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 # PASSFinder
-cluster PolyA supported sites from 3'End sequencing
+
+## Dependancies
+
+### [htslib](https://github.com/samtools/htslib)
+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```
+
+### [zlib](https://zlib.net/)
+Install Zlib
+
+Linux: ```apg-get install zlib1g-dev```
+
+Mac: 
+
+either install developer tools with
+```xcode-select --install```
+
+or use Homebrew ```brew install zlib```
+ 
+
+
+## Help
+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
+	
+## Bug reports
+Scientific Computing Facility @ Max-Planck Institute For Brain Research
+
+<sciclist@brain.mpg.de>