Issues · GuttmanLab/guttmanlab-core · GitHub

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FASTQ parser needs null check when closing reader

#26

· charcuterie opened

on Apr 18, 2016

TODO: FASTQ sequence names start with '@'

#25

· charcuterie opened

on Apr 17, 2016

Annotations returned by AnnotationCollection.sortedIterator() are not sorted

#24

· pamelarussell opened

on Apr 13, 2016

Strandedness/unstrandedness of annotation doesn't affect count over annotation

#22

· pamelarussell opened

on Feb 8, 2016

Counts for genomic populated windows are almost right but a little low

#17

· pamelarussell opened

on Dec 2, 2015

Genomic populated windows don't count full fragment

#16

· pamelarussell opened

on Dec 2, 2015

SAMFragment end position is wrong

#15

· pamelarussell opened

on Dec 2, 2015

PairedMappedFragment size and number of blocks are wrong

#14

· pamelarussell opened

on Dec 2, 2015

AnnotationCollection.sortedIterator(annotation, true) returns non-overlapping annotations

#11

· charcuterie opened

on Oct 23, 2015

SAMFragment.getReferenceEndPosition() returns wrong position when Fragments have deletions

#10

· charcuterie opened

on Oct 22, 2015

Wrong counts for BAMPairedFragmentCollection over regions read in from a bed file

#9

· pamelarussell opened

on Oct 22, 2015

Concurrent iteration exception when scoring gene, window at same time

#7

· pamelarussell opened

on Oct 14, 2015