#!/usr/bin/env perl

use strict;
use warnings;
use autodie;

my %search_terms;

{
    open my $search_terms_fh, '<', $ARGV[0];

    while (<$search_terms_fh>) {
        chomp;
        $search_terms{$_} = undef;
    }
} 

{
    open my $master_file_fh, '<', $ARGV[1];

    while (<$master_file_fh>) {
        my ($id, undef) = split ' ', $_, 2;
        print if exists $search_terms{$id};
    } 
}

##</code><code>##

$ cat pm_1170300_search_terms.txt
J00153:42:HC5NCBBXX:6:1101:10896:14959
J00153:42:HC5NCBBXX:6:1101:10896:14959
J00153:42:HC5NCBBXX:6:1101:26616:20709
J00153:42:HC5NCBBXX:6:1101:27549:19935

##</code><code>##

$ cat pm_1170300_master_file.txt
 J00153:42:HC5NCBBXX:6:1101:10896:14959	99	gnl|Btau_4.6.1|chr16	72729218	1	12M
J00153:42:HC5NCBBXX:6:1101:27549:19935	83	gnl|Btau_4.6.1|chr8	49556412	1	7M
 X00153:42:HC5NCBBXX:6:1101:10896:14959	99	gnl|Btau_4.6.1|chr16	72729218	1	12M
X00153:42:HC5NCBBXX:6:1101:27549:19935	83	gnl|Btau_4.6.1|chr8	49556412	1	7M

##</code><code>##

$ pm_1170300_hash_search.pl pm_1170300_search_terms.txt pm_1170300_master_file.txt
 J00153:42:HC5NCBBXX:6:1101:10896:14959	99	gnl|Btau_4.6.1|chr16	72729218	1	12M
J00153:42:HC5NCBBXX:6:1101:27549:19935	83	gnl|Btau_4.6.1|chr8	49556412	1	7M

##</code><code>##

#!/usr/bin/env perl

use strict;
use warnings;

use Benchmark qw{cmpthese};

my @keys = 'aa' .. 'zz';

cmpthese 1e5 => {
    a_inc => sub { my %hash; ++$hash{$_} for @keys },
    undef => sub { my %hash; $hash{$_} = undef for @keys },
    val_0 => sub { my %hash; $hash{$_} = 0 for @keys },
    val_1 => sub { my %hash; $hash{$_} = 1 for @keys },
    val42 => sub { my %hash; $hash{$_} = 42 for @keys },
};

##</code><code>##

$ pm_1170300_bench_undef_hash_value.pl; pm_1170300_bench_undef_hash_value.pl; pm_1170300_bench_undef_hash_value.pl; pm_1170300_bench_undef_hash_value.pl; pm_1170300_bench_undef_hash_value.pl
        Rate a_inc val_0 undef val42 val_1
a_inc 4129/s    --   -1%   -1%   -1%   -2%
val_0 4151/s    1%    --   -1%   -1%   -1%
undef 4188/s    1%    1%    --   -0%   -0%
val42 4191/s    2%    1%    0%    --   -0%
val_1 4198/s    2%    1%    0%    0%    --
        Rate a_inc undef val_1 val42 val_0
a_inc 4193/s    --   -2%   -2%   -2%   -2%
undef 4272/s    2%    --   -0%   -0%   -0%
val_1 4275/s    2%    0%    --   -0%   -0%
val42 4290/s    2%    0%    0%    --   -0%
val_0 4290/s    2%    0%    0%    0%    --
        Rate a_inc val_0 val_1 undef val42
a_inc 4228/s    --   -1%   -1%   -1%   -2%
val_0 4277/s    1%    --   -0%   -0%   -1%
val_1 4292/s    2%    0%    --    0%   -0%
undef 4292/s    2%    0%    0%    --   -0%
val42 4301/s    2%    1%    0%    0%    --
        Rate a_inc val_0 val_1 val42 undef
a_inc 4174/s    --   -1%   -2%   -2%   -2%
val_0 4207/s    1%    --   -1%   -1%   -1%
val_1 4239/s    2%    1%    --   -0%   -0%
val42 4243/s    2%    1%    0%    --   -0%
undef 4243/s    2%    1%    0%    0%    --
        Rate a_inc val_0 val_1 undef val42
a_inc 4239/s    --   -1%   -2%   -2%   -2%
val_0 4279/s    1%    --   -1%   -1%   -1%
val_1 4305/s    2%    1%    --   -0%   -0%
undef 4308/s    2%    1%    0%    --   -0%
val42 4316/s    2%    1%    0%    0%    --

##</code><code>##

#!/usr/bin/env perl

use strict;
use warnings;

use Benchmark qw{cmpthese};

my $string = ' J00153:42:HC5NCBBXX:6:1101:10896:14959   99  gnl|Btau_4.6.1|chr16    72729218    1   12M';

cmpthese 1e7 => {
    limit_undef => sub { my ($id, undef) = split ' ', $string, 2 },
    nolim_undef => sub { my ($id, undef) = split ' ', $string },
    limit_array => sub { my ($id, @rest) = split ' ', $string, 2 },
    nolim_array => sub { my ($id, @rest) = split ' ', $string },
};

##</code><code>##

$ pm_1170300_bench_split_limit.pl; pm_1170300_bench_split_limit.pl; pm_1170300_bench_split_limit.pl; pm_1170300_bench_split_limit.pl; pm_1170300_bench_split_limit.pl
                 Rate nolim_array limit_array nolim_undef limit_undef
nolim_array  346500/s          --        -68%        -68%        -77%
limit_array 1071811/s        209%          --         -2%        -29%
nolim_undef 1090513/s        215%          2%          --        -27%
limit_undef 1499250/s        333%         40%         37%          --
                 Rate nolim_array limit_array nolim_undef limit_undef
nolim_array  355492/s          --        -64%        -68%        -76%
limit_array 1000000/s        181%          --        -10%        -32%
nolim_undef 1107420/s        212%         11%          --        -24%
limit_undef 1461988/s        311%         46%         32%          --
                 Rate nolim_array limit_array nolim_undef limit_undef
nolim_array  346981/s          --        -68%        -69%        -76%
limit_array 1096491/s        216%          --         -1%        -24%
nolim_undef 1111111/s        220%          1%          --        -23%
limit_undef 1445087/s        316%         32%         30%          --
                 Rate nolim_array nolim_undef limit_array limit_undef
nolim_array  359195/s          --        -67%        -67%        -76%
nolim_undef 1089325/s        203%          --         -0%        -27%
limit_array 1092896/s        204%          0%          --        -27%
limit_undef 1492537/s        316%         37%         37%          --
                 Rate nolim_array nolim_undef limit_array limit_undef
nolim_array  362319/s          --        -68%        -68%        -76%
nolim_undef 1114827/s        208%          --         -1%        -26%
limit_array 1127396/s        211%          1%          --        -25%
limit_undef 1506024/s        316%         35%         34%          --