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optionally check that the records are sorted. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@131 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
jmaguire 2009-03-22 15:36:24 +00:00
parent 149ac3d96c
commit dfe50ce773
1 changed files with 19 additions and 0 deletions
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19
playground/java/src/org/broadinstitute/sting/ValidateSAM.java
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@ -15,6 +15,7 @@ public class ValidateSAM extends CommandLineProgram {
@Option(shortName="I", doc="SAM or BAM file for validation") public File INPUT_FILE; @Option(shortName="I", doc="SAM or BAM file for validation") public File INPUT_FILE;
@Option(shortName="M", doc="Maximum number of errors to detect before exiting", optional=true) public String MAX_ERRORS_ARG = "-1"; @Option(shortName="M", doc="Maximum number of errors to detect before exiting", optional=true) public String MAX_ERRORS_ARG = "-1";
@Option(shortName="S", doc="How strict should we be with validation", optional=true) public String STRICTNESS_ARG = "strict"; @Option(shortName="S", doc="How strict should we be with validation", optional=true) public String STRICTNESS_ARG = "strict";
@Option(shortName="SORTED", doc="Check that the SAM file is sorted", optional=true) public boolean CHECK_SORTED_ARG = false;
private long startTime = -1; private long startTime = -1;
@ -51,16 +52,34 @@ public class ValidateSAM extends CommandLineProgram {
int nRecords = 0; int nRecords = 0;
int nErrors = 0; int nErrors = 0;
SAMRecord last_record = null;
while ( iter.hasNext() ) { while ( iter.hasNext() ) {
nRecords++; nRecords++;
try { try {
final SAMRecord ri = iter.next(); final SAMRecord ri = iter.next();
if (CHECK_SORTED_ARG &&
(last_record != null) &&
(ri.getReferenceName() == last_record.getReferenceName()) &&
(ri.getAlignmentStart() < last_record.getAlignmentStart()))
{
System.out.println("Not sorted!");
System.out.println(last_record.format());
System.out.println(ri.format() + "\n");
System.exit(-1);
}
last_record = ri;
} catch (Exception ioe) { } catch (Exception ioe) {
nErrors++; nErrors++;
System.out.println("[VALIDATION FAILURE IN RECORD]: " + ioe); System.out.println("[VALIDATION FAILURE IN RECORD]: " + ioe);
ioe.printStackTrace(); ioe.printStackTrace();
} }
if ( MAX_ERRORS > -1 && nErrors >= MAX_ERRORS ) { if ( MAX_ERRORS > -1 && nErrors >= MAX_ERRORS ) {
System.out.println("Maximum number of errors encountered " + nErrors); System.out.println("Maximum number of errors encountered " + nErrors);
break; break;