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some documentation changes, add a couple of simple checks 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1445 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron 2009-08-20 05:20:27 +00:00
parent 026e09ec07
commit 0386e110cf
1 changed files with 25 additions and 10 deletions
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35
java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFValidator.java
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@ -11,7 +11,9 @@ import java.util.TreeMap;
* <p/> * <p/>
* Class VCFValidator * Class VCFValidator
* <p/> * <p/>
* validate a VCF file * This is the main class for providing a light weight validation of a VCF file.
* It has two parameters, an optional -A flag meaning that you'd like to collect all
* the errors and present them at the end, and the VCF file itself (a required parameter).
*/ */
public class VCFValidator { public class VCFValidator {
@ -20,9 +22,9 @@ public class VCFValidator {
/** /**
* about as simple as things come right now. We open the file, process all the entries in the file, * about as simple as things come right now. We open the file, process all the entries in the file,
* and if no errors pop up in processing, well hey, looks good to us. * and if no errors pop up in processing, well hey, looks good to us.
* TODO: add validation to individual records fields as they make sense
* *
* @param args the vcf file is the only parameter * @param args the vcf file is the only required parameter, with the optional -A indicating that errors
* should be held until the end of processing
*/ */
public static void main(String[] args) { public static void main(String[] args) {
boolean catchAll = false; boolean catchAll = false;
@ -43,25 +45,36 @@ public class VCFValidator {
} }
// count hom many records we see // count hom many records we see
int recordCount = 0; int recordCount = 0;
Map<Integer,Exception> problems = new TreeMap<Integer,Exception>(); Map<Integer, Exception> problems = new TreeMap<Integer, Exception>();
try { try {
// open up our reader // open up our reader
VCFReader reader = new VCFReader(vcfFile); VCFReader reader = new VCFReader(vcfFile);
// the number of samples should be set in the header and consistant over all records
final int sampleCount = reader.getHeader().getGenotypeSamples().size();
while (reader.hasNext()) { while (reader.hasNext()) {
try { try {
recordCount++; recordCount++;
VCFRecord rec = reader.next(); VCFRecord rec = reader.next();
// if the header indicates we have genotyping data, try to extract it for all samples // if the header indicates we have genotyping data, try to extract it for all samples
if (reader.getHeader().hasGenotypingData()) { if (reader.getHeader().hasGenotypingData()) {
int sampleCounter = 0;
for (VCFGenotypeRecord genorec : rec.getVCFGenotypeRecords()) { for (VCFGenotypeRecord genorec : rec.getVCFGenotypeRecords()) {
// just cycle through them, more checks go here sampleCounter++;
/**
* just cycle through the records right now; any additional checks for
* the records should go in this block.
**/
} }
if (sampleCounter != sampleCount)
throw new RuntimeException("Record " + recordCount + " does not have the required number " +
"of records (" + sampleCounter + " in the record, " + sampleCount + " in the header)");
} }
} catch (Exception e) { } catch (Exception e) {
if (catchAll) if (catchAll)
problems.put(recordCount,e); problems.put(recordCount, e);
else { else {
validationFailed(e, recordCount); validationFailed(e, recordCount);
return; return;
@ -70,15 +83,15 @@ public class VCFValidator {
} }
} catch (Exception e) { } catch (Exception e) {
if (catchAll) if (catchAll)
problems.put(new Integer(0),e); problems.put(new Integer(0), e);
else else
validationFailed(e, recordCount); validationFailed(e, recordCount);
} }
System.err.println("Viewed " + recordCount + " VCF record entries."); System.err.println("Viewed " + recordCount + " VCF record entries.");
if (problems.size() > 0) { if (problems.size() > 0) {
System.err.println("Encountered " + problems.size() + " number of issues. (record zero indicates a header problem)"); System.err.println("Encountered " + problems.size() + " number of issues. (record zero indicates a header problem)");
for (Integer e : problems.keySet()) { for (Integer e : problems.keySet()) {
System.err.println("\tProblem at record " + e + " : " + problems.get(e)); System.err.println("\tProblem at record " + e + " : " + problems.get(e));
} }
} }
} }
@ -95,7 +108,9 @@ public class VCFValidator {
e.printStackTrace(); e.printStackTrace();
} }
/** print the usage information for the VCF validator */ /**
* print the usage information for the VCF validator
*/
public static void printUsage() { public static void printUsage() {
System.err.println("VCF validator (VCF Version " + VCF_VERSION + ")"); System.err.println("VCF validator (VCF Version " + VCF_VERSION + ")");
System.err.println("Usage:"); System.err.println("Usage:");