Hey, have been using seqLib successfully for a while, but I just ran into an issue. I have a function, and within this function, I create a BamReader object, get reads out, etc. This works well, except I've recently noticed that when I use CRAM files and set the reference using BamReader::SetCramReference, the reference is not closed when calling BamReader::Close(), or when the BamReader object goes out of scope when the function ends. So when I call my function on several thousand CRAM files, the code crashes because I don't have enough file handles. Can you please implement a method to close the cram reference?
Error message wise, when running I get this
connect: Network is unreachable
one for each file (this is run on a cluster without internet access), then once I run out of file handles, I get
connect: Network is unreachable
test-data/mouse_data/mm10_2016_10_02.fa: Too many open files
Failed to populate reference for id 10
Unable to fetch reference #10 10001343..10999757
Failure to decode slice
Hey, have been using seqLib successfully for a while, but I just ran into an issue. I have a function, and within this function, I create a BamReader object, get reads out, etc. This works well, except I've recently noticed that when I use CRAM files and set the reference using BamReader::SetCramReference, the reference is not closed when calling BamReader::Close(), or when the BamReader object goes out of scope when the function ends. So when I call my function on several thousand CRAM files, the code crashes because I don't have enough file handles. Can you please implement a method to close the cram reference?
Error message wise, when running I get this
one for each file (this is run on a cluster without internet access), then once I run out of file handles, I get