public static void main(String[] args) {
System.err.println(
"Executing "
+ (new Object() {}.getClass().getEnclosingClass().getName())
+ " "
+ Arrays.toString(args)
+ "\n");
Timer t = new Timer();
String inPattern = args[0];
int minChrom = -1;
int maxChrom = -1;
int outgenome = -1;
Data.GENOME_BUILD = -1;
String name = null;
for (int i = 1; i < args.length; i++) {
final String arg = args[i].toLowerCase();
String[] split = arg.split("=");
String a = split[0];
String b = (split.length > 1 ? split[1] : null);
if (a.equals("ingenome")) {
Data.setGenome(Integer.parseInt(b));
if (minChrom == -1) {
minChrom = 1;
}
if (maxChrom == -1) {
maxChrom = Data.numChroms;
}
} else if (a.equals("outgenome")) {
outgenome = Integer.parseInt(b);
} else if (a.equals("minchrom")) {
minChrom = Integer.parseInt(b);
} else if (a.equals("maxchrom")) {
maxChrom = Integer.parseInt(b);
} else if (a.equals("threads") || a.equals("t")) {
THREADS = Integer.parseInt(b);
} else if (a.equals("nblocksize")) {
N_BLOCK_SIZE = Integer.parseInt(b);
} else if (a.equals("nblocktrigger")) {
N_BLOCK_TRIGGER = Integer.parseInt(b);
} else if (a.equals("staynearref")) {
STAY_NEAR_REF = Tools.parseBoolean(b);
} else if (a.equals("append") || a.equals("app")) {
append = ReadStats.append = Tools.parseBoolean(b);
} else if (a.equals("overwrite") || a.equals("ow")) {
overwrite = Tools.parseBoolean(b);
} else if (a.startsWith("regen")) {
REGEN_N_BLOCKS = Tools.parseBoolean(b);
} else if (a.startsWith("name=")) {
REGEN_N_BLOCKS = Tools.parseBoolean(b);
} else {
System.err.println("Unknown argument " + arg);
}
}
assert (Data.GENOME_BUILD > -1);
assert (outgenome > -1);
// assert(Data.GENOME_BUILD!=outgenome);
if (Data.GENOME_BUILD == outgenome) {
System.out.println("Warning! Overwriting input genome " + outgenome);
}
String fname = Data.chromFname(minChrom, outgenome);
File f = new File(fname.substring(0, fname.lastIndexOf('/')));
// assert(false) : f.getAbsolutePath();
if (!f.exists()) {
f.mkdirs();
}
for (int chrom = minChrom; chrom <= maxChrom; chrom++) {
String outName = Data.chromFname(chrom, outgenome);
assert (overwrite || !new File(outName).exists())
: "Destination " + outName + " already exists.";
// assert(false) : inPattern+", "+outName;
process(inPattern.replaceFirst("#", "" + chrom), outName, chrom);
}
FastaToChromArrays2.writeInfo(
outgenome,
maxChrom,
(name == null ? Data.name : name),
"" + Data.GENOME_BUILD + "_plus_variations",
false,
false);
t.stop();
{
String path = IndexMaker4.fname(1, 1, 12, 1);
int lastSlash = path.lastIndexOf('/');
path = path.substring(0, lastSlash);
File dir = new File(path);
if (dir.exists()) {
System.out.println("Deleting old index for " + outgenome);
for (File f2 : dir.listFiles()) {
if (f2.isFile() && (f2.getName().contains(".int2d") || f2.getName().endsWith(".txt"))) {
f2.delete();
}
}
}
}
// System.out.println("Vars in: \t"+VARS_IN);
// System.out.println("Vars out:\t"+VARS_OUT);
System.out.println();
System.out.println("Time: \t" + t);
}
public static void main(String[] args) {
Timer t = new Timer();
String in = args[0];
String outF = args.length > 1 ? args[1] : null;
String outR = args.length > 2 ? args[2] : null;
String outU = args.length > 3 ? args[3] : null;
if (args.length > 4) {
if (args[4].equalsIgnoreCase("header")) {
includeHeader = true;
}
}
ByteFile tf = ByteFile.makeByteFile(in, true, false);
Tools.testForDuplicateFiles(true, in, outF, outR, outU);
Tools.testOutputFiles(true, false, false, outF, outR, outU);
final ByteStreamWriter fStream, rStream, uStream;
fStream = (outF == null ? null : new ByteStreamWriter(outF, true, false, true));
rStream = (outR == null ? null : new ByteStreamWriter(outR, true, false, true));
uStream = (outU == null ? null : new ByteStreamWriter(outU, true, false, true));
if (fStream != null) {
fStream.start();
}
if (rStream != null) {
rStream.start();
}
if (uStream != null) {
uStream.start();
}
long plus = 0;
long minus = 0;
long other = 0;
byte[] s = null;
for (s = tf.nextLine(); s != null; s = tf.nextLine()) {
if (s.length > 0) {
byte c = s[0];
if (c == '@') {
if (includeHeader) {
if (fStream != null) {
fStream.println(s);
}
if (rStream != null) {
rStream.println(s);
}
if (uStream != null) {
uStream.println(s);
}
}
} else {
int flag = SamLine.parseFlagOnly(s);
if (SamLine.mapped(flag)) {
if (SamLine.strand(flag) == 0) {
if (fStream != null) {
fStream.println(s);
}
plus++;
} else {
if (rStream != null) {
rStream.println(s);
}
minus++;
}
} else {
if (uStream != null) {
uStream.println(s);
}
other++;
}
}
}
}
tf.close();
if (fStream != null) {
fStream.poisonAndWait();
}
if (rStream != null) {
rStream.poisonAndWait();
}
if (uStream != null) {
uStream.poisonAndWait();
}
System.err.println("Total reads: \t" + (plus + minus + other));
System.err.println("Plus reads: \t" + (plus));
System.err.println("Minus reads: \t" + (minus));
System.err.println("Unmapped reads:\t" + (other));
t.stop();
System.err.println("Time: \t" + t);
}
public static void main(String[] args) {
String in1 = args[0];
String in2 =
(args.length < 2 || args[1].equalsIgnoreCase("null") || args[1].contains("=")
? null
: args[1]);
if (in2 != null) {
assert (!in1.equalsIgnoreCase(in2));
FASTQ.TEST_INTERLEAVED = false;
} else {
FASTQ.TEST_INTERLEAVED = true;
FASTQ.FORCE_INTERLEAVED = true;
}
long maxReads = -1;
for (int i = 1; i < args.length; i++) {
final String arg = args[i];
final String[] split = arg.split("=");
String a = split[0].toLowerCase();
String b = (split.length > 1 ? split[1] : "true");
if (Parser.isJavaFlag(arg)) {
// jvm argument; do nothing
} else if (Parser.parseZip(arg, a, b)) {
// do nothing
} else if (Parser.parseQuality(arg, a, b)) {
// do nothing
} else if (Parser.parseFasta(arg, a, b)) {
// do nothing
} else if (a.equals("reads") || a.startsWith("maxreads")) {
maxReads = Tools.parseKMG(b);
} else {
throw new RuntimeException("Unknown parameter " + args[i]);
}
}
Parser.processQuality();
assert (FastaReadInputStream.settingsOK());
Timer t = new Timer();
ConcurrentReadInputStream cris = getReadInputStream(maxReads, false, true, in1, in2);
System.out.println("Fetched " + cris.getClass().getName());
{
Object[] p = cris.producers();
// while(p[0]==null){
// p=cris.producers();
// }
System.out.print("Producers: ");
String comma = "";
for (Object o : p) {
System.out.print(comma + (o == null ? "null" : o.getClass().getName()));
comma = ", ";
}
System.out.println();
}
boolean paired = cris.paired();
System.out.println("paired=" + paired);
cris.start(); // 4567
ListNum<Read> ln = cris.nextList();
ArrayList<Read> reads = (ln != null ? ln.list : null);
if (reads != null && !reads.isEmpty()) {
Read r = reads.get(0);
assert ((r.mate != null) == paired);
}
long readCount = 0;
long baseCount = 0;
while (reads != null && reads.size() > 0) {
for (Read r : reads) {
Read r2 = r.mate;
if (r != null) {
readCount++;
if (r.bases != null) {
baseCount += r.length();
}
}
if (r2 != null) {
readCount++;
if (r2.bases != null) {
baseCount += r2.length();
}
}
}
cris.returnList(ln.id, ln.list.isEmpty());
// System.err.println("fetching list");
ln = cris.nextList();
reads = (ln != null ? ln.list : null);
// System.out.println("reads: "+(reads==null ? "null" : reads.size()));
}
System.err.println("Finished reading");
cris.returnList(ln.id, ln.list.isEmpty());
cris.close();
t.stop();
System.out.println("Reads: \t" + readCount);
System.out.println("Bases: \t" + baseCount);
System.out.println("Avg Length: \t" + String.format("%.2f", baseCount * 1.0 / readCount));
System.out.println("Time: \t" + t);
}