#########################################################################
# LASTZ Malayan flying lemur galVar1 tree shrew tupBel1- (DONE - 2016-04-25 - Hiram)
    mkdir /hive/data/genomes/galVar1/bed/lastzTupBel1.2016-04-25
    cd /hive/data/genomes/galVar1/bed/lastzTupBel1.2016-04-25

    printf "#  Malayan flying lemur vs tree shrew
BLASTZ=/cluster/bin/penn/lastz-distrib-1.03.66/bin/lastz
BLASTZ_M=254 

# TARGET:  Malayan flying lemur galVar1
SEQ1_DIR=/hive/data/genomes/galVar1/galVar1.2bit
SEQ1_LEN=/hive/data/genomes/galVar1/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LIMIT=800
SEQ1_LAP=10000

# QUERY: Tree shrew tupBel1
SEQ2_DIR=/hive/data/genomes/tupBel1/tupBel1.2bit
SEQ2_LEN=/hive/data/genomes/tupBel1/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LIMIT=1000
SEQ2_LAP=0

BASE=/hive/data/genomes/galVar1/bed/lastzTupBel1.2016-04-25
TMPDIR=/dev/shm
" > DEF
    # << happy emacs

    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
        -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > do.log 2>&1
    # real    1032m29.536s

    cat fb.galVar1.chainTupBel1Link.txt
    # 1163275671 bases of 2802917674 (41.502%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` galVar1 tupBel1) \
        > rbest.log 2>&1 &
    # real    129m31.676s

    # and for the swap:
    mkdir /hive/data/genomes/tupBel1/bed/blastz.galVar1.swap
    cd /hive/data/genomes/tupBel1/bed/blastz.galVar1.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/galVar1/bed/lastzTupBel1.2016-04-25/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    386m50.217s

    cat fb.tupBel1.chainGalVar1Link.txt
    #  1088845329 bases of 2137225476 (50.947%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` tupBel1 galVar1) \
            > rbest.log 2>&1
    # real    183m49.967s

#########################################################################