annotate srf2fastq/io_lib-1.12.2/man/man1/srf_index_hash.1 @ 0:d901c9f41a6a default tip

Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository

.TH srf_index_hash 1 "September 29" "" "Staden io_lib"

.SH "NAME"

.PP
.BR srf_index_hash
\- Adds a hash-table index to an SRF file.

.SH "SYNOPSIS"
.PP
\fBsrf_index_hash\fR  [\fI-c] \fIsrf_archive\fR

.SH "DESCRIPTION"
.PP
\fBsrf_index_hash\fR adds and index to an SRF file or replaces an
existing index with a new one. In the case of concatenated SRF files
only the index at the end of a file will be replaced, but internal
indices will not be consulted by SRF tools.
.PP
The index is a hash table indexing the sequence names only. The name
itself does not appear in the index, rather the top 7-bits of a 64-bit
hash key are held in the index along with N-bits used to determine the
hash bucket. This reduces the index size to around 10-15 bytes per
sequence.

.SH "OPTIONS"
.PP
.TP
\fB-c\fR
Check only. This requests that the index is not produced, but the
checks performed during the creation of an index (such as looking for
duplicate sequence names) are still performed.

.SH "AUTHOR"
.PP
James Bonfield, Wellcome Trust Sanger Institute