#add fPIC to the MOREFLAGS in the Makefile, run make, then run these:
export LD_LIBRARY_PATH=..//lib
gcc -shared -fPIC -L ../lib zstd_zlibwrapper.o gzclose.o gzlib.o gzread.o gzwrite.o -lz -lzstd -o zstd_preload.so

nm -D zstd_preload.so

#in gdb
set environment LD_PRELOAD /home/cwilks/zstd-1.3.3/zlibWrapper/zstd_preload.so
set exec-wrapper env 'LD_PRELOAD=/home/cwilks/zstd-1.3.3/zlibWrapper/zstd_preload.so'


#add redirection methods
cat zstd_zlibwrapper.c | perl -ne 'chomp; $s=$_; if($s=~/ZEXTERN int ZEXPORT z_/) { $P=1; $s1=$s; $s1=~s/ZEXTERN int ZEXPORT z_/ZEXTERN int ZEXPORT /; print "$s1\n"; @f=split(/\s+/,$s); $s1=~/ZEXTERN int ZEXPORT ([^ ]+) /; $func=$1; $nl = "return z_$func("; for($i=5; $i<scalar(@f);$i+=2) { $nl.=" " if($i>5); $f[$i]=~s/\*//g; $f[$i]=~s/\)\)/\)/; $nl.=$f[$i]; } if($s=~/\)\s*$/) { print "{\n\t$nl;\n}\n"; $P=undef;} next;} if($P) { print "$s\n"; @f=split(/\s+/,$s); for($i=1; $i<scalar(@f);$i++) { if($f[$i]=~/[,\)]/) { $f[$i]=~s/\*//g; $f[$i]=~s/\)\)/\)/; $nl.=" ".$f[$i]; }} if($s=~/\)\s*$/) { print "{\n\t$nl;\n}\n"; $P=undef;} }' > redirections.add


#run this with normal bgzip (zlib)
rsync -av /data/test15.fq.10000000 /data/test15.fq.10000000.1
time LD_PRELOAD=/home/cwilks/zstd-1.3.3/zlibWrapper/zstd_preload.so ./bgzip /data/test15.fq.10000000.1


time cat /data2/test15.fq.bgzs | LD_PRELOAD=/home/cwilks/zstd/lib/zstd_preload.so bgzip -d


cat /data/h1_intervals.tsv | LD_PRELOAD=/home/cwilks/zstd/lib/zstd_preload.so bgzip > /data2/h1_intervals.tsv.bgzs
#doesn't work due to missing magic number?
LD_PRELOAD=/home/cwilks/zstd/lib/zstd_preload.so tabix -s2 -b3 -e4 /data2/h1_intervals.tsv.bgzs


for gdb debugging, after startup:
set environment LD_PRELOAD /home/cwilks/zstd/lib/zstd_preload.so
gdb --args env LD_PRELOAD=/home/cwilks/zstd/lib/zstd_preload.so tabix -s2 -b3 -e4 /data2/h1_intervals.tsv.bgzs


LD_PRELOAD=/home/cwilks/zstd/lib/zstd_preload.so tabix /data2/h1_intervals.tsv.bgzs chr1:11845-12009