HSI (Hex-encoded Sequence Indexer)

About

This is my personal branch of the super-lightweight sequence indexing program that I developed for use in Mirage2 and Diviner.

The main reason for moving this from the Wheeler Lab repo is just to have a version that uses make rather than cmake.

Setup

Just make it! The executables will live in the build directory.

Usage

There are three tools included in this package: sindex, sstat, and sfetch.

sindex

sindex is used to create a .hsi index on a FASTA-formatted sequence file. Running

sindex [filename].fa

will create an index file named [filename].fa.hsi

sstat

sstat prints out summary metadata regarding the sequences contained in an hsi-indexed FASTA file:

sstat [filename].fa

sfetch

sfetch is used to extract a sequence (or part of a sequence) from an hsi-indexed FASTA file. To extract the full contents of a sequence, use the command

sfetch [filename].fa [sequence-name]

To extract a subsequence beginning at the i^th residue and ending at the j^th residue (inclusive), use the command

sfetch -range i..j [filename].fa [sequence-name]