├── .gitattributes ├── .gitignore ├── LICENSE ├── README.md ├── bwameth.py ├── compare ├── README.md ├── cmp-bis2.sh ├── common.sh ├── data │ ├── mm10.capture-regions.bed.gz │ ├── real-quals.txt │ ├── real-trim-quals.txt │ ├── sim-quals.txt │ └── sim-trim-quals.txt ├── plots.sh ├── run-bis1.sh ├── run-bis2.sh ├── run-bison.sh ├── run-bsmap.sh ├── run-bsmooth.sh ├── run-bwa.sh ├── run-gnumapbs.sh ├── run-gsnap.sh ├── run-last.sh ├── search-bis2.sh └── src │ ├── bsmooth-adjust-crick.py │ ├── extract-read.py │ ├── gen-simulated.sh │ ├── gsnap-meth.py │ ├── last-bisulfite-paired.sh │ ├── parse-time-mem.py │ ├── plot-quals-bw.R │ ├── plot-quals.R │ ├── sim-roc.py │ ├── target-roc.py │ └── trim.sh ├── example ├── README.md ├── ref.fa ├── t_R1.fastq.gz ├── t_R2.fastq.gz └── test.sh ├── ez_setup.py ├── paper ├── Makefile ├── bioinfo.cls ├── document.bib ├── document.tex ├── natbib.bst ├── natbib.sty ├── noerrorsim-quals.eps ├── noerrorsim-trim-quals.eps ├── real-bwa-strand.eps ├── 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