#!/usr/bin/env bash

# this must be run into an active git repository

ver=$(fgrep '#define VERSION ' stringtie.cpp)

ver=${ver#*\"}

ver=${ver%%\"*}

pack=stringtie-$ver

echo "preparing $pack.tar.gz"

echo "-------------------"

/bin/rm -rf $pack

/bin/rm -f $pack.tar.gz

mkdir $pack

mkdir $pack/gclib

cd samtools-0.1.18

make clean

cd ..

# getting a clean SuperReads_RNA directory

srm=SuperReads_RNA

if [[ -d $srm ]]; then

mv $srm $srm.prepping

git checkout -- $srm

mv $srm $pack/

mv $srm.prepping $srm

fi

gldir=stringtie-$ver/gclib/

cp Makefile LICENSE README.md run_tests.sh stringtie.cpp prepDE.py prepDE.py3 {rlink,tablemaker,tmerge}.{h,cpp} $pack/

cp -r samtools-0.1.18 $pack/

/bin/rm -rf $pack/samtools-0.1.18/.svn

cp ./gclib/{GVec,GList,khashl,GHashMap}.hh ./gclib/GBitVec.h ./gclib/xxhash.h $gldir

cp ./gclib/{GArgs,GStr,GBam,GBase,gdna,codons,gff,GFaSeqGet,GFastaIndex,proc_mem,GThreads}.{h,cpp} $gldir

tar cvfz $pack.tar.gz $pack

ls -l $pack.tar.gz