GatherVcfs and MergeVcfs: add COMMENT= + GatherVcfs SORT #1480
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| @Argument(doc = "Comment(s) to include in the merged output file's header.", optional = true, shortName = "CO") | ||
| public List<String> COMMENT = new ArrayList<>(); | ||
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| @Argument(doc = "Re-order the INPUT files according to order of their first variant.", optional = true, shortName = "S") |
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This documentation is unclear...I needed to read the code to understand what you mean.
Explain that the program will assume that the variants in the files come from non overlapping regions, but that while each file is itself sorted, the order that the files are provided in is not to be trusted. If TRUE, instead of sorting all the variants, the program will concatenate the variants from the files using the order of the first variant in each file as the order of the files.
Also, "SORT" is not a good name, since it's is used elsewhere to mean that the outputs will be sorted....I suggest you use REORDER_INPUT_BY_FIRST_VARIANT
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@yfarjoun I got time to return to this PR. I fixed things according to your comments, and I hope the formatting is fixed now (eclipse... ) |
Co-authored-by: George Grant <[email protected]>
Co-authored-by: George Grant <[email protected]>
Co-authored-by: George Grant <[email protected]>
braces Co-authored-by: George Grant <[email protected]>
added spaces Co-authored-by: George Grant <[email protected]>
added spaces Co-authored-by: George Grant <[email protected]>
add spaces Co-authored-by: George Grant <[email protected]>
add spaces Co-authored-by: George Grant <[email protected]>
added spaces Co-authored-by: George Grant <[email protected]>
rename sort->reorder Co-authored-by: George Grant <[email protected]>
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Looks good. @lindenb could you update this with the latest master? |
Description
GatherVcfs and MergeVcfs are often my last steps in the workflow; This is the moment where I wish I could add a comment in my VCFS.
Here I added a an option
COMMENT=for both commands.Furthermore, I added an option
SORTto GatherVcfs to avoid sorting my VCF according to the dictionary. if SORT=true, the first variant of each VCF is extracted and we use those variants to sort the INPUT.I updated the test and fixed a one or two resource leak.
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