/*

* The MIT License

*

* Copyright (c) 2009 The Broad Institute

*

* Permission is hereby granted, free of charge, to any person obtaining a copy

* of this software and associated documentation files (the "Software"), to deal

* in the Software without restriction, including without limitation the rights

* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell

* copies of the Software, and to permit persons to whom the Software is

* furnished to do so, subject to the following conditions:

*

* The above copyright notice and this permission notice shall be included in

* all copies or substantial portions of the Software.

*

* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR

* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,

* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE

* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER

* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,

* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN

* THE SOFTWARE.

*/

package picard.sam;

import htsjdk.samtools.SAMValidationError;

import htsjdk.samtools.SamFileValidator;

import htsjdk.samtools.SamReader;

import htsjdk.samtools.SamReaderFactory;

import htsjdk.samtools.ValidationStringency;

import htsjdk.samtools.BamIndexValidator.IndexValidationStringency;

import htsjdk.samtools.reference.ReferenceSequenceFile;

import htsjdk.samtools.reference.ReferenceSequenceFileFactory;

import htsjdk.samtools.util.IOUtil;

import picard.PicardException;

import picard.cmdline.CommandLineProgram;

import picard.cmdline.CommandLineProgramProperties;

import picard.cmdline.Option;

import picard.cmdline.StandardOptionDefinitions;

import picard.cmdline.programgroups.SamOrBam;

import java.io.File;

import java.io.FileNotFoundException;

import java.io.PrintWriter;

import java.util.ArrayList;

import java.util.List;

/**

* Command line program wrapping SamFileValidator.

*

* @author Doug Voet

*/

@CommandLineProgramProperties(

usage = ValidateSamFile.USAGE_SUMMARY + ValidateSamFile.USAGE_DETAILS,

usageShort = ValidateSamFile.USAGE_SUMMARY,

programGroup = SamOrBam.class

)

public class ValidateSamFile extends CommandLineProgram {

static final String USAGE_SUMMARY = "Validates a SAM or BAM file. ";

static final String USAGE_DETAILS = "<p>This tool reports on the validity of a SAM or BAM file relative to the SAM format " +

"specification. This is useful for troubleshooting errors encountered with other tools that may be caused by improper " +

"formatting, faulty alignments, incorrect flag values, etc. </p> " +

"<p>By default, the tool runs in VERBOSE mode and will exit after finding 100 errors and output them to the console (stdout). " +

"Therefore, it is often more practical to run this tool initially using the MODE=SUMMARY option. This mode outputs a summary " +

"table listing the numbers of all 'errors' and 'warnings'.</p> "+

"<p>When fixing errors in your file, it is often useful to prioritize the severe validation errors and ignore the " +

"errors/warnings of lesser concern. This can be done using the IGNORE and/or IGNORE_WARNINGS arguments. For helpful " +

"suggestions on error prioritization, please follow this link to obtain additional documentation on <a href='https://www.broadinstitute.org/gatk/guide/article?id=7571'>ValidateSamFile</a>.</p>" +

"<p>After identifying and fixing your 'warnings/errors', we recommend that you rerun this tool to validate your SAM/BAM " +

"file prior to proceeding with your downstream analysis. This will verify that all problems in your file have been addressed.</p>" +

"<h4>Usage example:</h4>" +

"<pre>" +

"java -jar picard.jar ValidateSamFile \\<br />" +

" I=input.bam \\<br />" +

" MODE=SUMMARY" +

"</pre>" +

"<p>To obtain a complete list with descriptions of both 'ERROR' and 'WARNING' messages, please see our additional " +

" <a href='https://www.broadinstitute.org/gatk/guide/article?id=7571'>documentation</a> for this tool.</p>" +

""+

"<hr />";

public enum Mode {VERBOSE, SUMMARY}

@Option(shortName = StandardOptionDefinitions.INPUT_SHORT_NAME,

doc = "Input SAM/BAM file")

public File INPUT;

@Option(shortName = StandardOptionDefinitions.OUTPUT_SHORT_NAME,

doc = "Output file or standard out if missing",

optional = true)

public File OUTPUT;

@Option(shortName = "M",

doc = "Mode of output")

public Mode MODE = Mode.VERBOSE;

@Option(doc = "List of validation error types to ignore.")

public List<SAMValidationError.Type> IGNORE = new ArrayList<SAMValidationError.Type>();

@Option(shortName = "MO",

doc = "The maximum number of lines output in verbose mode")

public Integer MAX_OUTPUT = 100;

@Option(doc = "If true, only report errors and ignore warnings.")

public boolean IGNORE_WARNINGS = false;

@Option(doc = "DEPRECATED. Use INDEX_VALIDATION_STRINGENCY instead. If true and input is " +

"a BAM file with an index file, also validates the index. Until this parameter is retired " +

"VALIDATE INDEX and INDEX_VALIDATION_STRINGENCY must agree on whether to validate the index.")

public boolean VALIDATE_INDEX = true;

@Option(doc = "If set to anything other than IndexValidationStringency.NONE and input is " +

"a BAM file with an index file, also validates the index at the specified stringency. " +

"Until VALIDATE_INDEX is retired, VALIDATE INDEX and INDEX_VALIDATION_STRINGENCY " +

"must agree on whether to validate the index.")

public IndexValidationStringency INDEX_VALIDATION_STRINGENCY = IndexValidationStringency.EXHAUSTIVE;

@Option(shortName = "BISULFITE",

doc = "Whether the SAM or BAM file consists of bisulfite sequenced reads. " +

"If so, C->T is not counted as an error in computing the value of the NM tag.")

public boolean IS_BISULFITE_SEQUENCED = false;

@Option(doc = "Relevant for a coordinate-sorted file containing read pairs only. " +

"Maximum number of file handles to keep open when spilling mate info to disk. " +

"Set this number a little lower than the per-process maximum number of file that may be open. " +

"This number can be found by executing the 'ulimit -n' command on a Unix system.")

public int MAX_OPEN_TEMP_FILES = 8000;

public static void main(final String[] args) {

System.exit(new ValidateSamFile().instanceMain(args));

}

@Override

protected int doWork() {

IOUtil.assertFileIsReadable(INPUT);

ReferenceSequenceFile reference = null;

if (REFERENCE_SEQUENCE != null) {

IOUtil.assertFileIsReadable(REFERENCE_SEQUENCE);

reference = ReferenceSequenceFileFactory.getReferenceSequenceFile(REFERENCE_SEQUENCE);

}

final PrintWriter out;

if (OUTPUT != null) {

IOUtil.assertFileIsWritable(OUTPUT);

try {

out = new PrintWriter(OUTPUT);

} catch (FileNotFoundException e) {

// we already asserted this so we should not get here

throw new PicardException("Unexpected exception", e);

}

} else {

out = new PrintWriter(System.out);

}

boolean result;

final SamReaderFactory factory = SamReaderFactory.makeDefault().referenceSequence(REFERENCE_SEQUENCE)

.validationStringency(ValidationStringency.SILENT)

.enable(SamReaderFactory.Option.VALIDATE_CRC_CHECKSUMS);

final SamReader samReader = factory.open(INPUT);

if (samReader.type() != SamReader.Type.BAM_TYPE) VALIDATE_INDEX = false;

factory.setOption(SamReaderFactory.Option.CACHE_FILE_BASED_INDEXES, VALIDATE_INDEX);

factory.reapplyOptions(samReader);

final SamFileValidator validator = new SamFileValidator(out, MAX_OPEN_TEMP_FILES);

validator.setErrorsToIgnore(IGNORE);

if (IGNORE_WARNINGS) {

validator.setIgnoreWarnings(IGNORE_WARNINGS);

}

if (MODE == Mode.SUMMARY) {

validator.setVerbose(false, 0);

} else {

validator.setVerbose(true, MAX_OUTPUT);

}

if (IS_BISULFITE_SEQUENCED) {

validator.setBisulfiteSequenced(IS_BISULFITE_SEQUENCED);

}

if (VALIDATE_INDEX) {

validator.setValidateIndex(VALIDATE_INDEX);

}

if (IOUtil.isRegularPath(INPUT)) {

// Do not check termination if reading from a stream

validator.validateBamFileTermination(INPUT);

}

result = false;

switch (MODE) {

case SUMMARY:

result = validator.validateSamFileSummary(samReader, reference);

break;

case VERBOSE:

result = validator.validateSamFileVerbose(samReader, reference);

break;

}

out.flush();

return result ? 0 : 1;

}

@Override

protected String[] customCommandLineValidation() {

if ((!VALIDATE_INDEX && INDEX_VALIDATION_STRINGENCY != IndexValidationStringency.NONE) ||

(VALIDATE_INDEX && INDEX_VALIDATION_STRINGENCY == IndexValidationStringency.NONE)) {

return new String[]{"VALIDATE_INDEX and INDEX_VALIDATION_STRINGENCY must be consistent: " +

"VALIDATE_INDEX is " + VALIDATE_INDEX + " and INDEX_VALIDATION_STRINGENCY is " +

INDEX_VALIDATION_STRINGENCY};

}

return super.customCommandLineValidation();

}

}