Typo in index usage
$ oa index --help
usage: oa index [-h] [--single] [--mate-pairs] [--check-ids]
[--max-read INDEX:MAXREAD] [--length INDEX:LENGTH]
[--estimate-length FRACTION] [--fasta] [--no-pipe]
[--forward-fasta] [--check-pairing] [--reverse-fasta]
index forward [reverse]
positional arguments:
index name of the produced index
forward Filename of the forward reads
reverse Filename of the reverse reads
optional arguments:
-h, --help show this help message and exit
--single Single read mode
--mate-pairs Mate pair library mode
--check-ids Checks that forward and reverse ids are identical
--max-read INDEX:MAXREAD
the count of million of reads to index (default the
full file)
--length INDEX:LENGTH
The length of the read to index (default indexed
length is estimated from the first read)
--estimate-length FRACTION
Estimate the length to index for conserving FRACTION
of the overall dataset
--fasta sequence files are fasta formated
--no-pipe do not use pipe but temp files instead
--forward-fasta forward file is a fasta file
--check-pairing ensure that forward and reverse files are correctly
paired
--reverse-fasta forward file is a fasta file
The last line should read:
--reverse-fasta reverse file is a fasta file
UPDATE: Actually corrected forward to reverse.
(I'm not sure why you need --fasta
plus --forward-fasta
and --reverse-fasta
)