If you run:
java -jar jannovar-cli/target/jannovar-cli-0.16.jar annotate-pos -d data/hg38_refseq.ser -c 'chr17:46330511G>T'
you get this error:

[ERROR] Could not annotate variant chr17:46330511G>T!
java.lang.StringIndexOutOfBoundsException: String index out of range: 845
    at java.lang.String.substring(String.java:1963)
    at de.charite.compbio.jannovar.reference.TranscriptSequenceDecorator.getCodonAt(TranscriptSequenceDecorator.java:85)
    at de.charite.compbio.jannovar.annotation.builders.SNVAnnotationBuilder.buildCDSExonicAnnotation(SNVAnnotationBuilder.java:105)
    at de.charite.compbio.jannovar.annotation.builders.SNVAnnotationBuilder.build(SNVAnnotationBuilder.java:71)
    at de.charite.compbio.jannovar.annotation.builders.AnnotationBuilderDispatcher.build(AnnotationBuilderDispatcher.java:45)
    at de.charite.compbio.jannovar.annotation.VariantAnnotator.buildNonSVAnnotation(VariantAnnotator.java:168)
    at de.charite.compbio.jannovar.annotation.VariantAnnotator.buildAnnotations(VariantAnnotator.java:151)
    at de.charite.compbio.jannovar.cmd.annotate_pos.AnnotatePositionCommand.run(AnnotatePositionCommand.java:64)
    at de.charite.compbio.jannovar.Jannovar.main(Jannovar.java:111)

Maybe similar to #176

[visze]

same with this:

java -jar jannovar-cli-0.16.jar annotate-pos -d data/hg19_refseq.ser  -c "chr10:99638189C>T"

[ERROR] Could not annotate variant chr10:99638189C>T!
java.lang.StringIndexOutOfBoundsException: String index out of range: 2228
    at java.lang.String.substring(String.java:1963)
    at de.charite.compbio.jannovar.reference.TranscriptSequenceDecorator.getCodonAt(TranscriptSequenceDecorator.java:85)
    at de.charite.compbio.jannovar.annotation.builders.SNVAnnotationBuilder.buildCDSExonicAnnotation(SNVAnnotationBuilder.java:105)
    at de.charite.compbio.jannovar.annotation.builders.SNVAnnotationBuilder.build(SNVAnnotationBuilder.java:71)
    at de.charite.compbio.jannovar.annotation.builders.AnnotationBuilderDispatcher.build(AnnotationBuilderDispatcher.java:45)
    at de.charite.compbio.jannovar.annotation.VariantAnnotator.buildNonSVAnnotation(VariantAnnotator.java:168)
    at de.charite.compbio.jannovar.annotation.VariantAnnotator.buildAnnotations(VariantAnnotator.java:151)
    at de.charite.compbio.jannovar.cmd.annotate_pos.AnnotatePositionCommand.run(AnnotatePositionCommand.java:64)
    at de.charite.compbio.jannovar.Jannovar.main(Jannovar.java:111)

[visze]

AGAIN! Also with 0.17 development. It seems to me a problem with the ref_seq database. RefSeq_curated works fine! So we should think of a way to get rid of these problems...

jannovar-cli-0.17-SNAPSHOT.jar annotate-pos -d hg19_refseq.ser -c "chr3:194901092C>T"

java.lang.StringIndexOutOfBoundsException: String index out of range: 886
        at java.lang.String.substring(String.java:1963)
        at de.charite.compbio.jannovar.reference.TranscriptSequenceDecorator.getCodonAt(TranscriptSequenceDecorator.java:85)
        at de.charite.compbio.jannovar.annotation.builders.SNVAnnotationBuilder.buildCDSExonicAnnotation(SNVAnnotationBuilder.java:105)
        at de.charite.compbio.jannovar.annotation.builders.SNVAnnotationBuilder.build(SNVAnnotationBuilder.java:71)
        at de.charite.compbio.jannovar.annotation.builders.AnnotationBuilderDispatcher.build(AnnotationBuilderDispatcher.java:45)
        at de.charite.compbio.jannovar.annotation.VariantAnnotator.buildNonSVAnnotation(VariantAnnotator.java:163)
        at de.charite.compbio.jannovar.annotation.VariantAnnotator.buildAnnotations(VariantAnnotator.java:144)
        at de.charite.compbio.jannovar.cmd.annotate_pos.AnnotatePositionCommand.run(AnnotatePositionCommand.java:64)
        at de.charite.compbio.jannovar.Jannovar.main(Jannovar.java:111)

[visze]

well. it is not only an issue in refseq. Also in refseq curated!

I get a lot of errors annotating mutatuions! We have to fix this issue!

java -jar jannovar-cli-0.16.jar annotate-pos -d data/hg19_refseq_curated.ser -c "chr12:51745834C>T"

error

java.lang.StringIndexOutOfBoundsException: String index out of range: 4521
        at java.lang.String.substring(String.java:1963)
        at de.charite.compbio.jannovar.reference.TranscriptSequenceDecorator.getCodonAt(TranscriptSequenceDecorator.java:85)
        at de.charite.compbio.jannovar.annotation.builders.SNVAnnotationBuilder.buildCDSExonicAnnotation(SNVAnnotationBuilder.java:105)
        at de.charite.compbio.jannovar.annotation.builders.SNVAnnotationBuilder.build(SNVAnnotationBuilder.java:71)
        at de.charite.compbio.jannovar.annotation.builders.AnnotationBuilderDispatcher.build(AnnotationBuilderDispatcher.java:45)
        at de.charite.compbio.jannovar.annotation.VariantAnnotator.buildNonSVAnnotation(VariantAnnotator.java:168)
        at de.charite.compbio.jannovar.annotation.VariantAnnotator.buildAnnotations(VariantAnnotator.java:151)
        at de.charite.compbio.jannovar.cmd.annotate_pos.AnnotatePositionCommand.run(AnnotatePositionCommand.java:64)
        at de.charite.compbio.jannovar.Jannovar.main(Jannovar.java:111)

[holtgrewe]

No more crashing after #210.

$ java -jar jannovar-cli/target/jannovar-cli-0.17-SNAPSHOT.jar annotate-pos -d data/hg19_refseq.ser -c "chr12:51745834C>T" -c "chr10:99638189C>T" -c "chr3:194901092C>T"
ERROR StatusLogger No log4j2 configuration file found. Using default configuration: logging only errors to the console.
Options
verbosity: 1
dataFile: data/hg19_refseq.ser
vcfFilePaths: []
chromosomalChanges: [chr12:51745834C>T, chr10:99638189C>T, chr3:194901092C>T]
showAll: false
jannovarFormat: false
writeJannovarInfoFields: false
writeVCFAnnotationStandardInfoFields: true
output infix: .jv
Deserializing transcripts...
INFO Deserializing JannovarData from data/hg19_refseq.ser
INFO Deserialization took 5.56 sec.
#change effect  hgvs_annotation
chr12:51745834C>T   THREE_PRIME_UTR_VARIANT,THREE_PRIME_UTR_VARIANT GALNT6:NM_007210.3:c.*2329G>A:p.(=),GALNT6:XM_005268607.1:c.*2329G>A:p.(=)
chr10:99638189C>T   CODING_TRANSCRIPT_INTRON_VARIANT,THREE_PRIME_UTR_VARIANT    CRTAC1:NM_018058.6:c.1819+1817G>A:p.(=),CRTAC1:XM_005269938.1:c.*214G>A:p.(=)
chr3:194901092C>T   CODING_TRANSCRIPT_INTRON_VARIANT,CODING_TRANSCRIPT_INTRON_VARIANT,CODING_TRANSCRIPT_INTRON_VARIANT,CODING_TRANSCRIPT_INTRON_VARIANT,CODING_TRANSCRIPT_INTRON_VARIANT,CODING_TRANSCRIPT_INTRON_VARIANT,CODING_TRANSCRIPT_INTRON_VARIANT,THREE_PRIME_UTR_VARIANT  XXYLT1:NM_152531.4:c.653-23782G>A:p.(=),XXYLT1:XM_005269282.1:c.215-23782G>A:p.(=),XXYLT1:XM_005269284.1:c.92-23782G>A:p.(=),XXYLT1:XM_005269285.1:c.92-23782G>A:p.(=),XXYLT1:XM_005269286.1:c.92-23782G>A:p.(=),XXYLT1:XM_005269287.1:c.-181+28G>A:p.(=),XXYLT1:XM_005269288.1:c.92-23782G>A:p.(=),XXYLT1:XM_005269283.1:c.*79G>A:p.(=)

ERROR StatusLogger No log4j2 configuration file found. Using default configuration: logging only errors to the console.
Options
verbosity: 1
dataFile: data/hg38_refseq.ser
vcfFilePaths: []
chromosomalChanges: [chr17:46330511G>T]
showAll: false
jannovarFormat: false
writeJannovarInfoFields: false
writeVCFAnnotationStandardInfoFields: true
output infix: .jv
Deserializing transcripts...
INFO Deserializing JannovarData from data/hg38_refseq.ser
INFO Deserialization took 8.62 sec.
#change effect  hgvs_annotation
chr17:46330511G>T   MISSENSE_VARIANT,MISSENSE_VARIANT,MISSENSE_VARIANT,MISSENSE_VARIANT,MISSENSE_VARIANT,MISSENSE_VARIANT,MISSENSE_VARIANT,MISSENSE_VARIANT,MISSENSE_VARIANT,MISSENSE_VARIANT,MISSENSE_VARIANT,CODING_TRANSCRIPT_INTRON_VARIANT,CODING_TRANSCRIPT_INTRON_VARIANT,CODING_TRANSCRIPT_INTRON_VARIANT,CODING_TRANSCRIPT_INTRON_VARIANT,CODING_TRANSCRIPT_INTRON_VARIANT,CODING_TRANSCRIPT_INTRON_VARIANT,CODING_TRANSCRIPT_INTRON_VARIANT,THREE_PRIME_UTR_VARIANT,THREE_PRIME_UTR_VARIANT,THREE_PRIME_UTR_VARIANT   LRRC37A:NM_014834.4:c.3234G>T:p.(Lys1078Asn),LRRC37A:XM_005257879.3:c.3234G>T:p.(Lys1078Asn),LRRC37A:XM_005257880.3:c.3087G>T:p.(Lys1029Asn),LRRC37A:XM_005257882.3:c.2952G>T:p.(Lys984Asn),LRRC37A:XM_005257887.3:c.651G>T:p.(Lys217Asn),LRRC37A:XM_006722208.2:c.3234G>T:p.(Lys1078Asn),LRRC37A:XM_006722209.2:c.3234G>T:p.(Lys1078Asn),LRRC37A:XM_006722210.2:c.2934G>T:p.(Lys978Asn),LRRC37A:XM_006722211.2:c.2862G>T:p.(Lys954Asn),LRRC37A:XM_011525539.1:c.3081G>T:p.(Lys1027Asn),LRRC37A:XM_011525540.1:c.651G>T:p.(Lys217Asn),ARL17B:NM_001103154.1:c.259+22309C>A:p.(=),ARL17B:XM_005256918.3:c.259+22309C>A:p.(=),ARL17B:XM_011524160.1:c.525+8998C>A:p.(=),ARL17B:XM_011524161.1:c.525+8998C>A:p.(=),ARL17B:XM_011524162.1:c.525+8998C>A:p.(=),ARL17B:XM_011524163.1:c.525+8998C>A:p.(=),ARL17B:XM_011524167.1:c.260-19236C>A:p.(=),ARL17B:XM_011524164.1:c.*67C>A:p.(=),LRRC37A:XM_005257883.3:c.*58G>T:p.(=),LRRC37A:XM_005257884.3:c.*58G>T:p.(=)