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* Implemented a tribble (co)dec for IntervalList. * moved the business part of the dec from IntervalList to the Tribble dec. * testing the Tribble directly.
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Yossi Farjoun
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Apr 3, 2019
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164 changes: 164 additions & 0 deletions
164
src/main/java/htsjdk/tribble/IntervalList/IntervalListCodec.java
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| /* | ||
| * Copyright (c) 2019, 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. | ||
| */ | ||
|
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| package htsjdk.tribble.IntervalList; | ||
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| import htsjdk.samtools.*; | ||
| import htsjdk.samtools.util.FormatUtil; | ||
| import htsjdk.samtools.util.Interval; | ||
| import htsjdk.samtools.util.LineReader; | ||
| import htsjdk.samtools.util.Log; | ||
| import htsjdk.tribble.AsciiFeatureCodec; | ||
| import htsjdk.tribble.TribbleException; | ||
| import htsjdk.tribble.annotation.Strand; | ||
| import htsjdk.tribble.readers.LineIterator; | ||
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| /** | ||
| * A tribble codec for IntervalLists. | ||
| * | ||
| * Also contains the parsing code for the non-tribble parsing of IntervalLists | ||
| */ | ||
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| public class IntervalListCodec extends AsciiFeatureCodec<Interval> { | ||
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| private final Log log = Log.getInstance(IntervalListCodec.class); | ||
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| private SAMSequenceDictionary dictionary; | ||
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| public IntervalListCodec() { | ||
| this(null); | ||
| } | ||
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| public IntervalListCodec(final SAMSequenceDictionary dict) { | ||
| super(Interval.class); | ||
| dictionary = dict; | ||
| } | ||
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| String lastSeq = null; | ||
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| private Interval parseIntervalString(final String line, final SAMSequenceDictionary dict) { | ||
| final int SEQUENCE_POS = 0; | ||
| final int START_POS = 1; | ||
| final int END_POS = 2; | ||
| final int STRAND_POS = 3; | ||
| final int NAME_POS = 4; | ||
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| final FormatUtil format = new FormatUtil(); | ||
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| // Make sure we have the right number of fields | ||
| final String[] fields = line.split("\t"); | ||
| if (fields.length != 5) { | ||
| throw new TribbleException("Invalid interval record contains " + | ||
| fields.length + " fields: " + line); | ||
| } | ||
|
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| // Then parse them out | ||
| String seq = fields[SEQUENCE_POS]; | ||
| if (seq.equals(lastSeq)) { | ||
| seq = lastSeq; | ||
| } | ||
| lastSeq = seq; | ||
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| final int start = format.parseInt(fields[START_POS]); | ||
| final int end = format.parseInt(fields[END_POS]); | ||
| if (start < 1) { | ||
| throw new IllegalArgumentException("Coordinate less than 1: start value of " + start + | ||
| " is less than 1 and thus illegal"); | ||
| } | ||
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| if (start > end + 1) { | ||
| throw new IllegalArgumentException("Start value of " + start + | ||
| " is greater than end + 1 for end of value: " + end + | ||
| ". I'm afraid I cannot let you do that."); | ||
| } | ||
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| Strand strand = Strand.decode(fields[STRAND_POS]); | ||
| if (strand==Strand.NONE) throw new IllegalArgumentException("Invalid strand field: " + fields[STRAND_POS]); | ||
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| final String name = fields[NAME_POS]; | ||
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| final Interval interval = new Interval(seq, start, end, strand==Strand.NEGATIVE, name); | ||
| final SAMSequenceRecord sequence = dict.getSequence(seq); | ||
| if (sequence == null) { | ||
| log.warn("Ignoring interval for unknown reference: " + interval); | ||
| return null; | ||
| } else { | ||
| final int sequenceLength = sequence.getSequenceLength(); | ||
| if (sequenceLength > 0 && sequenceLength < end) { | ||
| throw new IllegalArgumentException("interval with end: " + end + " extends beyond end of sequence with length: " + sequenceLength); | ||
| } | ||
| return interval; | ||
| } | ||
| } | ||
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| @Override | ||
| public Interval decode(final String line) { | ||
| if (line.startsWith("@")) { | ||
| return null; | ||
| } | ||
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| if (line.trim().isEmpty()) { | ||
| return null; | ||
| } | ||
| // our header cannot be null, we need the dictionary from the header | ||
| if (dictionary == null) { | ||
| throw new TribbleException("IntervalList dictionary cannot be null when decoding a record"); | ||
| } | ||
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| return parseIntervalString(line, dictionary); | ||
| } | ||
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| @Override | ||
| public Object readActualHeader(LineIterator lineIterator) { | ||
| final SAMTextHeaderCodec headerCodec = new SAMTextHeaderCodec(); | ||
| final SAMFileHeader header = headerCodec.decode(new LineReader() { | ||
| int lineNo = 0; | ||
| @Override | ||
| public String readLine() { | ||
| lineNo++; | ||
| return lineIterator.next(); | ||
| } | ||
| @Override | ||
| public int getLineNumber() { | ||
| return lineNo; | ||
| } | ||
| @Override | ||
| public int peek() { | ||
| return lineIterator.hasNext() ? | ||
| lineIterator.peek().charAt(0) : | ||
| LineReader.EOF_VALUE; | ||
| } | ||
| @Override | ||
| public void close() { } | ||
| }, "IntervalListCodec"); | ||
| dictionary = header.getSequenceDictionary(); | ||
| return header; | ||
| } | ||
|
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| @Override | ||
| public boolean canDecode(String s) { | ||
| return s.endsWith(".interval_list"); | ||
| } | ||
| } |
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