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NGSEP / NGSEPcore

NGSEP is an integrated framework for analysis of high throughput sequencing (HTS) reads. The main functionality of NGSEP is the variants detector, which allows to make integrated discovery and genotyping of Single Nucleotide Variants (SNVs), insertions, deletions, and genomic regions with copy number variation (CNVs).
GNU General Public License v3.0
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fixed extractKmers to avoid Exception #2

Closed gcandrade10 closed 6 years ago

gcandrade10 commented 6 years ago

if source.length()<kmerSize this method throws this error: Exception in thread "main" java.lang.reflect.InvocationTargetException at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at ngsep.NGSEPcore.main(NGSEPcore.java:58) Caused by: java.lang.NegativeArraySizeException at ngsep.sequences.KmersCounter.extractKmers(KmersCounter.java:258) at ngsep.sequences.KmersCounter.extractKmers(KmersCounter.java:243) at ngsep.alignments.ReadsAligner.kmerBasedInexactSearchAlgorithm(ReadsAligner.java:163) at ngsep.alignments.ReadsAligner.search(ReadsAligner.java:147) at ngsep.alignments.ReadsAligner.alignRead(ReadsAligner.java:96) at ngsep.alignments.ReadsAligner.alignReads(ReadsAligner.java:77) at ngsep.alignments.ReadsAligner.main(ReadsAligner.java:57)