<?php

// dump a bedfile via http
require_once 'db.function.php';
require_once 'util.function.php';

session_start();
$db = getDB();
if((isset($_SESSION['researcher_id']) && bedfile_access_permission($_SESSION['researcher_id'], $_GET['id']))
   || (isset($_GET['token']) && $db->getOne("select bedfile_id from bedfile where befile_id = ? and token = ? and token_expires > now()", $_GET['id'], $_GET['token']))) {

    $bedfile = $db->getRow("select * from bedfile where bedfile_id = ?", array($_GET['id']));
    $chrom_length = ($bedfile['genome_id'] ? $db->getAssoc("select chrom, length from chrom_length where genome_id = ?", FALSE, $bedfile['genome_id']) : array());
    print $bedfile['header'] . "\n";
    if($bedfile['filetype'] == 'rawbed') {
        // esp for large files, it's better to pre-process for chromosome length, in the interest of speed
        //readfile($db->getOne("select filepath from rawbed where bedfile_id = ?", $_GET['id']));
        $fp = fopen($db->getOne("select filepath from rawbed where bedfile_id = ?", $_GET['id']), "r");
        fgets($fp);   // strip header from original file
        while($r = fgetcsv($fp, 0, "\t")) {
            if(isset($chrom_length[$r[0]]) && $r[2] > $chrom_length[$r[0]]) {
                $r[2] = $chrom_length[$r[0]]; //continue;
            }
            if(isset($chrom_length[$r[0]]) && $r[1] > $chrom_length[$r[0]]) {
                $r[1] = $chrom_length[$r[0]]; //continue;
            }
            print join("\t", $r) . "\n";
        }
        fclose($fp);
    } else {
        //print $bedfile['header'] . "\n";
        $rows = $db->query("select * from summarybed where bedfile_id = ?", $_GET['id']);
        $filterOutKeys = array('summarybed_id', 'bedfile_id');
        while($r = $rows->fetchRow()) {
            if(isset($chrom_length[$r['chrom']]) && $r['chromend'] > $chrom_length[$r['chrom']]) {
                $r['chromend'] = $chrom_length[$r['chrom']]; //continue;
            }
            if(isset($chrom_length[$r['chrom']]) && $r['chromstart'] > $chrom_length[$r['chrom']]) {
                $r['chromstart'] = $chrom_length[$r['chrom']]; //continue;
            }
            $r = array_diff_key($r, array_flip($filterOutKeys));
            print trim(join("\t", $r)) . "\n";
        }
    }
}

?>