htsjdk.tribble.util.ParsingUtils Java Examples
The following examples show how to use
htsjdk.tribble.util.ParsingUtils.
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Example #1
Source File: IndexUtils.java From gatk with BSD 3-Clause "New" or "Revised" License | 6 votes |
/** * Try to load the tabix index from disk, checking for out of date indexes and old versions * @return an Index, or null if we're unable to load */ public static Index loadTabixIndex(final File featureFile) { Utils.nonNull(featureFile); try { final String path = featureFile.getAbsolutePath(); final boolean isTabix = new AbstractFeatureReader.ComponentMethods().isTabix(path, null); if (! isTabix){ return null; } final String indexPath = ParsingUtils.appendToPath(path, FileExtensions.TABIX_INDEX); logger.debug("Loading tabix index from disk for file " + featureFile); final Index index = IndexFactory.loadIndex(indexPath); final File indexFile = new File(indexPath); checkIndexVersionAndModificationTime(featureFile, indexFile, index); return index; } catch (final IOException | RuntimeException e) { return null; } }
Example #2
Source File: Utils.java From gatk with BSD 3-Clause "New" or "Revised" License | 6 votes |
/** * Splits a String using indexOf instead of regex to speed things up. * This method produces the same results as {@link String#split(String)} and {@code String.split(String, 0)}, * but has been measured to be ~2x faster (see {@code StringSplitSpeedUnitTest} for details). * * @param str the string to split. * @param delimiter the delimiter used to split the string. * @return A {@link List} of {@link String} tokens. */ public static List<String> split(final String str, final char delimiter) { final List<String> tokens; if ( str.isEmpty() ) { tokens = new ArrayList<>(1); tokens.add(""); } else { tokens = ParsingUtils.split(str, delimiter); removeTrailingEmptyStringsFromEnd(tokens); } return tokens; }
Example #3
Source File: FuncotatorEngine.java From gatk with BSD 3-Clause "New" or "Revised" License | 6 votes |
/** * Split each element of the given {@link List} into a key and value. * Assumes each element of the given {@link List} is formatted as follows: * KEY:VALUE * @param annotationArgs {@link List} of strings formatted KEY:VALUE to turn into a {@link Map}. * @return A {@link LinkedHashMap} of KEY:VALUE pairs corresponding to entries in the given list. */ public static LinkedHashMap<String, String> splitAnnotationArgsIntoMap( final List<String> annotationArgs ) { final LinkedHashMap<String, String> annotationMap = new LinkedHashMap<>(); for ( final String s : annotationArgs ) { final List<String> keyVal = ParsingUtils.split(s, FuncotatorArgumentDefinitions.MAP_NAME_VALUE_DELIMITER); if ( keyVal.size() != 2) { throw new UserException.BadInput( "Argument annotation incorrectly formatted: " + s ); } annotationMap.put( keyVal.get(0), keyVal.get(1) ); } return annotationMap; }
Example #4
Source File: SageHotspotAnnotation.java From hmftools with GNU General Public License v3.0 | 5 votes |
@Override public int compare(final VariantContext firstVariantContext, final VariantContext secondVariantContext) { int positionResult = super.compare(firstVariantContext, secondVariantContext); if (positionResult != 0) { return positionResult; } final String firstAlleles = ParsingUtils.sortList(firstVariantContext.getAlleles()).toString(); final String secondAlleles = ParsingUtils.sortList(secondVariantContext.getAlleles()).toString(); return firstAlleles.compareTo(secondAlleles); }
Example #5
Source File: VcfToVariant.java From genomewarp with Apache License 2.0 | 5 votes |
@VisibleForTesting static List<String> getFilter(VariantContext vc) { if (vc.isFiltered()) { return (List<String>) ParsingUtils.sortList(vc.getFilters()); } if (vc.filtersWereApplied()) { return Arrays.asList(VCFConstants.PASSES_FILTERS_v4); } return Arrays.asList(VCFConstants.UNFILTERED); }
Example #6
Source File: CollectSamErrorMetrics.java From picard with MIT License | 5 votes |
/** * Parses a "Directive" of the form "ERROR,STRATIFIER,STRATIFIER...etc." into a {@link BaseErrorAggregation} consisting of the appropriate * {@link BaseCalculator} and the {@link ReadBaseStratification.CollectionStratifier CollectionStratifier} constructed from the various * individual stratifiers. * The conversion from string to object is performed by the enums * {@link ErrorType Errors} and {@link ReadBaseStratification.Stratifier Stratifier}. * * @param stratifierDirective The string directive describing the error type and collection of stratifiers to use * @return The appropriate {@link BaseErrorAggregation}. */ protected static BaseErrorAggregation parseDirective(final String stratifierDirective) { final String[] directiveUnits = new String[MAX_DIRECTIVES + 1]; final char directiveSeparator = ':'; final int numberOfTerms = ParsingUtils.split(stratifierDirective, directiveUnits, directiveSeparator, false); if (numberOfTerms > MAX_DIRECTIVES) { throw new IllegalArgumentException(String.format("Cannot parse more than the number of different stratifiers plus one (%d) terms in a single directive. (What are you trying to do?)", MAX_DIRECTIVES)); } if (numberOfTerms == 0) { throw new IllegalArgumentException("Found no directives at all. Cannot process."); } // make a linkedList due to removal and addition operations below final List<ReadBaseStratification.RecordAndOffsetStratifier<?>> stratifiers = Arrays.stream(directiveUnits, 1, numberOfTerms) .map(String::trim) .map(ReadBaseStratification.Stratifier::valueOf) .map(ReadBaseStratification.Stratifier::makeStratifier) .collect(Collectors.toList()); final ReadBaseStratification.RecordAndOffsetStratifier jointStratifier; if (stratifiers.isEmpty()) { jointStratifier = ReadBaseStratification.nonStratifier; } else { jointStratifier = new ReadBaseStratification.CollectionStratifier(stratifiers); } // build an error supplier from the first term final Supplier<? extends BaseCalculator> supplier = ErrorType.valueOf(directiveUnits[0].trim()).getErrorSupplier(); // return the aggregator made from the stratifier and the error supplier return new BaseErrorAggregation<>(supplier, jointStratifier); }
Example #7
Source File: SageHotspotAnnotation.java From hmftools with GNU General Public License v3.0 | 4 votes |
@NotNull private static String simpleString(@NotNull final VariantContext context) { return "[" + context.getContig() + ":" + context.getStart() + " Type:" + context.getType() + " Alleles:" + ParsingUtils.sortList( context.getAlleles()) + "]"; }