Nim Program to split bed files based on a maximum read count in each interval for a given bam file.

This program loops through all the reads in the regions. If exact counts are not needed take a look at split_bed_by_index which makes estimates using the bam index and is almost instantaneous.

Installation:

Install nim and compile nim script

curl https://nim-lang.org/choosenim/init.sh -sSf|sed "s/need_tty=yes/need_tty=no/g" | sh
export PATH=$HOME/.nimble/bin:$PATH

export PATH=${OPT_DIR}/.nimble/bin:$PATH
nimble install -y https://github.com/papaemmelab/split_bed_by_reads --nimbleDir:${OPT_DIR}/.nimble

Download the binaries:

wget -O ${BIN_DIR}/split_bed_by_reads https://github.com/papaemmelab/split_bed_by_reads/releases/download/0.1.0/split_bed_by_reads && \
chmod +x ${BIN_DIR}/split_bed_by_reads
export PATH=${BIN_DIR}:$PATH

Usage:

Split bed intervals by maximum read counts

Usage:
  split_bed_by_reads [options] <BED> <BAM> <OUT>

Arguments:
  <BED>     Input bed file
  <BAM>     Input bam file
  <OUT>     Output bed file

Options:
  -h --help                 Show this screen.
  -v --version              Show version.
  -t --threads <threads>    Number of BAM decompression threads [default: 4]
  -c --count <count>        Number of reads to split  [default: 1000000].

Credit

• Max Levine @mflevine
• hts-nim-tools by Brent Pederson @brentp