.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.12.
.TH PARASAIL_ALIGNER "1" "April 2020" "parasail_aligner 2.4.1" "User Commands"
.SH NAME
parasail_aligner \- Development heaaders and static libraries for parasail
.SH DESCRIPTION
usage: parasail_aligner [\-a funcname] [\-c cutoff] [\-x] [\-e gap_extend] [\-o gap_open] [\-m matrix] [\-t threads] [\-d] [\-M match] [\-X mismatch] [\-k band size (for nw_banded)] [\-l AOL] [\-s SIM] [\-i OS] [\-v] [\-V] \fB\-f\fR file [\-q query_file] [\-g output_file] [\-O output_format {EMBOSS,SAM,SAMH,SSW}] [\-b batch_size] [\-r memory_budget] [\-C] [\-A alphabet_aliases]
.SS "Defaults:"
.IP
funcname: sw_stats_striped_16
.IP
cutoff: 7, must be >= 1, exact match length cutoff
.IP
\fB\-x\fR: if present, don't use suffix array filter
.IP
gap_extend: 1, must be >= 0
.IP
gap_open: 10, must be >= 0
.IP
matrix: blosum62
.IP
\fB\-d\fR: if present, assume DNA alphabet ACGT
.IP
match: 1, must be >= 0
.IP
mismatch: 0, must be >= 0
.IP
threads: system\-specific default, must be >= 1
.IP
AOL: 80, must be 0 <= AOL <= 100, percent alignment length
SIM: 40, must be 0 <= SIM <= 100, percent exact matches
.TP
OS: 30, must be 0 <= OS <= 100, percent optimal score
over self score
.IP
\fB\-v\fR: verbose output, report input parameters and timing
\fB\-V\fR: verbose memory output, report memory use
.IP
file: no default, must be in FASTA format
.IP
query_file: no default, must be in FASTA format
.IP
output_file: parasail.csv
.IP
output_format: no default, must be one of {EMBOSS,SAM,SAMH,SSW}
.IP
batch_size: 0 (calculate based on memory budget),
.IP
how many alignments before writing output
.IP
memory_budget: 2GB or half available from system query (4.046 GB)
.IP
\fB\-C\fR: if present, use case sensitive alignments, matrices, etc.
.PP
alphabet_aliases: traceback will treat these pairs of characters as matches,
.IP
for example, 'TU' for one pair, or multiple pairs as 'XYab'
.SH AUTHOR
 This manpage was written by Nilesh Patra for the Debian distribution and
 can be used for any other usage of the program.