Aaron Quinlan comments

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                                            Aaron Quinlan

support CRAM input for genomecov

@38 could you have a look at this?

bamtobed can not open online references, it is the expected behavior?

Thanks for reporting this. @38 could you please have a look?

Suggested improvement for reldist

Thanks for these suggestions - will dig in and try to address this soon.

-n in makewindows sometimes makes the last bin to an extremely unequal size

This is a consequence of having to round fractional window sizes to an integer. For example, this interval's length is 3268 and dividing by 100 gives a window length of...

-n in makewindows sometimes makes the last bin to an extremely unequal size

@38 could you please have a look at updating the makewindows logic to follow the algorithm @jmarshall proposes above? The relevant function is here: https://github.com/arq5x/bedtools2/blob/master/src/windowMaker/windowMaker.cpp#L103 In the interest of backwards...

Error: Type checker found wrong number of fields while tokenizing data line.

Could you try cloning from master and testing with that version, as there are some unreleased improvements to the type checking?

Error: Type checker found wrong number of fields while tokenizing data line.

These errors suggest to me that you need to install the XCode Command Line tools, etc., as it seems your upgrade is missing standard C and C++ libraries.

Add aaf() option to --gt-filter

Isn't that for the allele frequency in a _single_ sample? What I meant to articulate was filtering based on the genotyped AF across all individuals meeting a specific phenotype.

bedtools sample is undocumented on RTD

Thank you for the reminder!

bedtools intersect: ERROR: Received illegal bin number -1 from getBin call.

@38 would you mind looking into this please?