hisat2-inspect-s - HISAT2 index inspector, small index binary
hisat2-inspect [options]*
<ht2_base>
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.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.
- -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 05 August 2021 Compiler: gcc version 10.2.1
20210110 (Debian 10.2.1-6) 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}