HISAT2-INSPECT-S(1)

🌸 the whole vibe first

okay bestie, this is HISAT2-INSPECT-S(1) 💖 and it lives in the User Commands manual, right next to all the other little tools. It's the glow-up guide for hisat2-inspect-s, the small index binary version of the HISAT2 index inspector. Come sit with me, we're gonna read it together and you're gonna get it on the first pass, fr fr.

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✨ NAME ✨

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

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🎀 SYNOPSIS 🎀

hisat2-inspect [options]* <ht2_base>

like… options first, then the base name. that's the whole shape of it, no notes 💅

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💜 DESCRIPTION 💜

This is HISAT2 version 2.2.1, made by Daehwan Kim (that's infphilo@gmail.com, and his corner of the internet is http://www.ccb.jhu.edu/people/infphilo) 👑 iconic behavior honestly.

• <ht2_base> — the ht2 filename minus the trailing .1.ht2/.2.ht2. so you chop that suffix off, bestie, don't hand it over whole.

So what does it do by default? By default it prints FASTA records of the indexed nucleotide sequences straight to standard out ✨. And then there's the little toggles that change the whole plot:

• With -n, it just prints names.
• With -s, it just prints a summary of the index parameters and sequences.
• With -e, it preserves colors if applicable 🌈.

that's the core plot twist, everything after is just garnish 🍓

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🔥 OPTIONS 🔥

• -a/--across <int> — Number of characters across in FASTA output (default: 60). so it's how wide the FASTA lines stretch, and the default is 60, no cap 📏
• -s/--summary — Print summary incl. ref names, lengths, index properties. the ✨everything✨ recap
• -n/--names — Print reference sequence names only. just the names, nothing else, it's giving minimalism
• --snp — Print SNPs 🧬
• --ss — Print splice sites ✂️
• --ss-all — Print splice sites including those not in the global index. the deluxe version bestie
• --exon — Print exons 🎁
• -e/--ht2-ref — Reconstruct reference from .ht2 (slow, preserves colors). yes it says slow, so pour a drink first 🐌 but it keeps the colors 🌈
• -v/--verbose — Verbose output (for debugging). chatty mode 🔍
• -h/--help — print detailed description of tool and its options. the classic, always there for you 🫶
• --usage — print this usage message. the quick lil reminder 📝

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🛠️ the build tea 🛠️

here's exactly what this binary was built as, verbatim, because numbers are sacred:

64-bit Built on Debian 21 January 2026 Compiler: gcc version 15.2.0
(Ubuntu 15.2.0-11ubuntu1) Options: -O3   -funroll-loops -g3 -Wdate-time
-D_FORTIFY_SOURCE=3 -std=c++11 Sizeof {int, long, long long, void*,
size_t, off_t}: {4, 8, 8, 8, 8, 8}

64-bit, built on Debian, 21 January 2026, gcc version 15.2.0 (Ubuntu 15.2.0-11ubuntu1), and the Sizeof lineup for {int, long, long long, void*, size_t, off_t} is {4, 8, 8, 8, 8, 8} 🌟

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bestie reminder: this page is hisat2-inspect-s version 2.2.1 and it's dated January 2026 💖 go forth, inspect those indexes, you absolutely ate 💅✨🦋