.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
.TH HISAT2-INSPECT "1" "August 2023" "hisat2-inspect version 2.2.1" "User Commands"
.SH NAME
hisat2-inspect \- HISAT2 index inspector, wrapper script
.SH SYNOPSIS
.B hisat2-inspect
[\fI\,options\/\fR]\fI\,* <ht2_base>\/\fR
.SH DESCRIPTION
HISAT2 version 2.2.1 by Daehwan Kim (infphilo@gmail.com, http://www.ccb.jhu.edu/people/infphilo)
.TP
<ht2_base>
ht2 filename minus trailing .1.ht2/.2.ht2
.IP
By default, prints FASTA records of the indexed nucleotide sequences to
standard out.  With \fB\-n\fR, just prints names.  With \fB\-s\fR, just prints a summary of
the index parameters and sequences.  With \fB\-e\fR, preserves colors if applicable.
.SH OPTIONS
.TP
\fB\-\-large\-index\fR
force inspection of the 'large' index, even if a
\&'small' one is present.
.TP
\fB\-a\fR/\-\-across <int>
Number of characters across in FASTA output (default: 60)
.TP
\fB\-s\fR/\-\-summary
Print summary incl. ref names, lengths, index properties
.TP
\fB\-n\fR/\-\-names
Print reference sequence names only
.TP
\fB\-\-snp\fR
Print SNPs
.TP
\fB\-\-ss\fR
Print splice sites
.TP
\fB\-\-ss\-all\fR
Print splice sites including those not in the global index
.TP
\fB\-\-exon\fR
Print exons
.TP
\fB\-e\fR/\-\-ht2\-ref
Reconstruct reference from .ht2 (slow, preserves colors)
.TP
\fB\-v\fR/\-\-verbose
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
.PP
64\-bit
Built on Debian
05 August 2023
Compiler: gcc version 13.2.0 (Debian 13.2.0\-1)
Options: \fB\-O3\fR   \fB\-funroll\-loops\fR \fB\-g3\fR \fB\-Wdate\-time\fR \fB\-D_FORTIFY_SOURCE\fR=\fI\,2\/\fR \fB\-std\fR=\fI\,c\/\fR++11
Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}