Man page - hisat2-inspect-l(1)

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hisat2

Manual

HISAT2-INSPECT-L

NAME
SYNOPSIS
DESCRIPTION
OPTIONS

NAME

hisat2-inspect-l - HISAT2 index inspector, large index binary

SYNOPSIS

hisat2-inspect [ options ] * <ht2_base>

DESCRIPTION

HISAT2 version 2.2.1 by Daehwan Kim (infphilo@gmail.com, http://www.ccb.jhu.edu/people/infphilo)
<ht2_base>

ht2 filename minus trailing .1.ht2l/.2.ht2l

By default, prints FASTA records of the indexed nucleotide sequences to standard out. With -n , just prints names. With -s , just prints a summary of the index parameters and sequences. With -e , preserves colors if applicable.

OPTIONS

-a /--across <int>

Number of characters across in FASTA output (default: 60)

-s /--summary

Print summary incl. ref names, lengths, index properties

-n /--names

Print reference sequence names only

	--snp		Print SNPs
	--ss		Print splice sites

--ss-all

Print splice sites including those not in the global index

--exon

Print exons

-e /--ht2-ref

Reconstruct reference from .ht2l (slow, preserves colors)

-v /--verbose

Verbose output (for debugging)

-h /--help

print detailed description of tool and its options

--usage

print this usage message

64-bit Built on Debian 28 March 2025 Compiler: gcc version 14.2.0 (Debian 14.2.0-19) Options: -O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE = 2 -std = c ++11 Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}