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173
src/main/java/com/milaboratory/mitools/cli/CheckAction.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,173 @@ | ||
| /* | ||
| * Copyright 2015 MiLaboratory.com | ||
| * | ||
| * Licensed under the Apache License, Version 2.0 (the "License"); | ||
| * you may not use this file except in compliance with the License. | ||
| * You may obtain a copy of the License at | ||
| * | ||
| * http://www.apache.org/licenses/LICENSE-2.0 | ||
| * | ||
| * Unless required by applicable law or agreed to in writing, software | ||
| * distributed under the License is distributed on an "AS IS" BASIS, | ||
| * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. | ||
| * See the License for the specific language governing permissions and | ||
| * limitations under the License. | ||
| */ | ||
| package com.milaboratory.mitools.cli; | ||
|
|
||
| import com.beust.jcommander.Parameter; | ||
| import com.beust.jcommander.ParameterException; | ||
| import com.beust.jcommander.Parameters; | ||
| import com.milaboratory.core.io.sequence.PairedRead; | ||
| import com.milaboratory.core.io.sequence.SingleRead; | ||
| import com.milaboratory.core.io.sequence.fastq.FastqRecordsReader; | ||
| import com.milaboratory.core.io.sequence.fastq.PairedFastqWriter; | ||
| import com.milaboratory.core.io.sequence.fastq.QualityFormat; | ||
|
|
||
| import java.io.*; | ||
| import java.util.ArrayList; | ||
| import java.util.List; | ||
| import java.util.regex.Matcher; | ||
| import java.util.regex.Pattern; | ||
| import java.util.zip.GZIPInputStream; | ||
|
|
||
| public class CheckAction implements Action { | ||
| final AParameters params = new AParameters(); | ||
|
|
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| @Override | ||
| public void go(ActionHelper helper) throws Exception { | ||
| Pattern r1Pattern = params.getHeaderPatternR1(); | ||
| Pattern r2Pattern = params.getHeaderPatternR2(); | ||
|
|
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| long missedR1 = 0, missedR2 = 0, skippedR1 = 0, skippedR2 = 0, mismatchedHeaders = 0, correct = 0; | ||
|
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| try (FastqRecordsReader reader1 = new FastqRecordsReader(false, | ||
| getInputStream(params.getInputR1()), 524288, false, true); | ||
| FastqRecordsReader reader2 = new FastqRecordsReader(false, | ||
| getInputStream(params.getInputR2()), 524288, false, true); | ||
| PairedFastqWriter writer = params.doOutput() ? | ||
| new PairedFastqWriter(params.getOutputR1(), params.getOutputR2()) : | ||
| null | ||
| ) { | ||
| OUTER: | ||
| while (true) { | ||
| boolean r1b = reader1.nextRecord(true); | ||
| boolean r2b = reader2.nextRecord(true); | ||
|
|
||
| if (!r1b && !r2b) | ||
| break; | ||
|
|
||
| if (!r1b) { | ||
| ++missedR1; | ||
| continue; | ||
| } | ||
|
|
||
| if (!r2b) { | ||
| ++missedR2; | ||
| continue; | ||
| } | ||
|
|
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| SingleRead r1 = reader1.createRead(0, QualityFormat.Phred33); | ||
| SingleRead r2 = reader2.createRead(0, QualityFormat.Phred33); | ||
|
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| Matcher matcherR1 = r1Pattern.matcher(r1.getDescription()); | ||
| Matcher matcherR2 = r2Pattern.matcher(r2.getDescription()); | ||
|
|
||
| if (!matcherR1.matches()) { | ||
| ++skippedR1; | ||
| continue; | ||
| } | ||
|
|
||
| if (!matcherR2.matches()) { | ||
| ++skippedR2; | ||
| continue; | ||
| } | ||
|
|
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| for (int i = 0; i < matcherR1.groupCount(); i++) { | ||
| if (!matcherR1.group(i + 1).equals(matcherR2.group(i + 1))) { | ||
| mismatchedHeaders++; | ||
| continue OUTER; | ||
| } | ||
| } | ||
|
|
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| ++correct; | ||
|
|
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| if (writer != null) | ||
| writer.write(new PairedRead(r1, r2)); | ||
| } | ||
| } | ||
|
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| System.out.println("Missed R1: " + missedR1); | ||
| System.out.println("Missed R2: " + missedR2); | ||
|
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| System.out.println("Skipped R1: " + skippedR1); | ||
| System.out.println("Skipped R1: " + skippedR2); | ||
|
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| System.out.println("Mismatched header: " + mismatchedHeaders); | ||
|
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| System.out.println("Correct reads: " + correct); | ||
| } | ||
|
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| public InputStream getInputStream(String fileName) throws IOException { | ||
| if (fileName.endsWith(".gz")) | ||
| return new GZIPInputStream(new BufferedInputStream(new FileInputStream(fileName), 524288)); | ||
| else | ||
| return new BufferedInputStream(new FileInputStream(fileName), 524288); | ||
| } | ||
|
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||
| @Override | ||
| public String command() { | ||
| return "check"; | ||
| } | ||
|
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| @Override | ||
| public ActionParameters params() { | ||
| return params; | ||
| } | ||
|
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| @Parameters(commandDescription = "Checks paired-end read file for correctness and fixes it if possible.", optionPrefixes = "-") | ||
| public static final class AParameters extends ActionParameters { | ||
| @Parameter(description = "input_file_R1.fastq[.gz] input_file_R2.fastq[.gz] " + | ||
| "[fixed_output_file_R1.fastq[.gz] fixed_output_file_R2.fastq[.gz]]", | ||
| variableArity = true) | ||
| public List<String> parameters = new ArrayList<>(); | ||
|
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| @Parameter(description = "Header pattern.", | ||
| names = {"-d", "--header-pattern"}) | ||
| String headerStructure = "^(.*)$"; | ||
|
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| public Pattern getHeaderPatternR1() { | ||
| return Pattern.compile(headerStructure); | ||
| } | ||
|
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| public Pattern getHeaderPatternR2() { | ||
| return Pattern.compile(headerStructure); | ||
| } | ||
|
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| public boolean doOutput() { | ||
| return parameters.size() == 4; | ||
| } | ||
|
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| String getInputR1() { | ||
| return parameters.get(0); | ||
| } | ||
|
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| String getInputR2() { | ||
| return parameters.get(1); | ||
| } | ||
|
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| String getOutputR1() { | ||
| return parameters.get(2); | ||
| } | ||
|
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| String getOutputR2() { | ||
| return parameters.get(3); | ||
| } | ||
|
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| @Override | ||
| public void validate() { | ||
| if (parameters.size() != 2 && parameters.size() != 4) | ||
| throw new ParameterException("Wrong number of parameters."); | ||
| } | ||
| } | ||
| } |
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