# Last edited on 2014-08-05 16:59:16 by stolfilocal
 
THE RAW NUCLEOTIDE SUBDIR

  The sub-directory "bas" contains samples of DNA sequences 

  250-base samples:

    The files 250A.bas and 250B.bas were created by hand.  They have an almost identical common segment.

    The file 250E.bas is a segment of 250 bases from Drosophila Simulans.  It is the reference sequence
    for the mutated versions 250E-in{NN}.bas and 250E-in{NN}.bas

  500-base samples:

    The files 500A.bas and 500B.bas were created by hand.  They have a "homologous" 
    part that covers about 80% of theor length.

  2500-base samples:

    The file 2500A.bas is the first 2500 bases from ../match/DSIM.bas (presumably
    /Drosophila simulans/ chromosome 4)

    The file 2500B.bas was created from 2500A.bas by replacing the first 800 bases and the last 800 bases
    by disjoint subsequences from the end of ../match/bas/DSIM.bas, respectively with 790 and 810
    bases.

    The file 2500C.bas was created from 2500B.bas by making small edits every 22 bases or so,
    with ../mutate_bas_lines.gawk 

  mutated versions:  

    The files {NAME}-mt{NN}.bas are copies of {NAME}.bas with a sequence of {NN} 
    consecutive bases replaced by arbitrary different bases.

    The files  {NAME}-in{NN}.bas are copies of NAME}.bas with a sequence of {NN} 
    consecutive bases inserted at some point.

FILTERED VERSIONS

  The filtered versions are in directory "eqs".  They were obtained as follows 

    tdir="${STOLFIHOME}/programs/c/JSLIBS/libdnaenc/tests/010_filter"
    ( cd ${tdir} && make -k all )
    fdir="${tdir}/out"
    seqs=( \
      100A \
      250A 250B 500A 500B 1500A 2500A 2500B 2500C  \
      500A-in01 500A-in02 500A-in04 500A-in08 \
      500A-mt01 500A-mt02 500A-mt04 500A-mt08 \
    )
    ls ${fdir}/*.eqs
    for seq in ${seqs[@]} ; do 
      if [[ -s ${fdir}/${seq}-ot-00.eqs ]]; then
        cp -avu ${fdir}/${seq}-ot-??.eqs eqs/ 
      fi
    done