#!/usr/bin/env perl
#
# Copyright 2010-2016, Julian Catchen <jcatchen@illinois.edu>
#
# This file is part of Stacks.
#
# Stacks is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# Stacks is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with Stacks.  If not, see <http://www.gnu.org/licenses/>.
#

#
# Process the data for a genetic map: build stacks in parents and progeny, 
# create a catalog from the parents, and match progeny against the catatlog.
# Call genotypes, and load all data into an MySQL database along the way.
#
# For the database interactions to work, the 'mysql' program is expected to be
# on the path and sufficient permissions set to access the specified database.
#

use strict;
use POSIX;
use File::Temp qw/ mktemp /;
use File::Spec;
use constant stacks_version => "1.42";

use constant true  => 1;
use constant false => 0;

my $dry_run      = false;
my $sql          = true;
my $create_db    = false;
my $overw_db     = false;
my $mysql_config = "/opt/anaconda1anaconda2anaconda3/share/stacks/" . "sql/mysql.cnf";
my $mysql_tables = "/opt/anaconda1anaconda2anaconda3/share/stacks/" . "sql/stacks.sql";
my $exe_path     = "/opt/anaconda1anaconda2anaconda3/bin/";
my $out_path     = "";
my $popmap_path  = "";
my $sample_path  = "";
my $db           = "";
my $data_type    = "map";
my $min_cov      = 0;
my $min_rcov     = 0;
my $batch_id     = -1;
my $sample_id    = 1;
my $desc         = ""; # Database description of this dataset
my $date         = ""; # Date relevent to this data, formatted for SQL: 2009-05-31
my $gzip         = false;

my @parents;
my @progeny;
my @samples;

my (@_pstacks, @_cstacks, @_sstacks, @_genotypes, @_populations);

my $cmd_str = $0 . " " . join(" ", @ARGV);

parse_command_line();

my $cnf = (-e $ENV{"HOME"} . "/.my.cnf") ? $ENV{"HOME"} . "/.my.cnf" : $mysql_config;

#
# Check for the existence of the necessary pipeline programs
#
die ("Unable to find '" . $exe_path . "pstacks'.\n")          if (!-e $exe_path . "pstacks"          || !-x $exe_path . "pstacks");
die ("Unable to find '" . $exe_path . "cstacks'.\n")          if (!-e $exe_path . "cstacks"          || !-x $exe_path . "cstacks");
die ("Unable to find '" . $exe_path . "sstacks'.\n")          if (!-e $exe_path . "sstacks"          || !-x $exe_path . "sstacks");
die ("Unable to find '" . $exe_path . "genotypes'.\n")        if (!-e $exe_path . "genotypes"        || !-x $exe_path . "genotypes");
die ("Unable to find '" . $exe_path . "populations'.\n")      if (!-e $exe_path . "populations"      || !-x $exe_path . "populations");
die ("Unable to find '" . $exe_path . "index_radtags.pl'.\n") if (!-e $exe_path . "index_radtags.pl" || !-x $exe_path . "index_radtags.pl");

my ($log, $log_fh, $sample);

my (@sample_list, %pop_ids, %pops, %grp_ids, %grps, %sample_ids);

parse_population_map(\@sample_list, \%pop_ids, \%pops, \%grp_ids, \%grps);

initialize_samples(\@parents, \@progeny, \@samples, \@sample_list, \%pop_ids, \%grp_ids);

#
# Open the log file
#
$log = "$out_path/ref_map.log";
open($log_fh, ">$log") or die("Unable to open log file '$log'; $!\n");

print $log_fh 
    "ref_map.pl version ", stacks_version, " started at ", strftime("%Y-%m-%d %H:%M:%S", (localtime(time))), "\n",
    $cmd_str, "\n\n";

initialize_database($log_fh, \@parents, \@progeny, \@samples, \%sample_ids) if ($sql == true);

execute_stacks($log_fh, $sample_id, \@parents, \@progeny, \@samples, \%sample_ids);

load_sql_data($log_fh, \%pops, \@parents, \@progeny, \@samples) if ($sql == true);

print $log_fh "\nref_map.pl completed at ", strftime("%Y-%m-%d %H:%M:%S", (localtime(time))), "\n";
close($log_fh);


sub execute_stacks {
    my ($log_fh, $sample_id, $parents, $progeny, $samples, $sample_ids) = @_;
    
    my (@results, @depths_of_cov);
    my ($pop_cnt, $sample, $num_files, $i, $cmd, $pipe_fh, $path, $cat_file);

    my $minc  = $min_cov  > 0 ? "-m $min_cov"  : "";
    my $minrc = $min_rcov > 0 ? "-m $min_rcov" : $minc;

    $i         = 1;
    $num_files = scalar(@{$parents}) + scalar(@{$progeny}) + scalar(@{$samples});

    #
    # Assemble RAD loci in each individual.
    #
    foreach $sample (@parents, @progeny, @samples) {

        printf("Identifying unique stacks; file % 3s of % 3s [%s]\n", $i, $num_files, $sample->{'file'});
        printf($log_fh "Identifying unique stacks; file % 3s of % 3s [%s]\n", $i, $num_files, $sample->{'file'});

        if (scalar(keys %{$sample_ids}) > 0) {
            $sample_id = $sample_ids->{$sample->{'file'}};
        }

        $path = $sample->{'path'} . $sample->{'file'} . "." . $sample->{'suffix'};
        
        if ($sample->{'type'} eq "sample") {
            $cmd = $exe_path . "pstacks -t $sample->{'fmt'} -f $path -o $out_path -i $sample_id $minc "  . join(" ", @_pstacks) . " 2>&1";
        } elsif ($sample->{'type'} eq "parent") {
            $cmd = $exe_path . "pstacks -t $sample->{'fmt'} -f $path -o $out_path -i $sample_id $minc "  . join(" ", @_pstacks) . " 2>&1";
        } elsif ($sample->{'type'} eq "progeny") {
            $cmd = $exe_path . "pstacks -t $sample->{'fmt'} -f $path -o $out_path -i $sample_id $minrc " . join(" ", @_pstacks) . " 2>&1";
        }
        print STDERR  "  $cmd\n";
        print $log_fh "$cmd\n";

        if ($dry_run == false) {
            @results = `$cmd`;

            #
            # Pull the depth of coverage from pstacks.
            #
            my @lines   = grep(/Mean coverage depth is/, @results);
            my ($depth) = ($lines[0] =~ /^  Mean coverage depth is (\d+\.?\d*); Std Dev: .+; Max: .+$/);
            push(@depths_of_cov, [$sample->{'file'}, $depth]);
        }
        write_results(\@results, $log_fh);

        $i++;
        $sample_id++;
    }

    write_depths_of_cov(\@depths_of_cov, $log_fh);

    #
    # Generate catalog of RAD loci.
    #
    print STDERR "Generating catalog...\n";
    my $file_paths = "";
    foreach $sample (@parents, @samples) {
        $file_paths .= "-s $out_path/$sample->{'file'} ";
    }

    $cmd = $exe_path . "cstacks -g -b $batch_id -o $out_path $file_paths " . join(" ", @_cstacks) . " 2>&1";
    print STDERR  "  $cmd\n";
    print $log_fh "$cmd\n\n";

    if ($dry_run == false) {
        open($pipe_fh, "$cmd |");
        while (<$pipe_fh>) {
            print $log_fh $_;
            if ($_ =~ /failed/i) { print STDERR "Catalog construction failed.\n"; exit(1); }
        }
        close($pipe_fh);
    }

    #
    # Match parents, progeny, or samples to the catalog.
    #
    $file_paths = "";
    print STDERR "Matching samples to the catalog...\n";

    foreach $sample (@parents, @progeny, @samples) {
        $file_paths .= "-s $out_path/$sample->{'file'} ";
    }

    $cat_file = "batch_" . $batch_id;
    $cmd      = $exe_path . "sstacks -g -b $batch_id -c $out_path/$cat_file -o $out_path $file_paths " . join(" ", @_sstacks) . " 2>&1";
    print STDERR  "  $cmd\n";
    print $log_fh "$cmd\n\n";

    if ($dry_run == false) {
        open($pipe_fh, "$cmd |");
        while (<$pipe_fh>) {
            print $log_fh $_;
        }
        close($pipe_fh);
    }

    if ($data_type eq "map") {
        #
        # Generate a set of observed haplotypes and a set of markers and generic genotypes
        #
        printf(STDERR "Generating genotypes...\n");

        $cmd = $exe_path . "genotypes -b $batch_id -P $out_path -r 1 -c -s " . join(" ", @_genotypes) . " 2>&1";
        print STDERR  "$cmd\n";
        print $log_fh "$cmd\n";

        if ($dry_run == 0) {
            open($pipe_fh, "$cmd |");
            while (<$pipe_fh>) {
                print $log_fh $_;
            }
            close($pipe_fh);
        }

    } else {
        printf(STDERR "Calculating population-level summary statistics\n");

        $cmd = $exe_path . "populations -b $batch_id -P $out_path -s " . join(" ", @_populations) . " 2>&1";
        print STDERR  "$cmd\n";
        print $log_fh "$cmd\n";

        if ($dry_run == 0) {
            open($pipe_fh, "$cmd |");
            while (<$pipe_fh>) {
                print $log_fh $_;
            }
            close($pipe_fh);
        }
    }
}

sub parse_population_map {
    my ($sample_list, $pop_ids, $pops, $grp_ids, $grps) = @_;

    my ($fh, @parts, $line, $sample);

    return if (length($popmap_path) == 0);
    
    open($fh, "<$popmap_path") or die("Unable to open population map, '$popmap_path', $!\n");

    while ($line = <$fh>) {
	chomp $line;

        next if ($line =~ /^\s*#/);
        
	@parts = split(/\t/, $line);

	if (scalar(@parts) > 3) {
	    die("Unable to parse population map, '$popmap_path' (map should contain no more than three columns).\n");
	}

        push(@{$sample_list}, $parts[0]);

	$pop_ids->{$parts[0]} = $parts[1];
	$pops->{$parts[1]}++;
        
	if (scalar(@parts) > 2) {
	    $grp_ids->{$parts[0]} = $parts[2];
	    $grps->{$parts[2]}++;
	}
    }

    if (scalar(keys %{$grps}) == 0) {
	$grps->{"1"}++;

        foreach $sample (@{$sample_list}) {
            $grp_ids->{$sample} = "1";
        }
    }

    print STDERR "Parsed population map: ", scalar(@{$sample_list}), " files in ", scalar(keys %{$pops});
    scalar(keys %{$pops}) == 1 ?  print STDERR " population" : print STDERR " populations";
    print STDERR " and ", scalar(keys %{$grps});
    scalar(keys %{$grps}) == 1 ? print STDERR " group.\n" : print STDERR " groups.\n";

    close($fh);
}

sub initialize_samples {
    my ($parents, $progeny, $samples, $sample_list, $pop_ids, $grp_ids) = @_;

    my ($local_gzip, $file, $prefix, $suffix, $path, $found, $i);

    if (scalar(@{$sample_list}) > 0 && scalar(@{$samples}) == 0) {
        my @suffixes = ("sam", "bam", "map", "bowtie");
        my @fmts     = ("sam", "bam", "map", "bowtie");

        #
        # If a population map was specified and no samples were provided on the command line.
        #
        foreach $sample (@{$sample_list}) {
            $found = false;
            
            for ($i = 0; $i < scalar(@suffixes); $i++) {
                $path = $sample_path . $sample . "." . $suffixes[$i];
                if (-e $path) {

                    if ($i == 1) {
                        $gzip = true;
                    }

                    push(@{$samples}, {'path'   => $sample_path,
                                       'file'   => $sample,
                                       'suffix' => $suffixes[$i],
                                       'type'   => "sample",
                                       'fmt'    => $fmts[$i]});
                    $found = true;
                    last;
                }
            }

            if ($found == false) {
                die("Unable to find sample '$sample' in directory '$sample_path' as specified in the population map, '$popmap_path'.\n");
            }
        }
        
    } else {
        #
        # Process any samples were specified on the command line.
        #
        foreach $sample (@{$parents}, @{$progeny}, @{$samples}) {

            ($prefix, $suffix) = ($sample->{'path'} =~ /^(.+)\.(.+)$/);

            $sample->{'suffix'}  = $suffix;

            if ($prefix =~ /^.*\/.+$/) {
                ($path, $file) = ($prefix =~ /^(.*\/)(.+)$/);
            } else {
                $file = $prefix;
                $path = "";
            }

            $sample->{'path'} = $path;
            $sample->{'file'} = $file;

	    if ($suffix =~ /^bam$/) {
		$sample->{'fmt'} = "bam";
		$gzip            = true;
	    } elsif ($suffix =~ /^sam$/) {
		$sample->{'fmt'} = "sam";
	    } elsif ($suffix =~ /^map$/) {
		$sample->{'fmt'} = "map";
	    } elsif ($suffix =~ /^bowtie$/) {
		$sample->{'fmt'} = "bowtie";
	    } else {
		die("Unknown input file type for file '" . $sample->{'path'} . "'.\n");
	    }

            $path = $sample->{'path'} . $sample->{'file'} . "." . $sample->{'suffix'};

            if (!-e $path) {
                die("Unable to locate sample file '$path'\n");
            }
        }

        foreach $sample (@{$parents}) {
            $sample->{'type'} = "parent";
        }
        foreach $sample (@{$progeny}) {
            $sample->{'type'} = "progeny";
        }
        foreach $sample (@{$samples}) {
            $sample->{'type'} = "sample";
        }
    }

    #
    # If a population map was specified, make sure all samples in the list were found (and vice versa) and assign popualtion IDs.
    #
    if (scalar(@{$sample_list}) > 0) {

        my %sample_hash;
        
        foreach $sample (@{$samples}) {
            $sample_hash{$sample->{'file'}}++;

            if (!defined($pop_ids->{$sample->{'file'}})) {
                die("Unable to find an entry for '" . $sample->{'file'} . "' in the population map, '$popmap_path'.\n");
            } else {
                $sample->{'pop_id'} = $pop_ids->{$sample->{'file'}};
            }
            if (!defined($grp_ids->{$sample->{'file'}})) {
                die("Unable to find an entry for '" . $sample->{'file'} . "' in the population map, '$popmap_path'.\n");
            } else {
                $sample->{'grp_id'} = $grp_ids->{$sample->{'file'}};
            }
        }

        foreach $sample (@{$sample_list}) {
            if (!defined($sample_hash{$sample})) {
                die("Unable to find a file corresponding to the population map entry '" . $sample . "' in the population map, '$popmap_path'.\n");
            }
        }

    } else {
        foreach $sample (@{$parents}, @{$progeny}, @{$samples}) {
            $sample->{'pop_id'} = "1";
            $sample->{'grp_id'} = "1";
            $pop_ids->{$sample->{'file'}} = $sample->{'pop_id'};
            $grp_ids->{$sample->{'file'}} = $sample->{'grp_id'};
        }
    }

    #
    # Check that no duplicate files were specified.
    #
    my (%files, $file);
    foreach $file (@{$parents}, @{$progeny}, @{$samples}) {
	$files{$file}++;
    }
    foreach $file (keys %files) {
	if ($files{$file} > 1) {
	    die("A duplicate file was specified which may create undefined results, '$file'\n");
	}
    }

    print STDERR "Found ", scalar(@{$parents}), " parental file(s).\n" if (scalar(@{$parents}) > 0);
    print STDERR "Found ", scalar(@{$progeny}), " progeny file(s).\n" if (scalar(@{$progeny}) > 0);
    print STDERR "Found ", scalar(@{$samples}), " sample file(s).\n" if (scalar(@{$samples}) > 0);
}

sub initialize_database {
    my ($log_fh, $parents, $progeny, $samples, $sample_ids) = @_;

    my (@results, $sample_id, $sample);

    print $log_fh "Initializing the database...\n";

    #
    # Create the database.
    #
    if ($create_db) {
        #
        # Check that the database doesn't already exist.
        #
        if ($dry_run == false) {
            @results = `mysql --defaults-file=$cnf -N -B -e "SHOW DATABASES LIKE '$db'"`;
            if (scalar(@results) > 0 && $overw_db == false) {
                die("Unable to create database '$db', it already exists.\n");
            }
        }

        if ($overw_db == true) {
            `mysql --defaults-file=$cnf -N -B -e "DROP DATABASE IF EXISTS $db"` if ($dry_run == false);
            print $log_fh "mysql --defaults-file=$cnf -N -B -e \"DROP DATABASE IF EXISTS '$db'\"\n";
        }

        `mysql --defaults-file=$cnf -e "CREATE DATABASE $db"` if ($dry_run == false);
        print $log_fh "mysql --defaults-file=$cnf $db -e \"CREATE DATABASE $db\"\n";
        `mysql --defaults-file=$cnf $db < $mysql_tables` if ($dry_run == false);
        print $log_fh "mysql --defaults-file=$cnf $db < $mysql_tables\n";
    }

    #
    # Set the SQL Batch ID for this set of loci, along with description and date of 
    # sequencing. Insert this batch data into the database.
    # 
    `mysql --defaults-file=$cnf $db -e "INSERT INTO batches SET id=$batch_id, description='$desc', date='$date', type='$data_type'"` if ($dry_run == false);

    print $log_fh "mysql --defaults-file=$cnf $db -e \"INSERT INTO batches SET id=$batch_id, description='$desc', date='$date', type='$data_type'\"\n";

    print $log_fh "Loading sample data into the MySQL database...\n";

    my $i = 1;

    foreach $sample (@{$parents}, @{$progeny}, @{$samples}) {

	if ($dry_run == false) {
	    `mysql --defaults-file=$cnf $db -e "INSERT INTO samples SET sample_id=$i, batch_id=$batch_id, type='$sample->{'type'}', file='$sample->{'file'}', pop_id='$sample->{'pop_id'}', group_id='$sample->{'grp_id'}'"`;
	    @results = `mysql --defaults-file=$cnf $db -N -B -e "SELECT id FROM samples WHERE sample_id=$i AND batch_id=$batch_id AND type='$sample->{'type'}' AND file='$sample->{'file'}'"`;
	    chomp $results[0];
	    $sample_id = $results[0];

            #
            # Save the sample ID to use when running pstacks.
            #
            $sample_ids->{$sample->{'file'}} = $sample_id;
	}
	print $log_fh "mysql --defaults-file=$cnf $db -e \"INSERT INTO samples SET sample_id=$i, batch_id=$batch_id, type='$sample->{'type'}', file='$sample->{'file'}', pop_id='$sample->{'pop_id'}', group_id='$sample->{'grp_id'}'\"\n";

        $i++;
    }

    print $log_fh "\n";
}

sub load_sql_data {
    my ($log_fh, $pops, $parents, $progeny, $samples) = @_;

    my ($pop_cnt, $sample, $num_files, $i, $file);

    print STDERR "\nComputation is complete, loading results to the database '$db'.\n";
    
    my $pop_cnt = scalar(keys %{$pops});

    $i         = 1;
    $num_files = scalar(@{$parents}) + scalar(@{$progeny}) + scalar(@{$samples});

    foreach $sample (@{$parents}, @{$progeny}, @{$samples}) {

        printf(STDERR "Loading pstacks output to $db; file % 3s of % 3s [%s]...", $i, $num_files, $sample->{'file'});

        if ($gzip == true) {
            $file = "$out_path/$sample->{'file'}" . ".tags.tsv.gz";
            import_gzsql_file($log_fh, $file, "unique_tags", 1);

            $file = "$out_path/$sample->{'file'}" . ".snps.tsv.gz";
            import_gzsql_file($log_fh, $file, "snps", 1);

            $file = "$out_path/$sample->{'file'}" . ".alleles.tsv.gz";
            import_gzsql_file($log_fh, $file, "alleles", 1);

        } else {
            $file = "$out_path/$sample->{'file'}" . ".tags.tsv";
            import_sql_file($log_fh, $file, "unique_tags", 1);

            $file = "$out_path/$sample->{'file'}" . ".snps.tsv";
            import_sql_file($log_fh, $file, "snps", 1);

            $file = "$out_path/$sample->{'file'}" . ".alleles.tsv";
            import_sql_file($log_fh, $file, "alleles", 1);
        }
        print STDERR "done.\n";
        
        $i++;
    }

    print STDERR "Importing catalog to $db...";

    my $cat_file = "batch_" . $batch_id;

    if ($gzip == true) {
        $file = "$out_path/$cat_file" . ".catalog.tags.tsv.gz";
        import_gzsql_file($log_fh, $file, "catalog_tags", 1);

        $file = "$out_path/$cat_file" . ".catalog.snps.tsv.gz";
        import_gzsql_file($log_fh, $file, "catalog_snps", 1);

        $file = "$out_path/$cat_file" . ".catalog.alleles.tsv.gz";
        import_gzsql_file($log_fh, $file, "catalog_alleles", 1);

    } else {
        $file = "$out_path/$cat_file" . ".catalog.tags.tsv";
        import_sql_file($log_fh, $file, "catalog_tags", 1);

        $file = "$out_path/$cat_file" . ".catalog.snps.tsv";
        import_sql_file($log_fh, $file, "catalog_snps", 1);

        $file = "$out_path/$cat_file" . ".catalog.alleles.tsv";
        import_sql_file($log_fh, $file, "catalog_alleles", 1);
    }
    print STDERR "done.\n";

    #
    # Load the sstacks results to the database if requested.
    #
    $i = 1;
    foreach $sample (@{$parents}, @{$progeny}, @{$samples}) {

	printf(STDERR "Loading sstacks output to $db; file % 3s of % 3s [%s]...", $i, $num_files, $sample->{'file'});

	if ($gzip == true) {
	    $file = "$out_path/" . $sample->{'file'} . ".matches.tsv.gz";
	    import_gzsql_file($log_fh, $file, "matches", 1);

	} else {
	    $file = "$out_path/" . $sample->{'file'} . ".matches.tsv";
	    import_sql_file($log_fh, $file, "matches", 1);
	}
        print STDERR "done.\n";

	$i++;
    }

    if ($data_type eq "map") {
        #
        # Load the outputs generated by genotypes to the database.
        #
        $file = "$out_path/batch_" . $batch_id . ".markers.tsv";
        import_sql_file($log_fh, $file, "markers", 1);

        $file = "$out_path/batch_" . $batch_id . ".genotypes_1.txt";
        import_sql_file($log_fh, $file, "catalog_genotypes", 1);
        
    } else {
        #
        # Load the outputs generated by populations to the database.
        #
        $file = "$out_path/batch_" . $batch_id . ".markers.tsv";
        import_sql_file($log_fh, $file, "markers", 1);

        $file = "$out_path/batch_" . $batch_id . ".sumstats.tsv";
        import_sql_file($log_fh, $file, "sumstats", $pop_cnt+1);

        $file = "$out_path/batch_" . $batch_id . ".hapstats.tsv";
        import_sql_file($log_fh, $file, "hapstats", $pop_cnt+1);

        #
        # Import the Fst files.
        #
        my $fst_cnt = 0;
        my (@keys, $m, $n);
        @keys = sort keys %pops;
        for ($m = 0; $m < scalar(@keys); $m++) {
            for ($n = 0; $n < scalar(@keys); $n++) {
                $file = "$out_path/batch_" . $batch_id . ".fst_" . $keys[$m] . "-" . $keys[$n] . ".tsv";

                if (-e $file) {
                    import_sql_file($log_fh, $file, "fst", 1);
                    $fst_cnt++;
                }
            }
        }
        print STDERR "Imported $fst_cnt Fst file(s).\n";

        #
        # Import the Phi_st files.
        #
        $fst_cnt = 0;
        for ($m = 0; $m < scalar(@keys); $m++) {
            for ($n = 0; $n < scalar(@keys); $n++) {
                $file = "$out_path/batch_" . $batch_id . ".phistats_" . $keys[$m] . "-" . $keys[$n] . ".tsv";

                if (-e $file) {
                    import_sql_file($log_fh, $file, "phist", 3);
                    $fst_cnt++;
                }
            }
        }
        print STDERR "Imported $fst_cnt Haplotype Fst file(s).\n";
    }

    print $log_fh "\n";

    #
    # Index the radtags database
    #
    my ($cmd, @results);
    print STDERR "Indexing the database...\n";
    $cmd = $exe_path . "index_radtags.pl -D $db -t -c 2>&1";
    print STDERR  "$cmd\n";
    print $log_fh "$cmd\n";
    @results =    `$cmd` if ($dry_run == false);
    print $log_fh @results;
}

sub write_results {
    my ($results, $log_fh) = @_;

    my $line;

    foreach $line (@{$results}) {
	if ($line =~ /\r/) { 
	    $line =~ s/^.+\r(.*\n)$/\1/; 
	}
	print $log_fh $line;
    }
}

sub write_depths_of_cov {
    my ($depths, $log_fh) = @_;

    print STDERR "\nDepths of Coverage for Processed Samples:\n";
    print $log_fh "\nDepths of Coverage for Processed Samples:\n";

    foreach $a (@{$depths}) {
	print STDERR  $a->[0], ": ", $a->[1], "x\n";
	print $log_fh $a->[0], ": ", $a->[1], "x\n";
    }
    print STDERR "\n";
    print $log_fh "\n";
}

sub import_sql_file {
    my ($log_fh, $file, $table, $skip_lines) = @_;

    my (@results, $ignore);

    $ignore = "IGNORE $skip_lines LINES" if ($skip_lines > 0);

    @results = `mysql --defaults-file=$cnf $db -e "LOAD DATA LOCAL INFILE '$file' INTO TABLE $table $ignore"` if ($sql == true && $dry_run == false);

    if ($sql == true) {
	print $log_fh "mysql --defaults-file=$cnf $db -e \"LOAD DATA LOCAL INFILE '$file' INTO TABLE $table $ignore\"\n", @results;
    }
}

sub import_gzsql_file {
    my ($log_fh, $file, $table, $skip_lines) = @_;

    my (@results, $ignore);

    $ignore = "IGNORE $skip_lines LINES" if ($skip_lines > 0);

    #
    # Get a temporary file name and create a named pipe.
    #
    my $tmpdir     = File::Spec->tmpdir();
    my $named_pipe = mktemp($tmpdir . "/denovo_map_XXXXXX");
    if ($sql == true && $dry_run == false) {
	mkfifo($named_pipe, 0700) || die("Unable to create named pipe for loading gzipped data: $named_pipe, $!");
	print $log_fh "Streaming $file into named pipe $named_pipe.\n";
    }

    #
    # Dump our gzipped data onto the named pipe.
    #
    system("gunzip -c $file > $named_pipe &") if ($sql == true && $dry_run == false);

    @results = `mysql --defaults-file=$cnf $db -e "LOAD DATA LOCAL INFILE '$named_pipe' INTO TABLE $table $ignore"` if ($sql == true && $dry_run == false);

    if ($sql == 1) {
	print $log_fh "mysql --defaults-file=$cnf $db -e \"LOAD DATA LOCAL INFILE '$named_pipe' INTO TABLE $table $ignore\"\n", @results;
    }

    #
    # Remove the pipe.
    #
    unlink($named_pipe) if ($sql == true && $dry_run == false);
}

sub parse_command_line {
    my ($arg);

    while (@ARGV) {
	$_ = shift @ARGV;
        if    ($_ =~ /^-v$/) { version(); exit(); }
	elsif ($_ =~ /^-h$/) { usage(); }
	elsif ($_ =~ /^-p$/) { push(@parents, { 'path' => shift @ARGV }); }
	elsif ($_ =~ /^-r$/) { push(@progeny, { 'path' => shift @ARGV }); }
	elsif ($_ =~ /^-s$/) { push(@samples, { 'path' => shift @ARGV }); }
	elsif ($_ =~ /^-d$/) { $dry_run   = true; }
	elsif ($_ =~ /^-o$/) { $out_path  = shift @ARGV; }
	elsif ($_ =~ /^-D$/) { $desc      = shift @ARGV; }
	elsif ($_ =~ /^-e$/) { $exe_path  = shift @ARGV; }
	elsif ($_ =~ /^-b$/) { $batch_id  = shift @ARGV; }
	elsif ($_ =~ /^-i$/) { $sample_id = shift @ARGV; }
	elsif ($_ =~ /^-a$/) { $date      = shift @ARGV; }
	elsif ($_ =~ /^-S$/) { $sql       = false; }
	elsif ($_ =~ /^-B$/) { $db        = shift @ARGV; }
	elsif ($_ =~ /^-m$/) { $min_cov   = shift @ARGV; }
	elsif ($_ =~ /^-P$/) { $min_rcov  = shift @ARGV; }
        elsif ($_ =~ /^--samples$/) {
            $sample_path = shift @ARGV;
            
        } elsif ($_ =~ /^-O$/) { 
	    $popmap_path = shift @ARGV;
	    push(@_populations, "-M " . $popmap_path); 

	} elsif ($_ =~ /^--create_db$/) {
            $create_db = true;

        } elsif ($_ =~ /^--overw_db$/) {
            $overw_db  = true;
            $create_db = true;

        } elsif ($_ =~ /^-A$/) { 
	    $arg = shift @ARGV;
	    push(@_genotypes, "-t " . $arg); 

	    $arg = lc($arg);
	    if ($arg ne "gen" && $arg ne "cp" && $arg ne "f2" && $arg ne "bc1" && $arg ne "dh") {
		print STDERR "Unknown genetic mapping cross specified: '$arg'\n";
		usage();
	    }

	} elsif ($_ =~ /^-t$/) { 
	    push(@_pstacks, "-d "); 

	} elsif ($_ =~ /^-T$/) {
	    $arg = shift @ARGV;
	    push(@_pstacks, "-p " . $arg); 
	    push(@_cstacks, "-p " . $arg); 
	    push(@_sstacks, "-p " . $arg); 
	    push(@_populations, "-t " . $arg); 

	} elsif ($_ =~ /^--bound_low$/) { 
	    push(@_pstacks, "--bound_low " . shift @ARGV); 
	    push(@_pstacks, "--model_type bounded");

	} elsif ($_ =~ /^--bound_high$/) { 
	    push(@_pstacks, "--bound_high " . shift @ARGV); 
	    push(@_pstacks, "--model_type bounded");

	} elsif ($_ =~ /^--alpha$/) { 
	    push(@_pstacks, "--alpha " . shift @ARGV); 

	} elsif ($_ =~ /^-X$/) {
	    #
	    # Pass an arbitrary command-line option to a pipeline program.
	    #
	    # Command line option must be of the form '-X "program:option"'
	    #
	    $arg = shift @ARGV;
	    my ($prog, $opt) = ($arg =~ /^(\w+):(.+)$/);

	    if ($prog eq "pstacks") {
		push(@_pstacks, $opt); 

	    } elsif ($prog eq "cstacks") {
		push(@_cstacks, $opt); 

	    } elsif ($prog eq "sstacks") {
		push(@_sstacks, $opt); 

	    } elsif ($prog eq "genotypes") {
		push(@_genotypes, $opt); 

	    } elsif ($prog eq "populations") {
		push(@_populations, $opt); 
	    } else {
		print STDERR "Unknown pipeline program, '$arg'\n";
		usage();
	    }
	}
	else {
	    print STDERR "Unknown command line option: '$_'\n";
	    usage();
	}
    }

    $exe_path = $exe_path . "/"          if (substr($exe_path, -1) ne "/");
    $out_path = substr($out_path, 0, -1) if (substr($out_path, -1) eq "/");

    if ($batch_id !~ /^\d+$/ || $batch_id < 0) {
	print STDERR "You must specify a batch ID and it must be an integer (e.g. 1, 2, 3).\n";
	usage();
    }

    if ($sql == true && length($date) == 0) {
	$date = strftime("%Y-%m-%d", (localtime(time)));
    }

    if (scalar(@parents) > 0 && scalar(@samples) > 0) {
	print STDERR "You must specify either parent or sample files, but not both.\n";
	usage();
    }

    if (scalar(@parents) == 0 && scalar(@samples) == 0 && length($popmap_path) == 0) {
	print STDERR "You must specify at least one parent or sample file.\n";
	usage();
    }

    if (length($sample_path) > 0) {
        $sample_path .= "/" if (substr($sample_path, -1) ne "/");
    }
    
    if (scalar(@samples) > 0 || length($popmap_path) > 0) {
	$data_type = "population";
    } else {
	$data_type = "map";
    }
}

sub version {
    print STDERR "ref_map.pl ", stacks_version, "\n";
}

sub usage {
    version();

    print STDERR <<EOQ; 
ref_map.pl -p path -r path [-s path] -o path [-t] [-m min_cov] [-M mismatches] [-T num_threads] [-A type] [-O popmap] [-B db -b batch_id -D "desc"] [-S -i num] [-e path] [-d] [-h]
    b: batch ID representing this dataset (an integer, e.g. 1, 2, 3).
    o: path to write pipeline output files.
    O: if analyzing one or more populations, specify a pOpulation map.
    A: if processing a genetic map, specify the cross type, 'CP', 'F2', 'BC1', 'DH', or 'GEN'.
    T: specify the number of threads to execute.
    e: executable path, location of pipeline programs.
    d: perform a dry run. Do not actually execute any programs, just print what would be executed.
    h: display this help message.

  Specify each sample separately:
    p: path to a Bowtie/SAM/BAM file containing one set of parent sequences from a mapping cross.
    r: path to a Bowtie/SAM/BAM file containing one set of progeny sequences from a mapping cross.
    s: path to a Bowtie/SAM/BAM file containing an individual sample from a population.
  Specify a path to samples and provide a population map:
    --samples <path>: specify a path to the directory of samples (samples will be read from population map).

  Stack assembly options:
    m: specify a minimum number of identical, raw reads required to create a stack (default 3).
    P: specify a minimum number of identical, raw reads required to create a stack in 'progeny' individuals.

  Database options:
    B: specify a database to load data into.
    D: a description of this batch to be stored in the database.
    S: disable recording SQL data in the database.
    i: starting sample_id, this is determined automatically if database interaction is enabled.
    --create_db: create the database specified by '-B' and populate the tables.
    --overw_db: delete the database before creating a new copy of it (turns on --create_db).

  SNP Model Options (these options are passed on to pstacks):
    --bound_low <num>: lower bound for epsilon, the error rate, between 0 and 1.0 (default 0).
    --bound_high <num>: upper bound for epsilon, the error rate, between 0 and 1.0 (default 1).
    --alpha <num>: chi square significance level required to call a heterozygote or homozygote, either 0.1, 0.05 (default), 0.01, or 0.001.

  Arbitrary command line options:
    -X "program:option": pass a command line option to one of the pipeline components, e.g.'-X "sstacks:-x"'.

EOQ

    exit(0);
}
