Fixed a bunch of test failures, including a couple bugs
main fix: the introduction of get_read_count_from_bam_index was breaking the use of streamed input because it reads from the BAM file. Fixed by adding seek(0) if the input is a file, and returning None otherwise.
A couple missing imports: os in tagfix, ssw in bam_utils
test_annotate had some issue with the way the stream was working. Using CliRunner seems to work better.
test_extract had a bad argument (-t is not a valid arg for extract. In the course of debugging, I also switched to using CliRunner there.
Fixed a bunch of test failures, including a couple bugs
main fix: the introduction of
get_read_count_from_bam_indexwas breaking the use of streamed input because it reads from the BAM file. Fixed by addingseek(0)if the input is a file, and returningNoneotherwise.A couple missing imports:
osintagfix,sswinbam_utilstest_annotatehad some issue with the way the stream was working. UsingCliRunnerseems to work better.test_extracthad a bad argument (-tis not a valid arg forextract. In the course of debugging, I also switched to usingCliRunnerthere.