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package shared;
import java.io.File;
import java.io.PrintStream;
import java.lang.management.ManagementFactory;
import java.lang.reflect.Method;
import java.net.UnknownHostException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import java.util.Comparator;
import java.util.List;
import java.util.Map;
import java.util.Random;
import java.util.concurrent.ThreadLocalRandom;
public class Shared {
/*--------------------------------------------------------------*/
/*---------------- Environment ----------------*/
/*--------------------------------------------------------------*/
public static boolean ENV=(System.getenv()!=null);
private static String HOSTNAME;
public static boolean WINDOWS=envContainsPair("OS", "Win", true);
public static boolean MAC=envContainsPair("OS", "Mac", true);
//https://stackoverflow.com/questions/14288185/detecting-windows-or-linux
public static boolean LINUX=envContainsPair("OS", "nix", true) || envContainsPair("OS", "nux", true) || envContainsPair("OS", "aix", true);
public static boolean SOLARIS=envContainsPair("OS", "sunos", true);
public static boolean GENEPOOL=envContainsPair("NERSC_HOST", "genepool", false);//Probably deprecated
public static boolean DENOVO=envContainsPair("NERSC_HOST", "denovo", false);//Almost certainly deprecated
public static boolean CORI=envContainsPair("NERSC_HOST", "cori", false);
public static boolean PERLMUTTER=envContainsPair("NERSC_HOST", "perlmutter", false);
public static boolean LOGIN=envContainsPair("HOSTNAME", "login", true);
public static boolean NERSC=envContainsKey("NERSC_HOST");
public static boolean AWS=envContainsKey("EC2_HOME");
public static boolean IGBVM="taxonomy-vm".equals(HOSTNAME()) || "taxonomy-vm-2".equals(HOSTNAME());
public static boolean DORI=envContainsPair("SLURM_PARTITION", "dori", false);
public static boolean AMD64="amd64".equalsIgnoreCase(System.getProperty("os.arch"));
public static void setTaxServer(String path){
taxServerNersc=taxServerAws=path;
}
private static String taxServerNersc="https://taxonomy.jgi.doe.gov/";
private static String ntSketchServerNersc="https://nt-sketch.jgi.doe.gov/";
private static String riboSketchServerNersc="https://ribo-sketch.jgi.doe.gov/";
private static String proteinSketchServerNersc="https://protein-sketch.jgi.doe.gov/";
private static String refseqSketchServerNersc="https://refseq-sketch.jgi.doe.gov/";
private static String demuxServer="https://demux.jgi.doe.gov/";//port 4096 on taxvm2
private static String taxServerAws="http://bbtaxonomy.org:3068/";
private static String ntSketchServerAws="http://nt-sketch.org:3071/";
private static String riboSketchServerAws="http://ribo-sketch.org:3073/";
private static String proteinSketchServerAws="http://protein-sketch.org:3074/";
private static String refseqSketchServerAws="http://refseq-sketch.org:3072/";
public static String taxServer(){return awsServers ? taxServerAws : taxServerNersc;}
public static String ntSketchServer(){return awsServers ? ntSketchServerAws : ntSketchServerNersc;}
public static String riboSketchServer(){return awsServers ? riboSketchServerAws : riboSketchServerNersc;}
public static String proteinSketchServer(){return awsServers ? proteinSketchServerAws : proteinSketchServerNersc;}
public static String refseqSketchServer(){return awsServers ? refseqSketchServerAws : refseqSketchServerNersc;}
public static String demuxServer(){return demuxServer;}
public static boolean awsServers=false;
public static boolean envContainsPair(String key, String value, boolean loose){
Map<String, String> map=System.getenv();
String v=map.get(key);
if(value==null || v==null){return v==value;}
return loose ? v.contains(value.toLowerCase()) : value.equalsIgnoreCase(v);
}
public static boolean envContainsKey(String key){
Map<String, String> map=System.getenv();
return map.containsKey(key);
}
public static String HOSTNAME(){
if(HOSTNAME==null){
try {
java.net.InetAddress localMachine = java.net.InetAddress.getLocalHost();
HOSTNAME=localMachine.getHostName();
} catch (UnknownHostException e) {
// TODO Auto-generated catch block
// e.printStackTrace();
HOSTNAME="unknown";
} catch (NullPointerException e) {
// TODO Auto-generated catch block
// e.printStackTrace();
HOSTNAME="unknown";
} catch (Throwable e) {
HOSTNAME="unknown";
}
}
return HOSTNAME;
}
/*--------------------------------------------------------------*/
/*---------------- Stuff ----------------*/
/*--------------------------------------------------------------*/
public static void main(String[] args){
COMMAND_LINE=args;
mainClass=Shared.class;
assert(false) : fullCommandline();
}
public static int LOGICAL_PROCESSORS=CALC_LOGICAL_PROCESSORS();
private static int THREADS=setThreads(-1);
private static int READ_BUFFER_NUM_BUFFERS=setBuffers();
private static int READ_BUFFER_LENGTH=200;
private static long READ_BUFFER_MAX_DATA=400000;
public static boolean OUTPUT_KMG=true;
/** Temporary, for testing; should be made non-global */
public static boolean AMINO_IN=false;
//TODO: For some reason, it seems as though GAPBUFFER must equal exactly 1/2 of GAPLEN. Not good; 1/4 would be far better.
public static final int GAPBUFFER=64; //TODO: Seems to break less than 64, for some reason
public static final int GAPBUFFER2=2*GAPBUFFER;
public static final int GAPLEN=128; //TODO: May break when over 128
public static final int MINGAP=GAPBUFFER2+GAPLEN;
public static final int GAPCOST=Tools.max(1, GAPLEN/64);
public static final byte GAPC='-';
public static String BBTOOLS_VERSION_STRING="39.20";
public static String BBMAP_VERSION_NAME="Grass Blade";
public static boolean TRIM_READ_COMMENTS=false;
public static boolean TRIM_RNAME=false; //For mapped sam reads
public static boolean USE_JNI=(CORI || DENOVO || GENEPOOL || NERSC || AWS || (AMD64 && (LINUX || MAC))) && !WINDOWS;
public static boolean USE_MPI=false;
public static boolean MPI_KEEP_ALL=true;
/** Use ConcurrentReadInputStreamMPI instead of D for this instance */
public static boolean USE_CRISMPI=true;
public static int MPI_RANK=0;
public static int MPI_NUM_RANKS=1;
public static int FASTA_WRAP=70;
public static byte FAKE_QUAL=30;
public static boolean FIX_EXTENSIONS=true;
/** True if assertions are enabled. */
private static boolean EA=false;
public static boolean EA(){return EA;}
public static String BBMAP_CLASS=null;
public static Class<?> mainClass=null;
public static String[] COMMAND_LINE=null;
public static final byte PLUS=0;
public static final byte MINUS=1;
/** Index with strand number */
public static final String[] strandCodes={"+", "-", "?"};
public static final char[] strandCodes2={'+', '-', '?'};
public static List<String> JVM_ARGS(){
return ManagementFactory.getRuntimeMXBean().getInputArguments();
}
public static String fullCommandline(){return fullCommandline(true, true);}
public static String fullCommandline(boolean includeCP){return fullCommandline(includeCP, true);}
public static String fullCommandline(boolean includeCP, boolean includeArgs){
StringBuilder sb=new StringBuilder();
if(includeArgs) {
sb.append("java ");
for(String s : JVM_ARGS()) {
sb.append(s).append(' ');
}
}
if(includeCP) {
sb.append("-cp "+System.getProperty("java.class.path")+" ");
}
sb.append(mainClass.getCanonicalName()).append(' ');
for(String s : COMMAND_LINE) {
sb.append(s).append(' ');
}
sb.setLength(sb.length()-1);
return sb.toString();
}
/** Directory in which to write temp files */
private static String TMPDIR=getTmpdir();
// static{assert(false) : "TMPDIR="+TMPDIR;}
private static String getTmpdir(){
String s=System.getenv("SLURM_TMP");
if(s==null){s=System.getenv("TMPDIR");}
if(s!=null){s=(s+"/").replaceAll("//", "/").replaceAll("\\\\", "/");}
return s;
}
public static String tmpdir(){return TMPDIR;}
public static String setTmpdir(String s){
if(s==null){TMPDIR=null;}
else{
s=s.replaceAll("\\\\", "/");
if(!s.endsWith("/")){s=s+"/";}
TMPDIR=s.replaceAll("//", "/");
}
return TMPDIR;
}
/** Anomaly probably resolved as of v.20.1
* This variable should be TRUE for normal users and FALSE for me. */
public static boolean anomaly=!(System.getProperty("user.dir")+"").contains("/bushnell/") && !WINDOWS;
public static final char[] getTLCB(int len){
char[] buffer=TLCB.get();
if(buffer==null || buffer.length<len){
buffer=new char[len];
if(len<1000000){TLCB.set(buffer);}
}
return buffer;
}
private static final ThreadLocal<char[]> TLCB=new ThreadLocal<char[]>();
/*--------------------------------------------------------------*/
/*---------------- Threads ----------------*/
/*--------------------------------------------------------------*/
public static int capThreads(int t) {
assert(THREADS>0) : THREADS;
final int old=THREADS;
THREADS=Tools.mid(1, t, old);
assert(THREADS>0) : THREADS;
return old;
}
public static int setThreads(String x){
int y=LOGICAL_PROCESSORS;
if(x!=null && !x.equalsIgnoreCase("auto")){
if(x.indexOf('.')>=0){
double d=Double.parseDouble(x);
if(d>1){
y=(int)d;
}else{
y=(int)Tools.max(1, Math.ceil(d*y));
}
}else{
y=Integer.parseInt(x);
}
}
return setThreads(y);
}
public static int setThreads(int x){
if(x>0){
THREADS=x;
}else{
THREADS=Tools.max(1, LOGICAL_PROCESSORS);
}
setBuffers();
assert(THREADS>0) : THREADS;
return THREADS;
}
public static int threads(){
assert(THREADS>0) : THREADS;
return THREADS;
}
public static int CALC_LOGICAL_PROCESSORS(){
final int procs=Tools.max(1, Runtime.getRuntime().availableProcessors());
int slots=procs;
if(PERLMUTTER && LOGIN) {slots=Tools.min(slots, 64);}
Map<String,String> env=System.getenv();
String s=env.get("NSLOTS");//Genepool
boolean success=false;
if(s!=null){
int x=slots;
try {
x=Tools.max(1, Integer.parseInt(s));
success=true;
} catch (NumberFormatException e) {
//ignore
}
if(x<=16){slots=x;}
}
if(!success){
s=env.get("SLURM_CPUS_ON_NODE");//All SLURM systems
if(s!=null){
int x=slots;
try {
x=Tools.max(1, Integer.parseInt(s));
success=true;
} catch (NumberFormatException e) {
//ignore
}
slots=x;
}
}
// if(slots>8 && (slots*2==procs || (slots==16 && procs==40))){return procs;}//hyperthreading
return Tools.min(slots, procs);
}
/*--------------------------------------------------------------*/
/*---------------- JNI ----------------*/
/*--------------------------------------------------------------*/
private static int loadedJNI=-1;
public static synchronized boolean loadJNI(){
return loadJNI("bbtoolsjni");
}
public static synchronized boolean loadJNI(String name){
if(loadedJNI<0){
boolean success=false;
String libpath=System.getProperty("java.library.path");
// System.err.println("libpath='"+libpath+"'");
if(libpath==null || libpath.length()==0){
libpath=System.getProperty("java.class.path").replace("/current", "/jni");
}else if(!libpath.contains("/jni")){
libpath=libpath+":"+System.getProperty("java.class.path").replace("/current", "/jni");
}
//Normal load
try{
System.loadLibrary(name);
success=true;
}catch(UnsatisfiedLinkError e){}
if(!success){
// System.loadLibrary() does not work with MPI.
// Need to use System.load() with an explicit full
// path to the native library file for the MPI case.
// String libpath=System.getProperty("java.library.path");
libpath=libpath.replace("-Djava.library.path=","");
String[] libpathEntries=libpath.split(File.pathSeparator);
for(int i=0; i<libpathEntries.length && !success; i++){
String lib=libpathEntries[i]+"/"+System.mapLibraryName(name);
try{
System.load(lib);
success=true;
}catch(UnsatisfiedLinkError e2){
success=false;
}
}
}
if(success){
loadedJNI=1;
}else{
loadedJNI=0;
System.err.println("Native library can not be found in java.library.path.");
new Exception().printStackTrace();
System.exit(1);
}
}
return loadedJNI==1;
}
/*--------------------------------------------------------------*/
/*---------------- Buffers ----------------*/
/*--------------------------------------------------------------*/
public static int capBuffers(int num){
return setBuffers(Tools.min(num, READ_BUFFER_NUM_BUFFERS));
}
public static int READ_BUFFER_NUM_BUFFERS() {
return READ_BUFFER_NUM_BUFFERS;
}
public static int setBuffers(){
return setBuffersFromThreads(THREADS);
}
public static int setBuffersFromThreads(int threads){
return setBuffers(Tools.max(4, (threads*3)/2));
}
/** Number of read lists buffered in input streams */
public static int setBuffers(int num){
// assert(READ_BUFFER_NUM_BUFFERS==0 || READ_BUFFER_NUM_BUFFERS==num) : READ_BUFFER_NUM_BUFFERS+" -> "+num; //TODO: 123
num=Tools.max(2, num);//TODO: Interesting, this is min 2 instead of the expected 1; maybe 1 didn't work?
return READ_BUFFER_NUM_BUFFERS=num;
}
/** Number of read lists buffered in input streams */
public static int numBuffers(){
return READ_BUFFER_NUM_BUFFERS;
}
public static int bufferLen(){
return READ_BUFFER_LENGTH;
}
public static long bufferData(){
return READ_BUFFER_MAX_DATA;
}
public static void capBufferLen(int x){
if(x!=READ_BUFFER_LENGTH){setBufferLen(Tools.min(x, READ_BUFFER_LENGTH));}
}
public static int setBufferLen(int x){
// assert(false) : READ_BUFFER_LENGTH+" -> "+x; //TODO: 123
assert(x>0);
return READ_BUFFER_LENGTH=x;
}
public static long setBufferData(long x){
// assert(false) : READ_BUFFER_MAX_DATA+" -> "+x; //TODO: 123
assert(x>0);
return READ_BUFFER_MAX_DATA=x;
}
/*--------------------------------------------------------------*/
/*---------------- Memory ----------------*/
/*--------------------------------------------------------------*/
public static boolean LOW_MEMORY=false;
/** Ratio of -Xms to -Xmx parameters */
public static final double xmsRatio(){
Runtime rt=Runtime.getRuntime();
return rt.totalMemory()*1.0/rt.maxMemory();
}
public static long memAvailable(int readThreads){
long usableMemory;
{
long memory=Runtime.getRuntime().maxMemory();
double xmsRatio=Shared.xmsRatio();
usableMemory=(long)Tools.max(((memory-48000000-(Tools.max(readThreads, 4)*400000))*(xmsRatio>0.97 ? 0.82 : 0.72)), memory*0.45);
}
return usableMemory;
}
public static long memTotal(){
Runtime rt=Runtime.getRuntime();
return rt.maxMemory();
}
public static long memFree(){
Runtime rt=Runtime.getRuntime();
return rt.freeMemory();
}
public static long memAvailable(){
Runtime rt=Runtime.getRuntime();
return rt.maxMemory()-rt.totalMemory()+rt.freeMemory();
}
/** An estimate, for preallocation */
public static long memAvailableAdvanced(){
Runtime rt=Runtime.getRuntime();
final long mmemory=rt.maxMemory();
final long tmemory=rt.totalMemory();
final long fmemory=rt.freeMemory();
final long umemory=tmemory-fmemory;
double xmsRatio=Shared.xmsRatio();
double usableMemory=Tools.max(((mmemory-96000000)*(xmsRatio>0.97 ? 0.82 : 0.72)), mmemory*0.45);
double availableMemory=Tools.max(fmemory*0.5, usableMemory-umemory); //The 0.5 is an untested conservative guess
return (long)availableMemory;
}
public static long memUsed(){
Runtime rt=Runtime.getRuntime();
return rt.maxMemory()-rt.freeMemory();
}
/** Print statistics about current memory use and availability */
public static final void printMemory(){
try{
if(GC_BEFORE_PRINT_MEMORY){
System.gc();
System.gc();
}
Runtime rt=Runtime.getRuntime();
long mmemory=rt.maxMemory()/1000000;
long tmemory=rt.totalMemory()/1000000;
long fmemory=rt.freeMemory()/1000000;
long umemory=tmemory-fmemory;
System.err.println("Memory: "+"max="+mmemory+"m, total="+tmemory+"m, "+
"free="+fmemory+"m, used="+umemory+"m");
}catch(Throwable t){}
}
public static final Random threadLocalRandom(){return threadLocalRandom(-1);}
public static final Random threadLocalRandom(long seed){
Random randy;
if(seed>=0){return new Random(seed);}//ThreadLocalRandom does not support seeds
try {
randy=ThreadLocalRandom.current();
} catch (Throwable e) {//In case the JVM does not support ThreadLocalRandom;
randy=new Random();
}
return randy;
}
/** Do garbage collection prior to printing memory usage */
public static boolean GC_BEFORE_PRINT_MEMORY=false;
/** For Matt N. */
public static String comment;
/*--------------------------------------------------------------*/
/*---------------- Java 8 ----------------*/
/*--------------------------------------------------------------*/
public static final void sort(int[] array){sort(array, 0, array.length);}
public static final void sort(int[] array, int from, int to){
try {
if(!parallelSort || array.length<=parallelSortLength){
Arrays.sort(array, from, to); //Supported in pre-Java 8.
return;
}
Arrays.parallelSort(array, from, to);
} catch (OutOfMemoryError e) {
KillSwitch.memKill(e);
}
}
public static final void sort(long[] array){sort(array, 0, array.length);}
public static final void sort(long[] array, int from, int to){
try {
if(!parallelSort || array.length<=parallelSortLength || THREADS<2){
Arrays.sort(array, from, to); //Supported in pre-Java 8.
return;
}
Arrays.parallelSort(array, from, to);
} catch (OutOfMemoryError e) {
KillSwitch.memKill(e);
}
}
public static final void sort(float[] array){sort(array, 0, array.length);}
public static final void sort(float[] array, int from, int to){
try {
if(!parallelSort || array.length<=parallelSortLength){
Arrays.sort(array, from, to); //Supported in pre-Java 8.
return;
}
Arrays.parallelSort(array, from, to);
} catch (OutOfMemoryError e) {
KillSwitch.memKill(e);
}
}
public static final void sort(double[] array){sort(array, 0, array.length);}
public static final void sort(double[] array, int from, int to){
try {
if(!parallelSort || array.length<=parallelSortLength){
Arrays.sort(array, from, to); //Supported in pre-Java 8.
return;
}
Arrays.parallelSort(array, from, to);
} catch (OutOfMemoryError e) {
KillSwitch.memKill(e);
}
}
public static final <T extends Comparable<? super T>> void sort(T[] array){sort(array, 0, array.length);}
public static final <T extends Comparable<? super T>> void sort(T[] array, int from, int to){
try {
if(!parallelSort || array.length<=parallelSortLength || THREADS<2){
Arrays.sort(array, from, to); //Supported in pre-Java 8.
return;
}
Arrays.parallelSort(array, from, to);
} catch (OutOfMemoryError e) {
KillSwitch.memKill(e);
}
}
public static final <T extends Comparable<? super T>> void sort(T[] array, Comparator<? super T> comparator){sort(array, 0, array.length, comparator);}
public static final <T extends Comparable<? super T>> void sort(T[] array, int from, int to, Comparator<? super T> comparator){
try {
if(!parallelSort || array.length<=parallelSortLength || THREADS<2){
Arrays.sort(array, from, to, comparator); //Supported in pre-Java 8.
return;
}
Arrays.parallelSort(array, from, to, comparator);
} catch (OutOfMemoryError e) {
KillSwitch.memKill(e);
}
}
public static final <T extends Comparable<? super T>> void sort(ArrayList<T> list){
try {
if(!parallelSort || list.size()<=parallelSortLength || THREADS<2){
Collections.sort(list); //Supported in pre-Java 8.
return;
}
{//If this block causes compile errors, just replace the whole function body with "Shared.sort(list, comparator);"
@SuppressWarnings("unchecked")
T[] array=list.toArray((T[])new Comparable[0]);
list.clear();
Arrays.parallelSort(array);
for(T r : array){list.add(r);}
}
} catch (OutOfMemoryError e) {
KillSwitch.memKill(e);
}
}
public static final <T> void sort(ArrayList<T> list, Comparator<? super T> comparator){
try {
if(!parallelSort){
Collections.sort(list, comparator); //Supported in pre-Java 8.
return;
}
{//If this block causes compile errors, just replace the whole function body with "Shared.sort(list, comparator);"
if(list.size()<=parallelSortLength || THREADS<2){
list.sort(comparator);
return;
}
@SuppressWarnings("unchecked")
T[] array=list.toArray((T[])new Object[0]);
list.clear();
Arrays.parallelSort(array, comparator);
for(T r : array){list.add(r);}
}
} catch (OutOfMemoryError e) {
KillSwitch.memKill(e);
}
}
/**
* Close this output stream if it is not stderr or stdout.
* Intended for files.
* @param outstream
*/
public static void closeStream(PrintStream outstream) {
if(outstream!=null){
synchronized(outstream){
if(outstream!=System.err && outstream!=System.out){
outstream.close();
}
}
}
}
public static final int MAX_ARRAY_LEN=Integer.MAX_VALUE-20;
public static final int parallelSortLength=10000;
private static boolean disableParallelSort=false;
public static boolean parallelSort=testParallelSort();
public static boolean SIMD=false;
public static double javaVersion=parseJavaVersion();
private static double parseJavaVersion(){
String s=System.getProperty("java.version");
if(s==null){return 1.6;}
int dots=0;
StringBuilder sb=new StringBuilder();
for(int i=0; i<s.length() && dots<2; i++){
char c=s.charAt(i);
if(c=='.'){dots++;}
else if(!Tools.isDigit(c)){break;}
if(dots>1){break;}
sb.append(c);
}
return Double.parseDouble(sb.toString());
}
public static void setParallelSort(boolean x){
if(x){
disableParallelSort=false;
parallelSort=testParallelSort();
}else{
disableParallelSort=true;
parallelSort=false;
}
}
/** This tests to see if the java version supports parallel sort, which was not true prior to 1.8. */
private static boolean testParallelSort(){
Method m=null;
try {
m=Arrays.class.getMethod("parallelSort", new Class[] {Object[].class, Comparator.class});
} catch (NoSuchMethodException e) {
// TODO Auto-generated catch block
// e.printStackTrace();
} catch (SecurityException e) {
// TODO Auto-generated catch block
// e.printStackTrace();
} catch (Throwable t) {
// TODO Auto-generated catch block
// e.printStackTrace();
}
return m!=null;
}
static{
assert(EA=true);//Sets the EA flag
KillSwitch.addBallast();
}
}
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