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Cannot read 10x bam file #15
Describe the bug
Cannot read 10x bam file
import bamnostic as bs bam_file = bs.AlignmentFile( os.path.join(folder, 'possorted_genome_bam.bam'), mode='rb')
Desktop (please complete the following information):
I saw your issue. I thought by the tag, field part that it might have been an unpacking issue in the binary part of the data. The problem was actually with how it parses the SAM header. The fields of the SAM header aren't expected to be 3-field because the field type is only really necessary for the BAM format to figure out how to unpack the tag data.
I fixed this to handle 3-field tags in SAM header though. Thank you for the heads-up.
I made an update to PyPI and conda. Conda might take awhile until it is finalized. If you want the updates now, feel free to just github install it.
Wow, thank you for the quick fix! --- Olga Botvinnik, PhD olgabotvinnik.com <http://www.olgabotvinnik.com>…
On Thu, Sep 6, 2018 at 2:23 PM Marcus D Sherman ***@***.***> wrote: Oops, forgot to quote something. Should be fixed with f7cfb0b <f7cfb0b> Sorry. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#15 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAxNcJcLuS97nkIkKLPj4lu3MjFMJqfmks5uYZJPgaJpZM4Wdrlq> .