Change default in RevertSam for restoring hard-clips to true #1509
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| @@ -155,8 +155,8 @@ | |||
| @Argument(shortName = "OBR", doc = "When true, outputs each read group in a separate file.") | |||
| public boolean OUTPUT_BY_READGROUP = false; | |||
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| @Argument(shortName = "RHC", doc = "Restore reads and qualities with hard-clips of records containing have XB and XQ tags.") | |||
| public boolean RESTORE_HARDCLIPS = false; | |||
| @Argument(shortName = "RHC", doc = "When false, does not attempt to restore reads and qualities of records with hard-clips containing XB and XQ tags.") | |||
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Not sure why changing this option to default to true would require changing the description to be in the negative form. Usually it's easier to understand if documentation is written in the positive
Suggested change
| @Argument(shortName = "RHC", doc = "When false, does not attempt to restore reads and qualities of records with hard-clips containing XB and XQ tags.") | |
| @Argument(shortName = "RHC", doc = "When true, attempt to restore reads and qualities of records with hard-clips containing XB and XQ tags.") |
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@pshapiro4broad back to you |
pshapiro4broad
approved these changes
May 15, 2020
2 tasks
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