#!/usr/bin/bash

#Note:
#Program name has been changed from `pbalign.py` in version 0.1.0 
#to `pbalign` in 0.2.0, pseudo namespace pbtools has been removed also.

CURDIR=$TESTDIR
DATDIR=$CURDIR/../data
OUTDIR=$CURDIR/../out
STDDIR=$CURDIR/../stdout
SIVDIR=/pbi/dept/secondary/siv/testdata/pbalign-unittest
DATSIVDIR=$SIVDIR/data/
STDSIVDIR=$SIVDIR/stdout/

TESTDATASETS=/pbi/dept/secondary/siv/testdata/SA3-DS
REFDIR=/pbi/dept/secondary/siv/references

TMP1=$$.tmp.out
TMP2=$$.tmp.stdout
SAMTOM4=samtom4
CMPH5TOOLS="/mnt/secondary/Smrtanalysis/smrtcmds/bin/smrtwrap cmph5tools.py "