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Published 20 hours ago • verified publisher icon rjpbonnal

index_stats is not working in 2.3.5

Open MatthewRalston opened this issue 8 years ago • 5 comments

I've indexed a bam file with samtools and receive true on the indexed command and index_stats returns an empty hash.

MatthewRalston avatar May 19 '16 19:05 MatthewRalston

Hi Mat, Can you provide an example? I am currently updating the gem to samtools-1.3.1 and it is passing the unit test for index_stat

homonecloco avatar May 24 '16 23:05 homonecloco

So are you saying a version >2.3.5 is passing?

MatthewRalston avatar May 31 '16 13:05 MatthewRalston

yes, but if you have any issues let us know. And if it fails, please attach an example so I can test it.

homonecloco avatar May 31 '16 13:05 homonecloco

An example as in a bam file? When I initially had this issue, the choice of BAM file was not important; ie the index stats command produced an empty hash {} in several instances.

MatthewRalston avatar May 31 '16 14:05 MatthewRalston

Can you check if it is working now? I couldn't reproduce the bug on the unit tests, and added a few more.

homonecloco avatar May 31 '16 14:05 homonecloco