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createChemistryHeader.py - Create a SAM header with PacBio sequencing chemistry

CREATECHEMISTRYHEADER.PY(1) User Commands CREATECHEMISTRYHEADER.PY(1)

NAME

createChemistryHeader.py - Create a SAM header with PacBio sequencing chemistry information

DESCRIPTION

usage: getChemistryHeader.py [-h] [--debug] --bas_files BAS_FILES
[BAS_FILES ...]
input_alignment_file output_header_file
createChemistryHeader creates a SAM header that contains the chemistry information used by Quiver.

positional arguments:

input_alignment_file
A SAM or BAM file produced by BLASR.
output_header_file
Name of the SAM or BAM header file that will be created with chemistry information loaded.

optional arguments:

-h, --help
show this help message and exit
--debug
Output detailed log information. (default: False)
--bas_files BAS_FILES [BAS_FILES ...]
The bas or bax files containing the reads that were aligned in the input_alignment_file. Also can be a fofn of bas or bax files. (default: None)
January 2017 createChemistryHeader.py 0.3.0