.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.7.
.TH HISAT2-BUILD-S "1" "September 2018" "hisat2-build-s version 2.1.0" "User Commands"
.SH NAME
hisat2-build-s \- HISAT2 indexer, small index binary
.SH SYNOPSIS
.B hisat2-build
[\fI\,options\/\fR]\fI\,* <reference_in> <ht2_index_base>\/\fR
.SH DESCRIPTION
HISAT2 version 2.1.0 by Daehwan Kim (infphilo@gmail.com, http://www.ccb.jhu.edu/people/infphilo)
.TP
reference_in
comma\-separated list of files with ref sequences
.TP
hisat2_index_base
write ht2 data to files with this dir/basename
.SH OPTIONS
.TP
\fB\-c\fR
reference sequences given on cmd line (as
<reference_in>)
.TP
\fB\-a\fR/\-\-noauto
disable automatic \fB\-p\fR/\-\-bmax/\-\-dcv memory\-fitting
.TP
\fB\-p\fR
number of threads
.TP
\fB\-\-bmax\fR <int>
max bucket sz for blockwise suffix\-array builder
.TP
\fB\-\-bmaxdivn\fR <int>
max bucket sz as divisor of ref len (default: 4)
.TP
\fB\-\-dcv\fR <int>
diff\-cover period for blockwise (default: 1024)
.TP
\fB\-\-nodc\fR
disable diff\-cover (algorithm becomes quadratic)
.TP
\fB\-r\fR/\-\-noref
don't build .3/.4.ht2 (packed reference) portion
.TP
\fB\-3\fR/\-\-justref
just build .3/.4.ht2 (packed reference) portion
.TP
\fB\-o\fR/\-\-offrate <int>
SA is sampled every 2^offRate BWT chars (default: 5)
.TP
\fB\-t\fR/\-\-ftabchars <int>
# of chars consumed in initial lookup (default: 10)
.TP
\fB\-\-localoffrate\fR <int>
SA (local) is sampled every 2^offRate BWT chars (default: 3)
.TP
\fB\-\-localftabchars\fR <int>
# of chars consumed in initial lookup in a local index (default: 6)
.TP
\fB\-\-snp\fR <path>
SNP file name
.TP
\fB\-\-haplotype\fR <path>
haplotype file name
.TP
\fB\-\-ss\fR <path>
Splice site file name
.TP
\fB\-\-exon\fR <path>
Exon file name
.TP
\fB\-\-seed\fR <int>
seed for random number generator
.TP
\fB\-q\fR/\-\-quiet
verbose output (for debugging)
.TP
\fB\-h\fR/\-\-help
print detailed description of tool and its options
.TP
\fB\-\-usage\fR
print this usage message
.TP
\fB\-\-version\fR
print version information and quit
.PP
64\-bit
Built on Debian
24 September 2018
Compiler: gcc version 8.2.0 (Debian 8.2.0\-7)
Options: \fB\-O3\fR   \fB\-funroll\-loops\fR \fB\-g3\fR \fB\-Wdate\-time\fR \fB\-D_FORTIFY_SOURCE\fR=\fI\,2\/\fR \fB\-DPOPCNT_CAPABILITY\fR
Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}