GDB_CMDS=gdb-cmds.tmp
FASTA=../fasta/test.fa
ARGS="$FASTA \
        -oc output/meme-output \
        -dna \
        -mod anr \
        -nmotifs 1 \
        -w 10 \
        -revcomp \
        -nomatrim \
        -spmap uni -spfuzz 0.5"

cat <<EOF >$GDB_CMDS
file /home/john/local/bin/meme_d.bin
set breakpoint pending on
#b main
#b subseq7.c:262
#b create_spoint_matrix
b init_theta_1
#b get_pY
#b get_max
#b score_llr_pop
#b init.c:832
#commands
#b get_llr_pv
#c
#end
run $ARGS
EOF

gdb -x $GDB_CMDS && rm $GDB_CMDS

