DOKK / manpages / debian 10 / hisat2 / hisat2-inspect-s.1.en
HISAT2-INSPECT-S(1) User Commands HISAT2-INSPECT-S(1)

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

hisat2-inspect [options]* <ht2_base>

HISAT2 version 2.1.0 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.

Number of characters across in FASTA output (default: 60)
Print summary incl. ref names, lengths, index properties
Print reference sequence names only
Print SNPs
Print splice sites
Print splice sites including those not in the global index
Print exons
Reconstruct reference from .ht2 (slow, preserves colors)
Verbose output (for debugging)
print detailed description of tool and its options
print this usage message

64-bit Built on Debian 24 September 2018 Compiler: gcc version 8.2.0 (Debian 8.2.0-7) Options: -O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -DPOPCNT_CAPABILITY Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}

September 2018 hisat2-inspect-s version 2.1.0