.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.46.4.
.TH CREATECHEMISTRYHEADER.PY "1" "December 2015" "createChemistryHeader.py 0.2.0" "User Commands"
.SH NAME
createChemistryHeader.py \- Create a SAM header with PacBio sequencing chemistry information
.SH DESCRIPTION
usage: getChemistryHeader.py [\-h] [\-\-debug] \fB\-\-bas_files\fR BAS_FILES
.TP
[BAS_FILES ...]
input_alignment_file output_header_file
.PP
createChemistryHeader creates a SAM header that contains the chemistry
information used by Quiver.
.SS "positional arguments:"
.TP
input_alignment_file
A SAM or BAM file produced by BLASR.
.TP
output_header_file
Name of the SAM or BAM header file that will be
created with chemistry information loaded.
.SS "optional arguments:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-\-debug\fR
Output detailed log information. (default: False)
.TP
\fB\-\-bas_files\fR 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)