@@ -0,0 +1,1012 @@
+package com.bina.varsim.util;%0A%0Aimport com.bina.varsim.types.ReadMapRecord;%0A%0Aimport java.io.BufferedReader;%0Aimport java.io.File;%0Aimport java.io.IOException;%0Aimport java.io.InputStreamReader;%0Aimport java.util.HashMap;%0Aimport java.util.Map;%0Aimport java.util.TreeMap;%0A%0A/**%0A * Created by mohiyudm on 2/29/16.%0A */%0Apublic class ReadMap extends GzFileParser%3CReadMapRecord%3E%7B%0A    protected Map%3CString, ReadMapRecord%3E readMap = new HashMap%3C%3E();%0A%0A    public ReadMap(final File file) throws IOException %7B%0A        _br = new BufferedReader(new InputStreamReader(decompressStream(file.getName())));%0A        while (hasMoreInput()) %7B%0A            final ReadMapRecord record = parseLine();%0A            readMap.put(record.getReadName(), record);%0A        %7D%0A    %7D%0A%0A    public ReadMapRecord parseLine() %7B%0A        return hasMoreInput() ? new ReadMapRecord(_line.trim()) : null;%0A    %7D%0A%0A    public ReadMapRecord getReadMapRecord(final String readName) %7B%0A        return readMap.containsKey(readName) ? readMap.get(readName) : null;%0A    %7D%0A%7D%0A

read in read maps from a read map file