/** @throws IOException */
private void readFileHeader() throws Exception {
// fisrt four bytes are empty
// it should be zero for new version of control file, backward compatibility
int emptyBytes = this.readFourBytes(inputStream);
if (emptyBytes != 0) {
log.warn(
"The first four bytes are not zero: "
+ emptyBytes
+ ". This is an old format control file.");
this.totalClusters = emptyBytes;
return;
}
// next four bytes should be version and greater or equal to the expected
int version = this.readFourBytes(inputStream);
if (version != this.EXPECTED_CONTROL_VERSION) {
log.error("Unexpected version byte: " + version);
throw new Exception("Unexpected version number in control file");
}
// next four bytes should be the total number of clusters
this.totalClusters = this.readFourBytes(inputStream);
log.info("The total number of clusters: " + this.getTotalClusters());
}
/**
* Lift over the given interval to the new genome build.
*
* @param interval Interval to be lifted over.
* @param liftOverMinMatch Minimum fraction of bases that must remap.
* @return Interval in the output build coordinates, or null if it cannot be lifted over.
*/
public Interval liftOver(final Interval interval, final double liftOverMinMatch) {
if (interval.length() == 0) {
throw new IllegalArgumentException(
"Zero-length interval cannot be lifted over. Interval: " + interval.getName());
}
Chain chainHit = null;
TargetIntersection targetIntersection = null;
// Number of bases in interval that can be lifted over must be >= this.
double minMatchSize = liftOverMinMatch * interval.length();
// Find the appropriate Chain, and the part of the chain corresponding to the interval to be
// lifted over.
for (final Chain chain : chains.getOverlaps(interval)) {
final TargetIntersection candidateIntersection = targetIntersection(chain, interval);
if (candidateIntersection != null
&& candidateIntersection.intersectionLength >= minMatchSize) {
if (chainHit != null) {
// In basic liftOver, multiple hits are not allowed.
return null;
}
chainHit = chain;
targetIntersection = candidateIntersection;
} else if (candidateIntersection != null) {
LOG.info(
"Interval "
+ interval.getName()
+ " failed to match chain "
+ chain.id
+ " because intersection length "
+ candidateIntersection.intersectionLength
+ " < minMatchSize "
+ minMatchSize
+ " ("
+ (candidateIntersection.intersectionLength / (float) interval.length())
+ " < "
+ liftOverMinMatch
+ ")");
}
}
if (chainHit == null) {
// Can't be lifted over.
return null;
}
return createToInterval(interval.getName(), targetIntersection);
}
protected int doWork() {
IoUtil.assertFileIsReadable(INPUT);
IoUtil.assertFileIsWritable(OUTPUT);
final SAMFileReader in = new SAMFileReader(INPUT);
// create the read group we'll be using
final SAMReadGroupRecord rg = new SAMReadGroupRecord(RGID);
rg.setLibrary(RGLB);
rg.setPlatform(RGPL);
rg.setSample(RGSM);
rg.setPlatformUnit(RGPU);
if (RGCN != null) rg.setSequencingCenter(RGCN);
if (RGDS != null) rg.setDescription(RGDS);
if (RGDT != null) rg.setRunDate(RGDT);
log.info(
String.format(
"Created read group ID=%s PL=%s LB=%s SM=%s%n",
rg.getId(), rg.getPlatform(), rg.getLibrary(), rg.getSample()));
// create the new header and output file
final SAMFileHeader inHeader = in.getFileHeader();
final SAMFileHeader outHeader = inHeader.clone();
outHeader.setReadGroups(Arrays.asList(rg));
if (SORT_ORDER != null) outHeader.setSortOrder(SORT_ORDER);
final SAMFileWriter outWriter =
new SAMFileWriterFactory()
.makeSAMOrBAMWriter(
outHeader, outHeader.getSortOrder() == inHeader.getSortOrder(), OUTPUT);
final ProgressLogger progress = new ProgressLogger(log);
for (final SAMRecord read : in) {
read.setAttribute(SAMTag.RG.name(), RGID);
outWriter.addAlignment(read);
progress.record(read);
}
// cleanup
in.close();
outWriter.close();
return 0;
}
private void read(InputStream in, String filename) throws IOException {
// Pattern comma=Pattern.compile("[,]");
Pattern pipe = Pattern.compile("[\\|]");
Pattern amp = Pattern.compile("&");
out.println("insert into FILE" + SUFFIX + "(filename) values (" + quote(filename) + ");");
VcfIterator r = new VcfIterator(in);
VCFHeader header = r.getHeader();
String csqColumns[] = null;
VCFInfoHeaderLine infoHeader = header.getInfoHeaderLine("CSQ");
if (infoHeader != null && this.USE_VEP) {
LOG.info("parsing VEP " + infoHeader.getDescription());
final String formatStr = "Format: ";
int i = infoHeader.getDescription().indexOf(formatStr);
if (i != -1) {
csqColumns =
pipe.split(infoHeader.getDescription().substring(i + formatStr.length()).trim());
LOG.debug(Arrays.asList(csqColumns));
} else {
LOG.error("Cannot parse " + infoHeader.getDescription());
}
}
String snpEffColumns[] = null;
infoHeader = header.getInfoHeaderLine("EFF");
if (infoHeader != null && this.USE_SNPEFF) {
LOG.info("parsing EFF " + infoHeader.getDescription());
final String formatStr = ".Format: '";
final String desc = infoHeader.getDescription();
int i = desc.indexOf(formatStr);
if (i != -1) i = desc.indexOf('(', i + formatStr.length());
int j = desc.lastIndexOf(')');
if (i != -1 && j > i) {
snpEffColumns =
pipe.split(desc.substring(i + 1, j).replaceAll("[ \\[\\]()\\.]", "").trim());
LOG.info(Arrays.asList(snpEffColumns));
} else {
LOG.error("Cannot parse " + infoHeader.getDescription());
}
}
String nmdColumns[] = null;
infoHeader = header.getInfoHeaderLine("NMD");
if (infoHeader != null && this.USE_SNPEFF) {
final String formatStr = " Format: '";
final String desc = infoHeader.getDescription();
int i = desc.indexOf(formatStr);
int j = (i == -1 ? -1 : desc.lastIndexOf('\''));
if (i != -1 && j > i) {
nmdColumns =
pipe.split(
desc.substring(i + formatStr.length(), j).replaceAll("[ \\[\\]()\\.]", "").trim());
} else {
LOG.error("Cannot parse " + infoHeader.getDescription());
}
}
String lofColumns[] = null;
infoHeader = header.getInfoHeaderLine("LOF");
if (infoHeader != null && this.USE_SNPEFF) {
final String formatStr = " Format: '";
final String desc = infoHeader.getDescription();
int i = desc.indexOf(formatStr);
int j = (i == -1 ? -1 : desc.lastIndexOf('\''));
if (i != -1 && j > i) {
lofColumns =
pipe.split(
desc.substring(i + formatStr.length(), j).replaceAll("[ \\[\\]()\\.]", "").trim());
} else {
LOG.error("Cannot parse " + infoHeader.getDescription());
}
}
for (String S : header.getSampleNamesInOrder()) {
// merge into SAMPLE using (select 1+MAX(id),'azdazd' from SAMPLE) as vals(x,y) on
// SAMPLE.name=vals.y when NOT MATCHED THEN INSERT VALUES vals.x,vals.y;
switch (this.engine) {
case hsql:
out.println(
"merge into SAMPLE"
+ SUFFIX
+ " using ( values("
+ quote(S)
+ ") ) "
+ "AS vals(y) ON SAMPLE"
+ SUFFIX
+ ".name = vals.y "
+ "WHEN NOT MATCHED THEN INSERT VALUES (NULL,vals.y);");
break;
default:
out.println(
"insert or ignore into SAMPLE" + SUFFIX + "(name) values (" + quote(S) + ");");
break;
}
}
List<String> headers = new ArrayList<String>();
for (VCFHeaderLine line : header.getMetaDataInSortedOrder()) {
if (VCFHeaderVersion.isFormatString(line.getKey())) continue;
headers.add(VCFHeader.METADATA_INDICATOR + line);
}
String chromLine = VCFHeader.HEADER_INDICATOR;
for (VCFHeader.HEADER_FIELDS field : header.getHeaderFields()) {
if (!VCFHeader.HEADER_INDICATOR.equals(chromLine))
chromLine += (VCFConstants.FIELD_SEPARATOR);
chromLine += (field);
}
if (header.hasGenotypingData()) {
chromLine += VCFConstants.FIELD_SEPARATOR + "FORMAT";
for (String sample : header.getGenotypeSamples()) {
chromLine += VCFConstants.FIELD_SEPARATOR;
chromLine += sample;
}
}
headers.add(chromLine);
for (String line : headers) {
out.println(
"insert into HEADER"
+ SUFFIX
+ "(file_id,header) values ("
+ "(select max(id) from FILE"
+ SUFFIX
+ "),"
+ quote(line)
+ ");");
}
while (r.hasNext()) {
VariantContext var = r.next();
if (var == null) {
LOG.error("Cannot parse VCF");
continue;
}
// "create table if not exists FILE(id,filename text)";
// "create table if not exists VARIATION(id,file_id,chrom,pos,start0,end0,rs_id,ref,qual)";
out.println(
"insert into VARIATION"
+ SUFFIX
+ "(file_id,chrom,pos,START0,END0,rs_id,ref,qual) values ("
+ "(select max(id) from FILE"
+ SUFFIX
+ "),"
+ quote(var.getChr())
+ ","
+ var.getStart()
+ ","
+ (var.getStart() - 1)
+ ","
+ var.getEnd()
+ ","
+ (var.getID() == null || var.getID().equals(VCFConstants.EMPTY_ID_FIELD)
? "NULL"
: quote(var.getID()))
+ ","
+ quote(var.getReference().getDisplayString())
+ ","
+ (var.getPhredScaledQual() < 0 ? "NULL" : var.getPhredScaledQual())
+ ");");
// "create table if not exists ALT(id,var_id,alt)";
for (Allele alt : var.getAlternateAlleles()) {
out.println(
"insert into ALT"
+ SUFFIX
+ "(var_id,alt) values ("
+ "(select max(id) from VARIATION"
+ SUFFIX
+ "),"
+ quote(alt.getDisplayString())
+ ");");
}
// "create table if not exists FILTER(id,var_id,filter)";
for (String filter : var.getFilters()) {
out.println(
"insert into FILTER"
+ SUFFIX
+ "(var_id,filter) values ("
+ "(select max(id) from VARIATION"
+ SUFFIX
+ "),"
+ quote(filter)
+ ");");
}
CommonInfo infos = var.getCommonInfo();
for (String key : infos.getAttributes().keySet()) {
Object val = infos.getAttribute(key);
// "create table if not exists INFO(id,var_id,k,v)";
if (SPLIT4 && key.equals("DP4")) {
String dp4[] = infotoString(val).split("[,]");
insertIntoInfo(quote(key + "[refFor]"), quote(dp4[0]));
insertIntoInfo(quote(key + "[refRev]"), quote(dp4[1]));
insertIntoInfo(quote(key + "[altFor]"), quote(dp4[2]));
insertIntoInfo(quote(key + "[altRev]"), quote(dp4[3]));
} else {
insertIntoInfo(quote(key), quote(infotoString(val)));
}
if (key.equals("CSQ") && csqColumns != null) {
List as_array = castToStringArray(val);
for (Object csqs : as_array) {
if (csqs.toString().isEmpty()) continue;
String tokens[] = pipe.split(csqs.toString());
List<String> extraInfo = new ArrayList<String>();
for (int t = 0; t < tokens.length && t < csqColumns.length; ++t) {
if (tokens[t].isEmpty()) continue;
if (csqColumns[t].equals("Consequence")) {
for (String pred : amp.split(tokens[t])) {
if (pred.isEmpty()) continue;
extraInfo.add(csqColumns[t]);
extraInfo.add(pred);
}
} else {
extraInfo.add(csqColumns[t]);
extraInfo.add(tokens[t]);
}
}
insertExtraInfos("CSQ", extraInfo);
}
}
if (key.equals("EFF") && snpEffColumns != null) {
for (Object item : castToStringArray(val)) {
String snpeff = item.toString();
if (snpeff.isEmpty()) continue;
int opar = snpeff.indexOf('(');
if (opar == -1) continue;
int cpar = snpeff.lastIndexOf(')');
if (cpar == -1) continue;
String tokens[] = pipe.split(snpeff.substring(opar + 1, cpar));
List<String> h = new ArrayList<String>();
h.add("Effect");
h.add(snpeff.substring(0, opar));
for (int t = 0; t < tokens.length && t < snpEffColumns.length; ++t) {
if (tokens[t].isEmpty()) continue;
h.add(snpEffColumns[t]);
h.add(tokens[t]);
}
insertExtraInfos(key, h);
}
}
if (key.equals("NMD") && nmdColumns != null) {
for (Object item : castToStringArray(val)) {
String nmd = item.toString();
if (nmd.isEmpty()) continue;
String tokens[] = pipe.split(nmd);
List<String> h = new ArrayList<String>(nmdColumns.length * 2);
for (int t = 0; t < tokens.length && t < nmdColumns.length; ++t) {
if (tokens[t].isEmpty()) continue;
h.add(nmdColumns[t]);
h.add(tokens[t]);
}
insertExtraInfos(key, h);
}
}
if (key.equals("LOF") && lofColumns != null) {
for (Object item : castToStringArray(val)) {
String lof = item.toString();
if (lof.isEmpty()) continue;
String tokens[] = pipe.split(lof);
List<String> h = new ArrayList<String>(lofColumns.length * 2);
for (int t = 0; t < tokens.length && t < lofColumns.length; ++t) {
if (tokens[t].isEmpty()) continue;
h.add(lofColumns[t]);
h.add(tokens[t]);
}
insertExtraInfos(key, h);
}
}
}
GenotypesContext genotypesCtx = var.getGenotypes();
for (Genotype g : genotypesCtx) {
// "create table if not exists GENOTYPE(id,var_id,k,v)";
List<Allele> alleles = g.getAlleles();
out.println(
"insert into GENOTYPE"
+ SUFFIX
+ "(var_id,sample_id,A1,A2,dp,ad,gq,pl,"
+ "is_phased,is_hom,is_homref,is_homvar,is_mixed,"
+ "is_nocall,is_noninformative,is_available,is_called,is_filtered"
+ ") values ("
+ "(select max(id) from VARIATION"
+ SUFFIX
+ "),"
+ "(select id from SAMPLE"
+ SUFFIX
+ " where name="
+ quote(g.getSampleName())
+ "),"
+ (alleles.size() == 2 ? quote(alleles.get(0).getBaseString()) : "NULL")
+ ","
+ (alleles.size() == 2 ? quote(alleles.get(1).getBaseString()) : "NULL")
+ ","
+ (g.hasDP() ? g.getDP() : "NULL")
+ ","
+ (g.hasAD() ? quote(infotoString(g.getAD())) : "NULL")
+ ","
+ (g.hasGQ() ? g.getGQ() : "NULL")
+ ","
+ (g.hasPL() ? quote(infotoString(g.getPL())) : "NULL")
+ ","
+ (g.isPhased() ? 1 : 0)
+ ","
+ (g.isHom() ? 1 : 0)
+ ","
+ (g.isHomRef() ? 1 : 0)
+ ","
+ (g.isHomVar() ? 1 : 0)
+ ","
+ (g.isMixed() ? 1 : 0)
+ ","
+ (g.isNoCall() ? 1 : 0)
+ ","
+ (g.isNonInformative() ? 1 : 0)
+ ","
+ (g.isAvailable() ? 1 : 0)
+ ","
+ (g.isCalled() ? 1 : 0)
+ ","
+ (g.isFiltered() ? 1 : 0)
+ ");");
for (String key : g.getExtendedAttributes().keySet()) {
Object val = g.getExtendedAttribute(key);
if (val == null) continue;
out.println(
"insert into GTPROP"
+ SUFFIX
+ "(genotype_id,k,v) values ("
+ "(select max(id) from GENOTYPE"
+ SUFFIX
+ "),"
+ quote(key)
+ ","
+ quote(infotoString(val))
+ ");");
}
}
}
r.close();
}
@Override
protected int doWork() {
try {
try {
this.engine = SQLEngine.valueOf(this.ENGINE);
} catch (Exception err) {
LOG.error("BAD SQL ENGINE " + this.ENGINE);
return -1;
}
out.println(
"create table if not exists FILE"
+ SUFFIX
+ "("
+ columnId()
+ "filename "
+ varchar(255)
+ " NOT NULL"
+ ");");
out.println(
"create table if not exists HEADER"
+ SUFFIX
+ "("
+ columnId()
+ "file_id INT NOT NULL REFERENCES FILE"
+ SUFFIX
+ "(id) ON DELETE CASCADE,"
+ "header "
+ text()
+ ");");
out.println(
"create table if not exists SAMPLE"
+ SUFFIX
+ "("
+ columnId()
+ "name "
+ varchar(100)
+ " NOT NULL UNIQUE"
+ ");");
out.println(
"create table if not exists VARIATION"
+ SUFFIX
+ "("
+ columnId()
+ "file_id INT NOT NULL REFERENCES FILE"
+ SUFFIX
+ "(id) ON DELETE CASCADE,"
+ "CHROM VARCHAR(20) NOT NULL,"
+ "POS INT NOT NULL,"
+ "START0 INT NOT NULL,"
+ "END0 INT NOT NULL,"
+ "RS_ID VARCHAR(50),"
+ "REF "
+ text()
+ " NOT NULL,"
+ "QUAL FLOAT"
+ ");");
out.println(
"create table if not exists ALT"
+ SUFFIX
+ "("
+ columnId()
+ "var_id INT NOT NULL REFERENCES VARIATION"
+ SUFFIX
+ "(id) ON DELETE CASCADE,"
+ "ALT "
+ text()
+ ");");
out.println(
"create table if not exists FILTER"
+ SUFFIX
+ "("
+ columnId()
+ "var_id INT NOT NULL REFERENCES VARIATION"
+ SUFFIX
+ "(id) ON DELETE CASCADE,"
+ "FILTER varchar(50) not null"
+ ");");
out.println(
"create table if not exists INFO"
+ SUFFIX
+ "("
+ columnId()
+ "var_id INT NOT NULL REFERENCES VARIATION"
+ SUFFIX
+ "(id) ON DELETE CASCADE,"
+ "k varchar(50) not null,"
+ "v "
+ text()
+ " not null"
+ ");");
out.println(
"create table if not exists EXTRAINFO"
+ SUFFIX
+ "("
+ columnId()
+ "info_id INT NOT NULL REFERENCES INFO"
+ SUFFIX
+ "(id) ON DELETE CASCADE,"
+ "type varchar(50) not null"
+ ");");
out.println(
"create table if not exists EXTRAINFOPROP"
+ SUFFIX
+ "("
+ columnId()
+ "extrainfo_id INT NOT NULL REFERENCES EXTRAINFO"
+ SUFFIX
+ "(id) ON DELETE CASCADE,"
+ "k varchar(50) not null,"
+ "v "
+ text()
+ " not null"
+ ");");
out.println(
"create table if not exists GENOTYPE"
+ SUFFIX
+ "("
+ columnId()
+ "var_id INT NOT NULL REFERENCES VARIATION"
+ SUFFIX
+ "(id) ON DELETE CASCADE,"
+ "sample_id INT NOT NULL REFERENCES SAMPLE"
+ SUFFIX
+ "(id) ON DELETE CASCADE,"
+ "A1 "
+ text()
+ ", A2 "
+ text()
+ ", dp int, ad varchar(50), gq float,pl "
+ text()
+ ","
+ "is_phased SMALLINT not null,is_hom SMALLINT not null,is_homref SMALLINT not null,is_homvar SMALLINT not null,is_mixed SMALLINT not null,"
+ "is_nocall SMALLINT not null,is_noninformative SMALLINT not null,is_available SMALLINT not null,is_called SMALLINT not null,is_filtered SMALLINT not null"
+ ");");
out.println(
"create table if not exists GTPROP"
+ SUFFIX
+ "("
+ columnId()
+ "genotype_id INT NOT NULL REFERENCES GENOTYPE"
+ SUFFIX
+ "(id) ON DELETE CASCADE,"
+ "k varchar(50) not null,"
+ "v "
+ text()
+ " not null"
+ ");");
switch (this.engine) {
case sqlite:
out.println("begin transaction;");
break;
default:
break;
}
if (IN.isEmpty()) {
LOG.info("reading from stdin");
read(System.in, "<stdin>");
} else {
for (File input : IN) {
LOG.info("opening " + input);
InputStream in = IOUtils.openFileForReading(input);
read(in, input.toString());
in.close();
}
}
if (SQLINDEX) {
index("SAMPLE", "name");
index("EXTRAINFO", "type");
index("EXTRAINFOPROP", "k");
index("EXTRAINFOPROP", "v");
index("INFO", "var_id");
index("INFO", "k");
index("EXTRAINFO", "info_id");
index("EXTRAINFOPROP", "extrainfo_id");
index("GENOTYPE", "var_id");
index("GENOTYPE", "sample_id");
}
switch (this.engine) {
case sqlite:
out.println("commit;");
break;
default:
break;
}
out.flush();
} catch (IOException err) {
err.printStackTrace();
return -1;
}
return 0;
}