Ryan Dale
Ryan Dale
This PR should not be merged into master. It is used as a mock branch that simulates the master branch, in which the circleci config has been modified to build...
Each of the example hubs that demonstrate the different kinds of track types have data that are on different chromosomes. These should either be moved (e.g., by downloading the example...
Decide if it would be useful to support cWig format http://bioinformatics.oxfordjournals.org/content/30/18/2543.full.html?etoc They report substantial query time improvements; could be useful for parallel array construction. They provide Python API via SWIG.
## Integration with other packages If `pybedtools.pkg_integration = True`, then: 1. Iterating over SAM or BAM yields `pysam.AlignedRead` objects 2. Iterating over VCF yields `cyvcf2.Variant` objects 3. (?) Iterating over...
`BedTool.genome_coverage` sometimes returns bedGraph-like output, sometimes not. In fact, by default, it doesn't return a valid BED-ish format file. See #110, #111, #112. _note to future self: this prob needs...
For streaming intersections of moderate-sized files (say, >5000 features), the following blocks:: ``` z = a.intersect(b, stream=True).intersect(c, stream=True) len(z) ``` The schematic below shows what's happening with stdin/stdout and pipes....
Imagine we have two bed files, and we do this: ``` python z = x.intersect(y, wao=True) ``` The resulting file could look like this, is incorrectly guessed to be SAM...
Add something like https://github.com/daler/pybedtools/issues/110#issuecomment-206353849 to `BedTool` to streamline working with 'coverage'-format files.
This takes the ideas from the code review on #953 and simplifies by refactoring how everything is configured. See https://github.com/bioconda/bioconda-utils/pull/953#issuecomment-1958104290 for the specific proposed items, which are addressed here. The...