unclear/wrong argument description of uLTRA align in help about ultra HOT 4 CLOSED

Thank you for reporting! I will try to fix all this asap (hopefully over the weekend).

I will implement:

1. A parameter --prefix to set custom outfile name
2. A parameter --index for specifying index location.
3. Removal of temporary files
4. Update documentation

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So I implemented the above points 1-4. The new version (v0.0.3.2) is available to install with conda/pip.

For example

./uLTRA pipeline test/SIRV_genes.fasta  \
                 /path/to/test/SIRV_genes_C_170612a.gtf \
                 test/reads.fa outfolder \
                --prefix sample_X  \
                --index index

Will create and use the index located in folder index/, and the final aligned file will be created as outfolder/sample_X.sam. Temporary files are also deleted. If they are wished to be kept, this could be specified with option --keep_temporary_files.

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Looks great!

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Some small notes:

for ultra index

• the difference between "outdir" (Path to output folder) and "index" (Path to where index files will be written to [default is the outfolder path].) parameters is unclear, as this step should only prepare the index files, right?
• gtf is explained as "Path to gtf or gtf file with gene models." Should this be gff3 file?
• --disable_infer "Makes splice creation step much faster. Thes parameter can be set if gene and
  transcript name fields are provided in gtf file." Isn't this always the case? (and typo "Thes")

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