I have been working on Java software to view reads from SAM/BAM files and want
to expand it to be able to read CRAM as well.
I converted a BAM file using samtools view - C to create the cram file and
samtools index to create the crai file.
Using htsjdk-1.1.30.jar, I ran into the following problems:
- The constructor CRAMFileReader(final File cramFile, final File
indexFile, final ReferenceSource referenceSource) does a null pointer
evaluation on a wrong variable.
- The constructor AbstractBAMFileIndex(final File file, final
SAMSequenceDictionary dictionary, final boolean useMemoryMapping) referenced by
CRAMFileReader#getIndex() assumes bai header in crai files.
These were easy to fix, but the CRAMFileReader does not return any records
after a call to queryAlignmentStart().
Seeking into the same cram file using samtools view works.
Am I wrong in assuming that the thsjdk library should be able to seek into cram
files created by samtools?
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