public BAMRecordWriter( Path output, SAMFileHeader header, boolean writeHeader, TaskAttemptContext ctx) throws IOException { init( output.getFileSystem(ctx.getConfiguration()).create(output), header, writeHeader); if (ctx.getConfiguration().getBoolean(BAMOutputFormat.WRITE_SPLITTING_BAI, false)) { Path splittingIndex = BAMInputFormat.getIdxPath(output); OutputStream splittingIndexOutput = output.getFileSystem(ctx.getConfiguration()).create(splittingIndex); splittingBAMIndexer = new SplittingBAMIndexer(splittingIndexOutput); } } public BAMRecordWriter(
public BAMRecordWriter( Path output, SAMFileHeader header, boolean writeHeader, TaskAttemptContext ctx) throws IOException { init( output.getFileSystem(ctx.getConfiguration()).create(output), header, writeHeader, BAMOutputFormat.useIntelDeflater(ctx.getConfiguration())); if (ctx.getConfiguration().getBoolean(BAMOutputFormat.WRITE_SPLITTING_BAI, false)) { Path splittingIndex = BAMInputFormat.getIdxPath(output); OutputStream splittingIndexOutput = output.getFileSystem(ctx.getConfiguration()).create(splittingIndex); splittingBAMIndexer = new SplittingBAMIndexer(splittingIndexOutput); } }
public BAMRecordWriter( Path output, SAMFileHeader header, boolean writeHeader, TaskAttemptContext ctx) throws IOException { init( output.getFileSystem(ctx.getConfiguration()).create(output), header, writeHeader, BAMOutputFormat.useIntelDeflater(ctx.getConfiguration())); if (ctx.getConfiguration().getBoolean(BAMOutputFormat.WRITE_SPLITTING_BAI, false)) { Path splittingIndex = BAMInputFormat.getIdxPath(output); OutputStream splittingIndexOutput = output.getFileSystem(ctx.getConfiguration()).create(splittingIndex); splittingBAMIndexer = new SplittingBAMIndexer(splittingIndexOutput); } }
/** A SAMFileHeader is read from the input Path. */ public BAMRecordWriter( Path output, Path input, boolean writeHeader, TaskAttemptContext ctx) throws IOException { init( output, SAMHeaderReader.readSAMHeaderFrom(input, ctx.getConfiguration()), writeHeader, ctx); if (ctx.getConfiguration().getBoolean(BAMOutputFormat.WRITE_SPLITTING_BAI, false)) { Path splittingIndex = BAMInputFormat.getIdxPath(output); OutputStream splittingIndexOutput = output.getFileSystem(ctx.getConfiguration()).create(splittingIndex); splittingBAMIndexer = new SplittingBAMIndexer(splittingIndexOutput); } } public BAMRecordWriter(
/** A SAMFileHeader is read from the input Path. */ public BAMRecordWriter( Path output, Path input, boolean writeHeader, TaskAttemptContext ctx) throws IOException { init( output, SAMHeaderReader.readSAMHeaderFrom(input, ctx.getConfiguration()), writeHeader, ctx); if (ctx.getConfiguration().getBoolean(BAMOutputFormat.WRITE_SPLITTING_BAI, false)) { Path splittingIndex = BAMInputFormat.getIdxPath(output); OutputStream splittingIndexOutput = output.getFileSystem(ctx.getConfiguration()).create(splittingIndex); splittingBAMIndexer = new SplittingBAMIndexer(splittingIndexOutput); } } public BAMRecordWriter(
/** A SAMFileHeader is read from the input Path. */ public BAMRecordWriter( Path output, Path input, boolean writeHeader, TaskAttemptContext ctx) throws IOException { init( output, SAMHeaderReader.readSAMHeaderFrom(input, ctx.getConfiguration()), writeHeader, ctx); if (ctx.getConfiguration().getBoolean(BAMOutputFormat.WRITE_SPLITTING_BAI, false)) { Path splittingIndex = BAMInputFormat.getIdxPath(output); OutputStream splittingIndexOutput = output.getFileSystem(ctx.getConfiguration()).create(splittingIndex); splittingBAMIndexer = new SplittingBAMIndexer(splittingIndexOutput); } } public BAMRecordWriter(
path.getFileSystem(cfg).open(getIdxPath(path)));
file.getFileSystem(cfg).open(getIdxPath(file)));
file.getFileSystem(cfg).open(getIdxPath(file)));