// TODO: HANDLE THE CASE WHERE ANY OF THE START/ENDS ARE 0
private String[] parseBarcode(FastqSequence r) {
if (this.IN_READ_NAME) {
return parseBarcodeFromName(r.getName());
} else {
return parseBarcodeFromSequence(r.getSequence());
}
}
private void setBarcode(FastqSequence r, String[] bcInfo) {
String compoundBC =
bcInfo[0] + (bcInfo[1] != null && bcInfo[1].length() > 0 ? "_" + bcInfo[1] : "");
String newName = buildBarcodeFromReadName(r.getName(), compoundBC);
r.setName(newName);
/*String comment = r.getDescription();
if (comment == null || comment.trim().isEmpty()) {
comment = compoundBC;
} else {
comment = comment + ":" + compoundBC;
}
r.setDescription(comment);*/
}
@Override
protected int doWork() {
sampleBarcodeCounts = new HashMap<String, Integer>();
randomBarcodeCounts = new HashMap<String, Integer>();
otherBarcodeCounts = new HashMap<String, Integer>();
sampleNonBarcodeCounts = new HashMap<String, Integer>();
randomNonBarcodeCounts = new HashMap<String, Integer>();
otherNonBarcodeCounts = new HashMap<String, Integer>();
HashMap<String, String> bcSampleMap = null;
try {
bcSampleMap = BCEvaluator.readBCMap(BC_SAMPLE_MAP);
} catch (FileNotFoundException e) {
System.out.println("Could not access the barcode sample mapping file");
e.printStackTrace();
return 1;
} catch (IOException e) {
System.out.println("Error accessing barcode sample mapping file");
e.printStackTrace();
return 1;
}
if (!OUTDIR.exists()) {
try {
System.out.println("Output directory does not exists " + OUTDIR + ", going to create it");
OUTDIR.mkdir();
} catch (SecurityException e) {
System.out.println("Could not create output directory");
e.printStackTrace();
return 1;
}
}
init();
FastqParser parser1 = new FastqParser();
FastqParser parser2 = new FastqParser();
HashMap<String, BufferedWriter[]> writerMap = null;
BufferedWriter unassignedP1 = null;
BufferedWriter unassignedP2 = null;
try {
try {
parser1.start(FASTQ1);
} catch (IOException e) {
System.out.println("Error reading fastq file " + FASTQ1);
e.printStackTrace();
return 1;
}
if (isPaired) {
try {
parser2.start(FASTQ2);
} catch (IOException e) {
System.out.println("Error reading fastq file " + FASTQ2);
e.printStackTrace();
return 1;
}
}
try {
writerMap = buildWriterMap(bcSampleMap);
unassignedP1 = new BufferedWriter(new FileWriter(OUTDIR + "/unassigned.P1.fq"));
if (isPaired) {
unassignedP2 = new BufferedWriter(new FileWriter(OUTDIR + "/unassigned.P2.fq"));
}
} catch (IOException e) {
System.out.println("Could not create output files for barcode splitting");
e.printStackTrace();
return 1;
}
while (parser1.hasNext()) {
FastqSequence r1 = parser1.next();
String[] bcInfo = parseBarcode(r1); // First position sample, second UMI, third OTHER
if (bcInfo[0] == null) {
logger.error(
"Obtained a null barcode for read " + r1.getName() + " sequence " + r1.getSequence());
}
BufferedWriter out1 = unassignedP1;
BufferedWriter out2 = unassignedP2;
String bc = getClosestBc(bcSampleMap, bcInfo[0]);
if (bc != null) {
// Need to update the BCInfo with the closest barcode once it is found
bcInfo[0] = bc;
BufferedWriter[] out = writerMap.get(bc);
out1 = out[0];
if (isPaired) {
out2 = out[1];
}
setBarcode(r1, bcInfo);
if (!IN_READ_NAME) {
r1.excise(this.BC_START_POS, this.bcLength);
}
updateCounts(bcInfo);
} else {
updateNonCounts(bcInfo);
}
r1.write(out1);
if (isPaired) {
FastqSequence r2 = parser2.next();
if (bc != null) {
setBarcode(r2, bcInfo);
}
// TODO: Handle when/if there is another barcode on R2
r2.write(out2);
}
if (bc != null) {
updateCounts(bcInfo);
}
}
writeReports();
} catch (IOException e) {
System.out.println("Error writing records to file");
e.printStackTrace();
return 1;
} finally {
try {
if (parser1 != null) parser1.close();
} catch (IOException e) {
System.out.println("Could not close fastq1 file");
}
if (isPaired) {
try {
parser2.close();
} catch (IOException e) {
System.out.println("Could not close fastq2 file");
}
}
try {
if (unassignedP1 != null) {
unassignedP1.close();
}
if (unassignedP2 != null) {
unassignedP2.close();
}
if (writerMap != null) {
closeWriters(writerMap);
}
} catch (IOException e) {
System.err.println("Error closing fastq writers");
e.printStackTrace();
}
}
return 0;
}