Package org.broadinstitute.gatk.utils.exceptions

Examples of org.broadinstitute.gatk.utils.exceptions.UserException$MissortedFile

292
293
294
295
296
297
298
299
300
301
        try {
            scheduleFile = File.createTempFile("bamschedule."+referenceSequence,null);
            scheduleFileChannel = new RandomAccessFile(scheduleFile,"rw").getChannel();
        }
        catch(IOException ex) {
            throw new UserException("Unable to create a temporary BAM schedule file.  Please make sure Java can write to the default temp directory or use -Djava.io.tmpdir= to instruct it to use a different temp directory instead.",ex);
        }
        scheduleFile.deleteOnExit();

    }
View Full Code Here
386
387
388
389
390
391
392
393
394
    }

    public DiffElement createDiffableFromFile(File file, int maxElementsToRead) {
        DiffableReader reader = findReaderForFile(file);
        if ( reader == null )
            throw new UserException("Unsupported file type: " + file);
        else
            return reader.readFromFile(file, maxElementsToRead);
    }
View Full Code Here
77
78
79
80
81
82
83
84
85
86
87
        }
        else if(stub.getOutputStream() != null){
            this.writer = factory.makeSAMWriter( stub.getFileHeader(), stub.isPresorted(), stub.getOutputStream());
        }
        else
            throw new UserException("Unable to write to SAM file; neither a target file nor a stream has been specified");

        // if we want to send the BAM file through the simplifying writer, wrap it here
        if ( stub.simplifyBAM() ) {
            this.writer = new SimplifyingSAMFileWriter(this.writer);
        }
View Full Code Here
40
41
42
43
44
45
46
47
48
49
50
        PrintStream o;
        try {
            o = new PrintStream(output);
        } catch (FileNotFoundException e) {
            throw new UserException(String.format("File %s to be output by GATKReportGatherer function was not found", output));
        }

        GATKReport current = new GATKReport();
        boolean isFirst = true;
        for (File input : inputs) {
View Full Code Here
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
            } catch (FileNotFoundException e) {
                String message = "Error loading black list: " + file.getAbsolutePath();
                if (parentFile != null) {
                    message += ", " + parentFile.getAbsolutePath() + ":" + parentLineNum;
                }
                throw new UserException(message);
            }
        } else {
            String[] filterEntry = filter.split(":", 2);

            String message = null;
            if (filterEntry.length != 2) {
                message = "Invalid read group filter: " + filter;
            } else if (filterEntry[0].length() != 2) {
                message = "Tag is not two characters: " + filter;
            }

            if (message != null) {
                if (parentFile != null) {
                    message += ", " + parentFile.getAbsolutePath() + ":" + parentLineNum;
                }
                message += ", format is <TAG>:<SUBSTRING>";
                throw new UserException(message);
            }

            if (!filters.containsKey(filterEntry[0]))
                filters.put(filterEntry[0], new TreeSet<String>());
            filters.get(filterEntry[0]).add(filterEntry[1]);
View Full Code Here
98
99
100
101
102
103
104
105
106
107
108
        // Read the first line for the version and number of tables.
        version = GATKReportVersion.fromHeader(reportHeader);
        if (version.equals(GATKReportVersion.V0_1) ||
                version.equals(GATKReportVersion.V0_2))
            throw new UserException("The GATK no longer supports reading legacy GATK Reports. Please use v1.0 or newer.");

        int nTables = Integer.parseInt(reportHeader.split(":")[2]);

        // Read each table according ot the number of tables
        for (int i = 0; i < nTables; i++) {
View Full Code Here
56
57
58
59
60
61
62
63
64
65
66
     * @param fastaFile Fasta file to be used as reference
     */
    public ReferenceDataSource(File fastaFile) {
        // does the fasta file exist? check that first...
        if (!fastaFile.exists())
            throw new UserException("The fasta file you specified (" + fastaFile.getAbsolutePath() + ") does not exist.");

        final boolean isGzipped = fastaFile.getAbsolutePath().endsWith(".gz");
        if ( isGzipped ) {
            throw new UserException.CannotHandleGzippedRef();
        }
View Full Code Here
375
376
377
378
379
380
381
382
     * @throws UserException if the header is from a reduced bam
     */
    private void checkForUnsupportedBamFile(final SAMFileHeader header) {
        for ( final SAMProgramRecord PGrecord : header.getProgramRecords() ) {
            if ( unsupportedPGs.containsKey(PGrecord.getId()) )
                throw new UserException("The GATK no longer supports running off of BAMs produced by " + unsupportedPGs.get(PGrecord.getId()));
        }
    }
View Full Code Here
235
236
237
238
239
240
241
242
243
            else {
                // both o1 and o2 have a value
                if ( o1 == o2 )
                    return o1;
                else
                    throw new UserException("Inconsistent values detected for " + name + " for field " + field + " value1 " + o1 + " value2 " + o2);
            }
        }
    }
View Full Code Here
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
            for ( final SAMReadGroupRecord readGroup : header.getReadGroups() ) {
                final String thisReadGroupSample = readGroup.getSample();

                if ( thisReadGroupSample == null ) {
                    throw new UserException(String.format("On-the fly sample renaming was requested for bam file %s, however this " +
                                                          "bam file contains a read group (id: %s) with a null sample attribute",
                                                          readerID.getSamFilePath(), readGroup.getId()));
                }
                else if ( firstEncounteredSample == null ) {
                    firstEncounteredSample = thisReadGroupSample;
                }
                else if ( ! firstEncounteredSample.equals(thisReadGroupSample) ) {
                    throw new UserException(String.format("On-the-fly sample renaming was requested for bam file %s, " +
                                                          "however this bam file contains reads from more than one sample " +
                                                          "(encountered samples %s and %s in the bam header). The GATK requires that " +
                                                          "all bams for which on-the-fly sample renaming is requested " +
                                                          "contain reads from only a single sample per bam.",
                                                          readerID.getSamFilePath(), firstEncounteredSample, thisReadGroupSample));
View Full Code Here
TOP

Related Classes of org.broadinstitute.gatk.utils.exceptions.UserException$MissortedFile

  • org.broadinstitute.gatk.engine.CommandLineExecutable
  • org.broadinstitute.gatk.engine.CommandLineGATK
  • org.broadinstitute.gatk.engine.datasources.reads.BAMSchedule
  • org.broadinstitute.gatk.engine.datasources.reads.BAMScheduler
  • org.broadinstitute.gatk.engine.datasources.reads.SAMDataSource
  • org.broadinstitute.gatk.engine.datasources.reads.SAMDataSource$SAMReaders
  • org.broadinstitute.gatk.engine.datasources.reads.utilities.PrintBAMRegion
  • org.broadinstitute.gatk.engine.datasources.reference.ReferenceDataSource
  • org.broadinstitute.gatk.engine.downsampling.DownsamplingMethod
  • org.broadinstitute.gatk.engine.filters.ReadGroupBlackListFilter
    • Copyright © 2018 www.massapicom. All rights reserved.
    All source code are property of their respective owners. Java is a trademark of Sun Microsystems, Inc and owned by ORACLE Inc. Contact coftware#gmail.com.