238 lines
8.1 KiB
Java
238 lines
8.1 KiB
Java
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package org.broadinstitute.sting.utils;
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import org.broad.tribble.util.variantcontext.VariantContext;
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import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
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import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
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import java.util.ArrayList;
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import java.util.Arrays;
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/**
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* Created by IntelliJ IDEA.
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* User: delangel
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* Date: Feb 3, 2011
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* Time: 2:44:22 PM
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* To change this template use File | Settings | File Templates.
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*/
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public class IndelUtils {
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protected final static String[] COLUMN_KEYS;
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static {
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COLUMN_KEYS= new String[41];
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COLUMN_KEYS[0] = "Novel_A";
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COLUMN_KEYS[1] = "Novel_C";
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COLUMN_KEYS[2] = "Novel_G";
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COLUMN_KEYS[3] = "Novel_T";
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COLUMN_KEYS[4] = "NOVEL_1";
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COLUMN_KEYS[5] = "NOVEL_2";
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COLUMN_KEYS[6] = "NOVEL_3";
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COLUMN_KEYS[7] = "NOVEL_4";
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COLUMN_KEYS[8] = "NOVEL_5";
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COLUMN_KEYS[9] = "NOVEL_6";
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COLUMN_KEYS[10] = "NOVEL_7";
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COLUMN_KEYS[11] = "NOVEL_8";
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COLUMN_KEYS[12] = "NOVEL_9";
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COLUMN_KEYS[13] = "NOVEL_10orMore";
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COLUMN_KEYS[14] = "RepeatExpansion_A";
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COLUMN_KEYS[15] = "RepeatExpansion_C";
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COLUMN_KEYS[16] = "RepeatExpansion_G";
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COLUMN_KEYS[17] = "RepeatExpansion_T";
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COLUMN_KEYS[18] = "RepeatExpansion_AC";
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COLUMN_KEYS[19] = "RepeatExpansion_AG";
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COLUMN_KEYS[20] = "RepeatExpansion_AT";
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COLUMN_KEYS[21] = "RepeatExpansion_CA";
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COLUMN_KEYS[22] = "RepeatExpansion_CG";
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COLUMN_KEYS[23] = "RepeatExpansion_CT";
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COLUMN_KEYS[24] = "RepeatExpansion_GA";
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COLUMN_KEYS[25] = "RepeatExpansion_GC";
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COLUMN_KEYS[26] = "RepeatExpansion_GT";
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COLUMN_KEYS[27] = "RepeatExpansion_TA";
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COLUMN_KEYS[28] = "RepeatExpansion_TC";
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COLUMN_KEYS[29] = "RepeatExpansion_TG";
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COLUMN_KEYS[30] = "RepeatExpansion_1";
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COLUMN_KEYS[31] = "RepeatExpansion_2";
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COLUMN_KEYS[32] = "RepeatExpansion_3";
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COLUMN_KEYS[33] = "RepeatExpansion_4";
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COLUMN_KEYS[34] = "RepeatExpansion_5";
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COLUMN_KEYS[35] = "RepeatExpansion_6";
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COLUMN_KEYS[36] = "RepeatExpansion_7";
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COLUMN_KEYS[37] = "RepeatExpansion_8";
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COLUMN_KEYS[38] = "RepeatExpansion_9";
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COLUMN_KEYS[39] = "RepeatExpansion_10orMore";
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COLUMN_KEYS[40] = "Other";
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}
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private static final int START_IND_NOVEL = 4;
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private static final int STOP_IND_NOVEL = 13;
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private static final int START_IND_FOR_REPEAT_EXPANSION_1 = 14;
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private static final int IND_FOR_REPEAT_EXPANSION_A = 14;
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private static final int IND_FOR_REPEAT_EXPANSION_C = 15;
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private static final int IND_FOR_REPEAT_EXPANSION_G = 16;
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private static final int IND_FOR_REPEAT_EXPANSION_T = 17;
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private static final int STOP_IND_FOR_REPEAT_EXPANSION_2 = 29;
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private static final int START_IND_FOR_REPEAT_EXPANSION_COUNTS = 30;
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private static final int STOP_IND_FOR_REPEAT_EXPANSION_COUNTS = 39;
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private static final int IND_FOR_OTHER_EVENT = 40;
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private static final int START_IND_NOVEL_PER_BASE = 0;
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private static final int STOP_IND_NOVEL_PER_BASE = 3;
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private static String findMinimalEvent(String eventString) {
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// for each length up to given string length, see if event string is a repetition of units of size N
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String minEvent = eventString;
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for (int k=1; k < eventString.length(); k++) {
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if (eventString.length() % k > 0)
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continue;
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String str = eventString.substring(0,k);
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// now see if event string is a repetition of str
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int numReps = eventString.length() / k;
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String r = "";
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for (int j=0; j < numReps; j++)
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r = r.concat(str);
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if (r.matches(eventString)) {
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minEvent = str;
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break;
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}
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}
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return minEvent;
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}
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public static ArrayList<Integer> findEventClassificationIndex(VariantContext vc, ReferenceContext ref) {
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int eventLength;
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String indelAlleleString;
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boolean done = false;
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ArrayList<Integer> inds = new ArrayList<Integer>();
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if ( vc.isInsertion() ) {
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indelAlleleString = vc.getAlternateAllele(0).getDisplayString();
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} else if ( vc.isDeletion() ) {
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indelAlleleString = vc.getReference().getDisplayString();
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}
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else {
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inds.add(IND_FOR_OTHER_EVENT);
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return inds;
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}
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byte[] refBases = ref.getBases();
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indelAlleleString = findMinimalEvent(indelAlleleString);
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eventLength = indelAlleleString.length();
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// See first if indel is a repetition of bases before current
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int indStart = refBases.length/2-eventLength+1;
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int numRepetitions = 0;
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while (!done) {
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if (indStart < 0)
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done = true;
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else {
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String refPiece = new String(Arrays.copyOfRange(refBases,indStart,indStart+eventLength));
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if (refPiece.matches(indelAlleleString))
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{
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numRepetitions++;
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indStart = indStart - eventLength;
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}
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else
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done = true;
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}
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}
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// now do it forward
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done = false;
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indStart = refBases.length/2+1;
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while (!done) {
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if (indStart + eventLength >= refBases.length)
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break;
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else {
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String refPiece = new String(Arrays.copyOfRange(refBases,indStart,indStart+eventLength));
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if (refPiece.matches(indelAlleleString))
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{
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numRepetitions++;
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indStart = indStart + eventLength;
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}
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else
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done = true;
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}
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}
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if (numRepetitions == 0) {
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//unrepeated sequence from surroundings
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int ind = START_IND_NOVEL + (eventLength-1);
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if (ind > STOP_IND_NOVEL)
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ind = STOP_IND_NOVEL;
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inds.add(ind);
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if (eventLength == 1) {
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// log single base indels additionally by base
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String keyStr = "Novel_" + indelAlleleString;
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int k;
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for (k=START_IND_NOVEL_PER_BASE; k <= STOP_IND_NOVEL_PER_BASE; k++) {
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if (keyStr.matches(COLUMN_KEYS[k]))
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break;
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}
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inds.add(k);
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}
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}
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else {
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int ind = START_IND_FOR_REPEAT_EXPANSION_COUNTS + (numRepetitions-1);
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if (ind > STOP_IND_FOR_REPEAT_EXPANSION_COUNTS)
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ind = STOP_IND_FOR_REPEAT_EXPANSION_COUNTS;
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inds.add(ind);
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if (eventLength<=2) {
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// for single or dinucleotide indels, we further log the base in which they occurred
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String keyStr = "RepeatExpansion_" + indelAlleleString;
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int k;
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for (k=START_IND_FOR_REPEAT_EXPANSION_1; k <= STOP_IND_FOR_REPEAT_EXPANSION_2; k++) {
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if (keyStr.matches(COLUMN_KEYS[k]))
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break;
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}
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// log now event
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inds.add(k);
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}
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}
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return inds;
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}
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public static String[] getIndelClassificationNames() {
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return COLUMN_KEYS;
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}
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public static String getIndelClassificationName(int k) {
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if (k >=0 && k < COLUMN_KEYS.length)
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return COLUMN_KEYS[k];
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else
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throw new ReviewedStingException("Invalid index when trying to get indel classification name");
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}
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public static boolean isATExpansion(VariantContext vc, ReferenceContext ref) {
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ArrayList<Integer> inds = findEventClassificationIndex(vc, ref);
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boolean isIt = false;
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for (int k : inds) {
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if (k == IND_FOR_REPEAT_EXPANSION_A || k == IND_FOR_REPEAT_EXPANSION_A) {
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isIt = true;
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break;
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}
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}
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return isIt;
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}
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public static boolean isCGExpansion(VariantContext vc, ReferenceContext ref) {
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return !isATExpansion(vc,ref);
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}
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}
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