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genomedensity's Introduction

Density of events around objects

== Build ==

$ make

or

$ make DEBUG=1

== Run ==

# bin size: 100bp
# number of bins either side of objects: 200

$ ./density_around 100 200 objects.csv events.csv

== Notes ==

Convert ensGene.txt to .bed file:

> awk '{print $3"\t"$5"\t"$6"\t"$4}' ensGene.txt > ensGene.bed

== Development ==

Short term goals
- none - please suggest some

long term
- add binary search ?
  * sort start positions
  * sort end positions
  * binary search to find start position in both arrays when looping
- probably not -- performance is very good

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