README update, confused about output

[evanbiederstedt]

Hi everyone,

Thanks for the excellent tool!

(1) Could you update the README so the --prefix flag isn't shown? I missed the note above following the examples; it would help productivity if you just created a "legacy code" section or eliminate all references to --prefix all together

(2) I'm a bit confused, as it appears that I do not have an output for bwameth.py --reference ref.fa t_R1.fastq.gz t_R2.fastq.gz -t X.

When running this command, I see the output using bwa mem with the last item as NA. Normally, if I were to use bwa mem alone, I would pipe this to an output. When running bwameth.py --reference ref.fa t_R1.fastq.gz t_R2.fastq.gz -t X as in the example https://github.com/brentp/bwa-meth/tree/master/example/, how exactly do I access the output?

[brentp]

I updated the readme. I'm not sure I understand (2).

If I do:

cd examples/
python ../bwameth.py --reference ref.fa t_R1.fastq.gz t_R2.fastq.gz -t 5 > s.sam
samtools view -b s.sam > s.bam

I see no problems, and I get a sam and then bam file with the expected output. Can you clarify the problme that you are having?

[evanbiederstedt]

Sorry---I could have been more clear myself.

I think the example in https://github.com/brentp/bwa-meth/tree/master/example/ is unclear for those uninitiated with the underlying bwa mem code outputting to stdout.

In the tutorial, you show

bwameth.py index ref.fa
bwameth.py --reference ref.fa t_R1.fastq.gz t_R2.fastq.gz -t 12

It might be more useful for first time users to show this

bwameth.py index ref.fa
bwameth.py --reference ref.fa t_R1.fastq.gz t_R2.fastq.gz -t 12 > myfile.sam

Right? Otherwise users just running a python script may expect an output file in whichever subdirectory they're running the script.

[brentp]

updated. thanks.

[evanbiederstedt]

Thanks for the help!