Package htsjdk.samtools.util

Examples of htsjdk.samtools.util.RuntimeIOException

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                IOUtil.assertFileIsWritable(soleInput);
                IOUtil.assertDirectoryIsWritable(dir);
                OUTPUT = File.createTempFile(soleInput.getName() + ".being_fixed.", BamFileIoUtils.BAM_FILE_EXTENSION, dir);
            }
            catch (final IOException ioe) {
                throw new RuntimeIOException("Could not create tmp file in " + dir.getAbsolutePath());
            }
        }

        // Get the input records merged and sorted by query name as needed
        final PeekableIterator<SAMRecord> iterator;
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                            start += fifo.write(buffer, start, read-start);
                        }
                    }
                }
                catch (final IOException ioe) {
                    throw new RuntimeIOException(ioe);
                }
                finally {
                    fifo.close();
                }
            }
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            }
        }
        try {
            out.close();
        } catch (IOException e) {
            throw new RuntimeIOException(e);
        }
        return 0;
    }
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            // And lastly add the Terminator block and close up
            out.write(BlockCompressedStreamConstants.EMPTY_GZIP_BLOCK);
            out.close();
        }
        catch (final IOException ioe) {
            throw new RuntimeIOException(ioe);
        }
    }
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            for (int i = 0; i < cycles; ++i) {
                final File bclFile = bclsForOneTile.get(i);
                if (bclFile == null) {
                    close();
                    throw new RuntimeIOException(String.format("Could not find BCL file for cycle %d", i));
                }
                final String filePath = bclFile.getName();
                final boolean isGzip = filePath.endsWith(".gz");
                final boolean isBgzf = filePath.endsWith(".bgzf");
                final InputStream stream = open(bclFile, seekable, isGzip, isBgzf);
                final int read = stream.read(byteBuffer.array());
                if (read != HEADER_SIZE) {
                    close();
                    throw new RuntimeIOException(String.format("BCL %s has invalid header structure.", bclFile.getAbsoluteFile()));
                }
                numClustersPerCycle[i] = byteBuffer.getInt();
                if (!isBgzf && !isGzip) {
                    assertProperFileStructure(bclFile, numClustersPerCycle[i], stream);
                }
                this.streams[i] = stream;
                byteBuffer.clear();
            }
        } catch (final IOException ioe) {
            throw new RuntimeIOException(ioe);
        }
    }
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            final boolean isBgzf = filePath.endsWith(".bgzf");
            final InputStream stream = open(bclFile, seekable, isGzip, isBgzf);
            final int read = stream.read(byteBuffer.array());

            if (read != HEADER_SIZE) {
                throw new RuntimeIOException(String.format("BCL %s has invalid header structure.", bclFile.getAbsoluteFile()));
            }

            byteBuffer.order(ByteOrder.LITTLE_ENDIAN);
            this.numClustersPerCycle[0] = byteBuffer.getInt();
            if (!isBgzf && !isGzip) {
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                        data.bases[read][cycle] = BASE_LOOKUP[readByte & BASE_MASK];
                        data.qualities[read][cycle] = bclQualityEvaluationStrategy.reviseAndConditionallyLogQuality((byte) (readByte >>> 2));
                    }
                    totalCycleCount++;
                } catch (final IOException ioe) {
                    throw new RuntimeIOException(ioe);
                }

            }
        }
        this.queue = data;
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                    }
                    else {
                        out = null;
                    }
                }
                catch (IOException ioe) { throw new RuntimeIOException(ioe); }

                final int bins = 101;
                final long[] targetBasesByGc  = new long[bins];
                final long[] alignedBasesByGc = new long[bins];
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            }

            out.close();
        }
        catch (final IOException ioe) {
            throw new RuntimeIOException("IOException while writing to file " + file.getAbsolutePath(), ioe);
        }
    }
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  • picard.sam.FixMateInformation
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