`--USE_END_IN_UNPAIRED_READS` and `--USE_UNPAIRED_CLIPPED_END` options for `picard MarkDuplicates` have no effect about picard HOT 9 OPEN

@meganshand and @kockan, @ChrisHIV - unless you see a clear use case for single end reads (that are not of a constant length in bases) we will update the help string as suggested by the issue to indicate that it should only be used for flow reads

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Looks like those options are specific to flow-based reads, therefore they will not be used at all unless you also set --FLOW_MODE true in your command(s).

I've tried this with the example alignments you've provided and while it did run successfully, I'd recommend extra caution if you ever decide to use these options with non-flow-based single-end reads, since I'd assume they were not intended for such use.

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Thanks. Indeed using --FLOW_MODE on that test data, --USE_END_IN_UNPAIRED_READS changes which reads are duplicates. However, --USE_UNPAIRED_CLIPPED_END still has no effect and it's unclear to me to why: the description suggests that it toggles whether clipped ends are included or excluded, which I think should affect where reads are deemed to start and end, and thus affect which are considered duplicates.

Maybe helpful to add to the two help messages that --FLOW_MODE must be used? Also good to make the help clearer which of true/false corresponds to inclusion/exclusion of clipped ends for --USE_UNPAIRED_CLIPPED_END.

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I agree with adding clarification(s) to the documentation. I'll try getting more details on whether these options are safe to be used with non-flow single-end reads before closing the issue.

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perhaps there should be some error if those options are used without --FLOW_MODE turned on?

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Absolutely, if these are truly only meant to be used with flow-based reads.

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@meganshand @ilyasoifer tagging for opinions on this (and potentially similar issues with other options in this/other tools)

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@kockan - thanks! We will discuss and propose how to best deal with this.

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@ilyasoifer Sounds reasonable to me. One small additional request: if these options are set in the command-line arguments without --FLOW_MODE, we should throw an exception (edit: decided an exception would be better than a warning after some initial thought)

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