$humanBowtieStats = BowtieStatsFinder::getBowtieStatsLogFile($dir->getPathname(), BowtieStatsFinder::HUMAN_FILE);
if (!$humanBowtieStats || !($humanMappingPercent = $humanBowtieStats->getAlignedReadsPercent())) {
$humanMappingPercent = 'NA';
}
$referenceBowtieStats = BowtieStatsFinder::getBowtieStatsLogFile($dir->getPathname(), BowtieStatsFinder::REFERENCE_FILE);
if (!$referenceBowtieStats || !($refernceMappingPercent = $referenceBowtieStats->getAlignedReadsPercent())) {
$relativeToUnmappedMappingPercent = 'NA';
} else {
$relativeToUnmappedMappingPercent = round((100 - $humanMappingPercent) * $refernceMappingPercent / 100, 2);
}
// search for reads filtering stats
$nReadsTotal = 'NA';
$nReadsFiltered = $humanBowtieStats ? $humanBowtieStats->getProcessedReadsCount() : 'NA';
$percentFiltered = 'NA';
$path = $dir->getPathname() . DIRECTORY_SEPARATOR . 'log';
$file = FileIterator::getFileByPattern('/reads-filter\\.pl\\.o\\d+/', $path);
$filepath = $path . DIRECTORY_SEPARATOR . $file;
if ($file == null) {
printf("Warning: file reads-filter.pl.o[:digits:] not found in [%s/log] directory\n", basename($dir->getPathname()));
} else {
if (!file_exists($filepath)) {
printf("Warning: file [%s] not found\n", $filepath);
} else {
$content = file_get_contents($filepath);
$result = preg_match('/Filtered (\\d+) of (\\d+) reads/', $content, $matches);
if ($result == 0) {
printf("Warning: file [%s] has no statistics\n", $filepath);
} else {
$nReadsTotal = $matches[2];
}
}
