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HISAT2-INSPECT-S(1) User Commands HISAT2-INSPECT-S(1)

NAME

hisat2-inspect-s - HISAT2 index inspector, small index binary

SYNOPSIS

hisat2-inspect [options]* <ht2_base>

DESCRIPTION

HISAT2 version 2.2.0 by Daehwan Kim (infphilo@gmail.com, http://www.ccb.jhu.edu/people/infphilo)
<ht2_base>
ht2 filename minus trailing .1.ht2/.2.ht2
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 .ht2 (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 06 May 2020 Compiler: gcc version 9.3.0 (Debian 9.3.0-11) 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}

May 2020 hisat2-inspect-s version 2.2.0