Install HTSLib, so that include files are available under /usr/local/include and library file is available under /usr/local/lib. Make sure that those paths are in your search path.
Linux: from source and follow instructions
Mac: brew install htslib
Install Zlib
Linux: apg-get install zlib1g-dev
Mac:
either install developer tools with
xcode-select --install
or use Homebrew brew install zlib
Makefile is provided. make command will create an executable.
Tool: PASSFinder
Version: v0.01
Summary: Cluster PolyA supported sites from 3'End sequencing.
Usage:
PASSFinder [OPTIONS] -i/--input <bam/stdin> -m/--maskpoly <bed> -o/--output <bed/stdout>
Options:
-i/--input BAM/stdin file [required]
-o/--output BED/stdout file [required]
-m/--maskpoly BED/stdin file with genomic poly regions [required]
-w/--window sliding window size
-d/--depth minimum number of polyA reads to define PASS
-p/--polysize minimum number of As for tail and Ts for head to define poly stretch
-h/--help print help message
-v/--version print current version
Scientific Computing Facility @ Max-Planck Institute For Brain Research