BGS-TestNote.log

The testing of BGS software relies on comparison between 2BWT-Flex and BGS.
The basic flow of the test is:
1. Make sure latest object program is referenced under the directory ~/experiments/compareResult/.
2. Generate output file in 2BWT-Flex
3. Remove the strand indicator, to replace + and - with ?
4. Sort the output
5. Generate output file in BGS
6. Sort the output
7. Compare the output from step 3 and 5.

|----------------------------------
| Detail Procedure                |
|----------------------------------

% cd $LT; make
% cd $BWT; make
% cd ~/experiments/compareResult/
% rm *
% ln -s /home/mkewu/db/ncbi.genome.fa.index* .
% ln -s /home/mkewu/db3/ncbi.chr1.fa.index* .
% ln -s /home/mkewu/control/2bwt-flex/latest/2bwt-combined .
% ln -s /home/mkewu/control/2bwt-flex/latest/2bwt-combined.ini .
% ln -s /home/mkewu/control/2bwt-flex/latest/2bwt-viewer .
% ln -s /home/mkewu/control/gpubwt/latest/BGS-2M .
% ln -s /home/mkewu/control/gpubwt/latest/BGS-3M .
% ln -s /home/mkewu/control/gpubwt/latest/BGS-View .

!Pick the appropriate index and query
% export INDEX=ncbi.genome.fa.index
% export INDEX=ncbi.chr1.fa.index
% export QUERY=ACGT.100bp1M.fa
% export QUERY=ACGT.35bp1M.1113.fa

% ./2bwt-combined short $INDEX $QUERY -m 3 -h 2
% ./2bwt-viewer $QUERY ${QUERY}.combined.out > 2bwt.out
% cat 2bwt.out | sed 's/+[ \t]*$/?\t/g' | sed 's/-[ \t]*$/?\t/g' | sort > 2bwt.out2

% ./BGS-3M $INDEX $QUERY 1000000 100
% ./BGS-View $QUERY ${QUERY}.gout.1 >  bgs.out
% ./BGS-View $QUERY ${QUERY}.gout.2 >> bgs.out
% ./BGS-View $QUERY ${QUERY}.gout.3 >> bgs.out
% ./BGS-View $QUERY ${QUERY}.gout.4 >> bgs.out
% cat bgs.out | sort > bgs.out2
% diff2 2bwt.out2 bgs.out2