Add flag to keep zero length intervals when converting bed -> interval_list #1928
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kockan
approved these changes
Dec 15, 2023
| @@ -107,9 +107,13 @@ public class BedToIntervalList extends CommandLineProgram { | |||
| @Argument(doc = "If true, entries that are on contig-names that are missing from the provided dictionary will be dropped.") | |||
| public boolean DROP_MISSING_CONTIGS = false; | |||
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| @Argument(doc = "If true, write length zero intervals in input bed file to resulting interval list file.") | |||
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Should we say "zero-length intervals" instead of "length zero intervals". I know it's not critical, just for the sake of consistency
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I actually like "length zero" better than "zero length" so I switched the labelings everywhere to make it consistent.
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Description
This PR is a follow-up to the discussion in #1914. In particular, it implements a boolean flag
KEEP_ZERO_LENGTH_INTERVALSfor theBedToIntervalListtool, and sets the default tofalse. This means that if the input bed file has length 0 intervals, e.g.chr1 1000 1000, they will be skipped in the.interval_listoutput file, unless the flag is manually toggled totrue. Note this will change default behavior from previous versions, but based on the discussion there seems like a very sensible default.A new test was added to test the functionality, and previous tests were modified to toggle this flag to true to ensure that existing tests meant to ensure length zero intervals were properly handled are still handled correctly when the flag is turned on.
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