<commit_before>package illumina_baseRecal;

use FindBin;
use lib "$FindBin::Bin";
use discipline;

use File::Basename;
use File::Spec::Functions;

use illumina_jobs qw(bamOperationWithSliceChecks);


sub runBaseRecalibration {
    my ($opt) = @_;

    say "\n### SCHEDULING BASERECALIBRATION ###";
    say "Running base recalibration for the following BAM-files:";

    my $known_files = "";
    $known_files = join " ", map { "-knownSites $_" } split '\t', $opt->{BASERECALIBRATION_KNOWN} if $opt->{BASERECALIBRATION_KNOWN};

    foreach my $sample (keys %{$opt->{SAMPLES}}) {
        bamOperationWithSliceChecks("BaseRecalibration", $sample, $known_files, "recalibrated", "recal", $opt);
    }
    return;
}

1;
<commit_msg>Fix executable bit<commit_after>package illumina_baseRecal;

use FindBin;
use lib "$FindBin::Bin";
use discipline;

use File::Basename;
use File::Spec::Functions;

use illumina_jobs qw(bamOperationWithSliceChecks);


sub runBaseRecalibration {
    my ($opt) = @_;

    say "\n### SCHEDULING BASERECALIBRATION ###";
    say "Running base recalibration for the following BAM-files:";

    my $known_files = "";
    $known_files = join " ", map { "-knownSites $_" } split '\t', $opt->{BASERECALIBRATION_KNOWN} if $opt->{BASERECALIBRATION_KNOWN};

    foreach my $sample (keys %{$opt->{SAMPLES}}) {
        bamOperationWithSliceChecks("BaseRecalibration", $sample, $known_files, "recalibrated", "recal", $opt);
    }
    return;
}

1;

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{'dir': 'git-commits-cleaned', 'id': '3474929', 'n_tokens_mistral': 530, 'n_tokens_neox': 506, 'n_words': 114}