ok 1 - ANDmask ok 2 - unpackM Rate u950 u1050 u900 u1100 u1000 A950 A1050 A1100 A900 A1000 u950 1.28/s -- -0% -0% -1% -1% -39% -39% -39% -39% -41% u1050 1.28/s 0% -- -0% -0% -1% -39% -39% -39% -39% -41% u900 1.28/s 0% 0% -- -0% -1% -39% -39% -39% -39% -41% u1100 1.28/s 1% 0% 0% -- -1% -39% -39% -39% -39% -41% u1000 1.29/s 1% 1% 1% 1% -- -38% -38% -39% -39% -40% A950 2.10/s 65% 64% 64% 64% 62% -- -0% -0% -0% -3% A1050 2.10/s 65% 64% 64% 64% 63% 0% -- -0% -0% -3% A1100 2.10/s 65% 64% 64% 64% 63% 0% 0% -- -0% -3% A900 2.11/s 65% 65% 65% 64% 63% 0% 0% 0% -- -2% A1000 2.16/s 69% 69% 69% 68% 67% 3% 3% 3% 2% -- 1..2 ##

##

use strict;
use warnings;

use Benchmark  qw{ cmpthese };
use Test::More qw{ no_plan };

open my $inFH, q{<}, \ <<__EOD__ or die $!;
TATCGC.TGCCC.ATTAAGCCATACTTCAAGGATCCCCCCG.GA.GGGCA
GGAGTCGTC.ACACATCTTCACTAC.CATATCTTGCTACGGCCACTGACA
CGA.A.CAATTTTCGAATGGAGGGCGAATGCCGTTGTGCGCTGCGTGACG
TCT.AGCCT.CGAA.A.GCAGGCGTGGGGCGTACCACGGCTTGGCCTAT.
ATGCACTT.AA.CCCTCGTAT.CTCTACTCT.ACAACCTTGGGCAG.T.T
TAGGGC.CCGCG.TAAACTGCAGATAGTACTCCAAGAATCGCTCCGACCC
.CGTCTAAACAATTAGCGGAGGTCGTC.CTGCAA.CAATGATCTTAACAC
AG.AAGAAGT.CAAAGT.GTAGTGGCTGGGTACTTGATCA.TCAATTTCA
ACC.TTCCAG.AAATGAGGTCTC.AAAAG.AGTT.CCTG.GGCTGTGTAG
ACAT.A.TGTTAACACCACCTATAATAGAAGC.TTATATTCACC.TTAAC
GAATTGT.TTCAATGCCACATA.GCTGGGCCAC.GCCTTAGGCTATTT.A
AGCTTTACAGATGT.ACCAAA.CCAG.GACTAGATGGGGGGG.ATATGCC
AGAAAGCCC.TCCCTGCGAAT.TGGGGGAGTACT.ATAGACTA.GGCCAG
.CACTCCGG.CTAACACTACTTCCTGTAACAAA.CTGAAGAGA.CGTTTG
CAGTCCTGAGCGTGCTAC..GTTCT.CTGTCG.TTAGATGGGCGC..GTA
AGCAAGAAAACACGTACAGAAAAAGCCGACGGC.GGGGTTC.GTCAACC.
T.ACTTATCGACATTAGCATCTGG.TGCCGCCTTT.GAACCCATTACTCG
TAAACGA.CACCGCTTAGGGCTGACCTCCGAA.TTATCAGAGTACCGGGC
ACGGATATCCTA.ATAGA.TACCTATGTAGGAAG.TCGAACTC.TAAACT
ACCCCCGTCC.TATCCTC.CGA.ATTGCCCCCGGCCGTACTCCA.AAACC
T..TC.AGCCGGG.TTG.TGTGGATCAGAAGTGATTGAGACTGG.GCCTA
TCAACCTTGAAGTTGAAACTCCGAGAGT.CGCGGTCAACC.AGCCTGCGC
GATCAGTGAGGAGCTGT.C.AAAGC.TC.AG.GCC.G.GA.GTGAGATT.
G.C.AGTTTGCCACTT.CATCCAGAGTTCATCCAGCAGG.ATTGAAGTTA
GCGCTGCA.CTGT.CATTTTTTATTCCCACCCGGTCTCCCCAACCCCGAT
TGTATAGCCAGG.CGGAG.TTTCTT.TAGATCTAGTAAGACATT.CCCGA
AC.CCCCT.G.TAGCTAAATCGACGGG..GTCAATATACACGGAT.CTTT
AAGC.GGGCTGATGCTTATCTCCTAGCCCGC.CCTCGATGAT.ATTATTG
TCACCC.ACCGC..T.CGGAACGAAAACT..AT.CCTATTAGAACATCCT
.GCGTGAACC.TG.G.TACACCG.GATGGTCCCGAC.GGCTACCGAT.CA
.CGCTGCCCCCATCTCCAGCTATC.AAA.AGGGACGCGATATGCGGAAGC
CGTTCAGACAATCCTTTTGGGGTGTAAATGTCTCC.ACCTC.GAGA.CTG
AAGACATAGGAG.CCAGAAT.A.CGTCATACAGAGGCACTC.TAT..TCT
AGGCCTGCCTACTT.TTGGCTAA.C.AGACTTGG.AAG.ATGTAGAAC.G
GTCAACCCGTGCTAACTGGGGTGAGGAATCTTCCGAGCC.TGCTCGTCGC
TCG.TGGCAGCTC.AACTGGTGCGCGGCAG.CCTCCTGCCAAGTATTCAG
CGGGGGCTAC..GTT.TCATCGAACACGGCACACTAACAAACTCCTGTGT
TTCCGGGGTCGACCCTTTGGCCCAAGAGTGA.AGGGCTTCG.ACTGCG..
AA.CGTGCGGGTAGCCTAGACACGTAGC.TTGTGCGC.CG.CGCA.CAAG
AT.TATGTCA.ACTTCCGCCGGG.CTTCTGTGTACATT.AA.GAGAATAA
CGGCAAGGATTGCTCGACGTAGGAGTCCGTGGAGCTCGTGC.GACC.ACC
.GTTAA.CACGCCTTAACTTTTCGGAACAGAGTAAC.AATCCCGG.TA.C
CAGGTAATGTGTCACCAGGTTCGGGCCCT.CACCGTCCCAGCTAC.TGTT
TAGCCCCTCTTTT.GAT.GGCCC.AGCGACATCAA.TGATC..CTGTAGG
CGATCATATTTCATTGTTCCGC.TG.AGCGGT.A.TG.GCAAT.CAGCCG
ATCGATGTTCTGATATG..GTGTGAATAC.AGAAACCGGCTTTGTCGGGG
CCTTT.AGGAA.AC.TAGGT.TT.CTCAATGAAC.GACATCAAC.T.AGC
AAGGAGGTACACAGCGTTCAGCGGATCC.CT.AAGC.TAGCATCTGCTGA
GCAGATA.A.TCTGCTTCAACTGTGAAAGGGTTG.CTAATCAG.GCGTAG
GGTACGATC.GCAAC.AGTCCACAAGTACACGGTGGAATT.CC..C.TTG
__EOD__

my $fileStart = tell $inFH;

my $offset = 9;    # Column 10 if numbering from 1

my $testOK = q{C.T.AGCTGTTG..GAGACCCAGGCAGTCCCAGTTGCCGATCTTTCAC..};

my %methods = (
   unpackM => sub { # Multi-line unpack suggested by LanX
       seek $inFH, 0, 0;

       my $buffer     = <$inFH>;
       my $lineLen    = length $buffer;
       my $nLines     = shift;
       my $chunkSize  = $lineLen * $nLines;

       seek $inFH, 0, 0;

       my $retStr;
       my $fmt = qq{(x${offset}ax@{ [ $lineLen - $offset - 1 ] })*};
       while ( my $bytesRead = read $inFH, $buffer, $chunkSize )
       {
           $retStr .= join q{}, unpack $fmt, $buffer;
       }

       return \ $retStr;
   },
   ANDmask => sub { # Multi-line AND mask by johngg
       seek $inFH, 0, 0;

       my $buffer     = <$inFH>;
       my $lineLen    = length $buffer;
       my $nLines     = shift;
       my $chunkSize  = $lineLen * $nLines;

       seek $inFH, 0, 0;

       my $retStr;
       my $mask
          = qq{\x00} x ${offset}
          . qq{\xff}
          . qq{\x00} x ( $lineLen - $offset - 1 );
       $mask x= $nLines;
       while ( my $bytesRead = read $inFH, $buffer, $chunkSize )
       {
           ( my $anded = $buffer & $mask ) =~ tr{\x00}{}d;
           $retStr .= $anded;
       }

       return \ $retStr;
   },
   );

foreach my $method ( sort keys %methods )
{
    ok( ${ $methods{ $method }->( 20 ) } eq $testOK, $method );
}

close $inFH or die $!;

my $filename = q{spw1202693.txt};
open $inFH, q{<}, $filename
   or die qq{open: < $filename: $!\n};

cmpthese(
   -15,
   {
       map
       {
           my $method = $_;
           map
           {
               my $nLines = $_;
               my $label  = substr( $method, 0, 1 ) . $nLines;
               my $codeStr
                  = q[sub { my $col = $methods{ ]
                  . $method
                  . q[ }->( $nLines ); }];
               $label => eval $codeStr;
           }
           900, 950, 1_000, 1_050, 1_100
       }
       keys %methods
   }
   );

close $inFH
   or die qq{close: < $filename: $!\n};