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Make captureRegionsBedFile optional
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Thomas Kuilman committed Aug 19, 2014
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Expand Up @@ -79,13 +79,13 @@ Minor bugs
# Changes and additions we are currently working on

- [ ] Extract binSize from bins.bed file
- [ ] Make captureRegionsBedFile optional
- [ ] Different input structure to indicate which bam files should be used as controls
- [ ] Change from MACS 1.4 to other ChIP seq tool available in R (chipseq from bioconductor?)
- [ ] Change from Samtools to Rsamtools
- [ ] Remove all unix specific functions and commands
- [ ] Clean up code
- [ ] Compile into bioConductor package
- [x] Make captureRegionsBedFile optional
- [x] Allow processing of single-end sequences
- [x] Increase speed for generating bins in `preENCODER`

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