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.
Just make it! The executables will live in the build directory.
There are three tools included in this package: sindex, sstat, and sfetch.
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 prints out summary metadata regarding the sequences contained in
an hsi-indexed FASTA file:
sstat [filename].fa
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 ith residue and ending at the jth residue (inclusive), use the command
sfetch -range i..j [filename].fa [sequence-name]