/** new blast command based on default parameters */
public BlatCommand() throws IOException {
// look in configuration file to determine default values
commandLine = DEFAULTCOMMANDLINE;
commandPath = DEFAULTCOMMANDPATH;
tmpDir = DEFAULTTMPDIR;
tmpDirFile = MetaUtils.createTempDir("blat_", tmpDir);
}
/**
* new blast command based on values stored in the configuration.
*
* <p>Looks for the following config values: blast.commandline, blast.commandpath, and
* blast.tmpdir
*
* @param config is the hadoop configuration with overriding values for commandline options and
* paths
*/
public BlatCommand(Configuration config) throws IOException {
String c;
if ((c = config.get("blat.commandline")) != null) {
commandLine = c;
} else {
commandLine = DEFAULTCOMMANDLINE;
}
if ((c = config.get("blat.commandpath")) != null) {
commandPath = c;
} else {
commandPath = DEFAULTCOMMANDPATH;
}
if ((c = config.get("blat.tmpdir")) != null) {
tmpDir = c;
} else {
tmpDir = DEFAULTTMPDIR;
}
doCleanup = config.getBoolean("blat.cleanup", true);
paired = config.getBoolean("blat.paired", true);
/*
do sanity check to make sure all paths exist
*/
// checkFileExists(commandLine);
// checkFileExists(commandPath);
// checkDirExists(tmpDir);
/*
if all is good, create a working space inside tmpDir
*/
tmpDirFile = MetaUtils.createTempDir("blat_", tmpDir);
}