Couple of things that can be slightly improved in the SAM-to-BAM tool:
1. "Reference list" is not informative (it's the technical way to say: "list of 
chromosomes and their sizes based on a FASTA file").  Users do not generally 
know what "reference list" is.

2. The "Locally Cached" option is not informative (I had to look in the source 
code to understand what it means).
What it should say is something like: "Get list of chromosomes/sizes based on 
the dataset's organism/database" (could be shorter, but should be friendly 

3. There's no option of having the chromosome list in the SAM file header. Some 
SAM files will contain the header (can even be done in the standard bowtie tool 
wrapper) - saves the need to specify where to get the "reference list" from.

4. Autodetection in the "set-metadata" step will go a long way here: if the SAM 
file already have a header, then no need to even ask about it.
If it doesn't have a header but have a DBKEY, then we're still OK.
If no DBKEY and no header, then complain or ask for a FASTA file from current 
(I realize the implementing this feature is hard and annoying, I don't imply 
that it's easy to do, just that it's needed).

5. Inside the python script (sam_to_bam.py) there's a comment that says: "for 
some reason the samtools view command gzips the resulting bam file without 
warning" .
Not sure why one cares about that, but "samtools view -u" will output an 
uncompressed BAM file.

6. samtools support piping, so a lot of I/O (and some time) can be spared by 
piping the two commands together:
   samtools view -u -b -S "INPUT.SAM" | samtools sort - OUTPUT
Instead of running two commands and generating a temporary unsorted BAM file.


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