create universal reader and writer #209
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our internal file read and writer
holmeso
requested changes
Nov 4, 2020
| protected T next; | ||
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| protected List<String> headerLines = new ArrayList<>(); | ||
| public RecordReader(final File file) throws IOException { this(file, DEFAULT_BUFFER_SIZE); } |
| /** | ||
| * Here, BufferedReader.close() calls InputStreamReader.close(), which API told us that it Closes the stream and releases any system resources associated with it. | ||
| */ | ||
| public void close() throws IOException { bin.close(); } |
| * This reader can maxmum take Integer.max lines of file header. Please make other header if bigger than this. | ||
| * @return a list of header lines | ||
| */ | ||
| public List<String> getHeader() { return headerLines; } |
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does this pass checkstyle's checks?
| if(headerPrefix == null) return nextLine; | ||
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| //reader header, hence file pointer to first line after header | ||
| while ( headerPrefix != null && null != nextLine && nextLine.startsWith(headerPrefix+"") ) { |
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null guards have already been performed
| try { | ||
| next = nextLine == null? null : getRecord(nextLine); | ||
| }catch(Exception e) { | ||
| throw new IOException("error during retrive first record " + e.getMessage()); |
| } | ||
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| //some record cross multi lines, eg id\nseq\n, this method may call bin.readLine() inside | ||
| public abstract T getRecord(String line) throws Exception; |
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Could a more specific Exception by thrown here?
| * @return the first line just after header | ||
| * @throws IOException | ||
| */ | ||
| public String readHeader(CharSequence headerPrefix ) throws IOException{ |
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maybe change to more meaningful name ie. readHeaderAndReturnFirstNonHeaderLine
| } | ||
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| return rec; | ||
| } catch (Exception e) { |
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should avoid catching Exception - be more specific
holmeso
requested changes
Nov 4, 2020
holmeso
reviewed
Nov 5, 2020
| * This reader can maxmum take Integer.max lines of file header. Please make other header if bigger than this. | ||
| * @return a list of header lines | ||
| */ | ||
| public List<String> getHeader() { return headerLines; } |
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does this pass checkstyle's checks?
This was referenced Jan 31, 2021
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This was referenced Feb 12, 2021
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Description
Our current qio project contains more than 20 different file readers and writers, most of them are similar. Some of them are hardly maintained due to old or deprecated file format. Here a universal file reader and writer is created, which can cover most file format, and also can be used as a base class for special and the complicated file format, such as VCF, FASTA, GFF, Illumina, etc.
Fixes #196 #197 #198
Type of change
Please delete options that are not relevant.
How Has This Been Tested?
A unit test class is added. At moment these three class is not yet used in any projects, it will be further tested after replace current old other reader and writer
Checklist: