112 lines
3.6 KiB
Java
Executable File
112 lines
3.6 KiB
Java
Executable File
package edu.mit.broad.sting.utils;
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import edu.mit.broad.sam.SAMRecord;
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import edu.mit.broad.sam.SAMSequenceRecord;
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import edu.mit.broad.picard.reference.ReferenceSequenceFileFactory;
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import edu.mit.broad.picard.reference.ReferenceSequence;
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import edu.mit.broad.picard.reference.ReferenceSequenceFile;
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import java.util.*;
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/**
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* Created by IntelliJ IDEA.
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* User: depristo
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* Date: Feb 24, 2009
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* Time: 10:12:31 AM
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* To change this template use File | Settings | File Templates.
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*/
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public class Utils {
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public static <T> List<T> filter(Predicate pred, Collection<T> c) {
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List<T> filtered = new ArrayList<T>();
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// loop through all the elements in c
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for (T obj : c) {
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// if the predicate is true for the current element
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if (pred.apply(obj)) {
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// append it to the result list
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filtered.add(obj);
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}
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}
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return filtered;
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}
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private static final Map<Integer,String> readFlagNames
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= new HashMap<Integer,String>();
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static {
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readFlagNames.put(0x1, "Paired");
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readFlagNames.put(0x2, "Proper");
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readFlagNames.put(0x4, "Unmapped");
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readFlagNames.put(0x8, "MateUnmapped");
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readFlagNames.put(0x10, "Forward");
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//readFlagNames.put(0x20, "MateForward");
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readFlagNames.put(0x4, "FirstOfPair");
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readFlagNames.put(0x8, "SecondOfPair");
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readFlagNames.put(0x100, "NotPrimary");
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readFlagNames.put(0x200, "NON-PF");
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readFlagNames.put(0x400, "Duplicate");
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}
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public static String readFlagsAsString(SAMRecord rec) {
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String flags = "";
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for ( int flag : readFlagNames.keySet() ) {
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if ( ( rec.getFlags() & flag ) != 0 ) {
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flags += readFlagNames.get(flag) + " ";
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}
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}
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return flags;
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}
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public static String join(String separator, String[] strings) {
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if (strings.length == 0) {
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return "";
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}
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StringBuilder ret = new StringBuilder(strings[0]);
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for (int i = 1; i < strings.length; ++i) {
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ret.append(separator);
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ret.append(strings[i]);
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}
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return ret.toString();
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}
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public static String join(String separator, Collection<String> strings) {
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return join( separator, strings.toArray(new String[0]) );
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}
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public static double average(List<Long> vals, int maxI) {
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long sum = 0L;
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int i = 0;
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for ( long x : vals ) {
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if ( i > maxI )
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break;
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sum += x;
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i++;
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//System.out.printf(" %d/%d", sum, i);
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}
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//System.out.printf("Sum = %d, n = %d, maxI = %d, avg = %f%n", sum, i, maxI, (1.0 * sum) / i);
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return (1.0 * sum) / i;
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}
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public static double average(List<Long> vals) {
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return average(vals, vals.size());
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}
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public static void setupRefContigOrdering(final ReferenceSequenceFile refFile) {
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List<SAMSequenceRecord> refContigs = refFile.getSequenceDictionary();
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HashMap<String, Integer> refContigOrdering = new HashMap<String, Integer>();
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int i = 0;
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System.out.printf("Prepared reference sequence contig dictionary%n order ->");
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for ( SAMSequenceRecord contig : refContigs ) {
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System.out.printf(" %s", contig.getSequenceName());
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refContigOrdering.put(contig.getSequenceName(), i);
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i++;
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}
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System.out.printf("%n Total elements -> %d%n", refContigOrdering.size());
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GenomeLoc.setContigOrdering(refContigOrdering);
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}
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}
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