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Published 20 hours ago • verified publisher icon galaxyproject

picard_SortSam and sam_sort appear to be performing the same operation

Open jennaj opened this issue 9 years ago • 4 comments

Duplication is desired? This may be confusing for end users. Both samtools and picard are nearly always installed in locals as the first go-to tool packages.

jennaj avatar Jun 18 '15 02:06 jennaj

Do you really mean MergeSamFiles and sam_sort? I don't think duplication is desired and we should demultiplex tools into it's own repository, offering more suites that fits specific needs.

bgruening avatar Jun 18 '15 08:06 bgruening

Yes, both of these. And I like that idea. We pulled the problematic MergeSAMFiles from the upcoming cloudman build. The sam_sort is only problematic for the single tag and is across all tools I have tested that include it. It is not on Main, just MTS and now the cloudman build (for now).

jennaj avatar Jun 18 '15 19:06 jennaj

@jennaj I don't see were MergeSamFile do the same than sam_sort. The one is merging multiple BAM files and can accept multiple inputs the other one accepts one input and sorts it.

Do you mean the specific option: Assume the input file is already sorted? This can be removed I guess. If you are referring to this let me know and I will patch it.

bgruening avatar Jun 18 '15 19:06 bgruening

Ok, there are two duplicated tool pairs. This is one of them. Here is the other duplicated tool pair: #166

I guess MergeSAMFiles could be added back to the cloudman build since we determined root cause was with upstream tools (read group tag handling) and fixed it.

The "Assume the input file is already sorted" issue is also distinct. Removing it is one option. If we go that way, mentioning in the usage on the tool form to use one of these sort tools first (whichever we retain or wish to recommend) would be very helpful for users.

jennaj avatar Jun 19 '15 07:06 jennaj