--only-download-trimmed-reads will be broken after ReadTools integration

[magicDGS]

If the reads are trimmed on upload after #53, the --only-download-trimmed-reads won't work any longer. There are several options:

• Remove support for the option: the user can trim locally if he wants the reads, and then upload; or perform the whole pipeline and get the reads after mapping, converting back to FASTQ using ReadTools/Picard.
• Add reading support in ReadTools for distmap format. The format will be detected by extension (.distmap, and .tfq after https://github.com/magicDGS/ReadTools/issues/404). Then, download can be done by just calling any of the "Reads conversion" tools to download as FASTQ or standardized SAM/BAM/CRAM.
• Download using custom scripts to read the format. For .tfq will be an easy one-liner; for legacy format, it will require a python/perl script (I think that already implemented)

I am in favor of removing, but it is your decision @robmaz!

[magicDGS]

Actually, in #76 I detected that the option is not documented, although in the Wiki is. What should we do with it?

[robmaz]

Die when anyone tries to use it and print an "OBSOLETE: Hasn't worked for a while." message?

2018-02-27 14:35 GMT+01:00 Daniel Gómez-Sánchez notifications@github.com:

Actually, in #76 https://github.com/robmaz/distmap/pull/76 I detected that the option is not documented, although in the Wiki is. What should we do with it?

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[magicDGS]

I would do that. In addition, I would document in the help adding a short-note saying that because trimming is done while uploading, the user can trim locally if they require the trimmed unmapped reads; otherwise, the mapped files would be trimmed and can be converted to FASTQ using ReadTools or picard.