Python code for analysis of ChIP-seq and RNA-seq data.

* DATA SOURCES FOR HMM
- OMP meDIP (eventually)
- Ngn meDIP (eventually)

- OMP hmeDIP 
- Ngn hmeDIP
- ICAM hmeDIP

- OMP mk4
- Ngn mk4

- OMP mRNA-seq
- Ngn mRNA-seq

* DATA SOURCES FOR CORRELATION
- transcript (knownGene)
- gene (kgXref)
- PhastCons 30way align (phastCons30Way)
- GC content (gc5Base)
- CpG island (cpgIslandExt)
- repeat (simpleRepeat)

* DATA MODEL
Each row is a 100 bp window of the genome.
WindowRow:
    - chr (int)
    - start (int)
    - end (int)
    - omp_expressed (binary)
    - ngn_expressed (binary)
    - omp_hmedip (int)
    - ngn_hmedip (int)
    - icam_hmedip (int)
    - omp_mk4 (int)
    - ngn_mk4 (int)
    - tss_dist (int) [-2kb..2kb] or INF
    - tse_dist (int) [-2kb..2kb] or INF
    - exon_start (binary)
    - coding_seq (binary)
    - in_gene (binary)
    - in_exon (binary)