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bash5tools - Tool for extracting data from .bas.h5 files


bash5tools [-h] [--verbose] [--version] [--profile] [--debug] [--outFilePrefix
OUTFILEPREFIX] [--readType {ccs,subreads,unrolled}] [--outType OUTTYPE] [--minLength
MINLENGTH] [--minReadScore MINREADSCORE] [--minPasses MINPASSES] input.bas.h5


positional arguments:
input .bas.h5 filename

optional arguments:
-h, --help
show this help message and exit

--verbose, -v
Set the verbosity level (default: None)

show program's version number and exit

Print runtime profile at exit (default: False)

Catch exceptions in debugger (requires ipdb) (default: False)

output filename prefix [None]

--readType {ccs,subreads,unrolled}
read type (ccs, subreads, or unrolled) []

--outType OUTTYPE
output file type (fasta, fastq) [fasta]

Read filtering arguments:
--minLength MINLENGTH
min read length [0]

min read score, valid only with --readType={unrolled,subreads} [0]

--minPasses MINPASSES
min number of CCS passes, valid only with --readType=ccs [0]

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