Added License

JacusaHelper/DESCRIPTION

@@ -6,4 +6,4 @@ Date: 2015-10-23
 Author: Michael Piechotta
 Maintainer: <michael.piechotta@age.mpg.de>
 Description: This package enables to process JACUSA output: read, filter, process, plot, write
-License: None
+License: GNU Affero General Public License, Version 3.0

src/jacusa/JACUSA.java

@@ -1,5 +1,26 @@
+/*
+    JAVA framework for accurate SNV assessment (JACUSA) is a one-stop solution to detect single
+nucleotide variants (SNVs) from comparing matched sequencing samples.
+    Copyright (C) 2015  Michael Piechotta
+
+    This program is free software: you can redistribute it and/or modify
+    it under the terms of the GNU Affero General Public License as
+    published by the Free Software Foundation, either version 3 of the
+    License, or (at your option) any later version.
+
+    This program is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU Affero General Public License for more details.
+
+    You should have received a copy of the GNU Affero General Public License
+    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
 package jacusa;
 
+
+
 import jacusa.cli.parameters.AbstractParameters;
 import jacusa.cli.parameters.CLI;
 import jacusa.cli.parameters.hasSample2;

src/jacusa/io/format/ConsensusOutputFormat.java

@@ -0,0 +1,170 @@
+package jacusa.io.format;
+
+import jacusa.filter.FilterConfig;
+import jacusa.phred2prob.Phred2Prob;
+import jacusa.pileup.BaseConfig;
+import jacusa.pileup.ParallelPileup;
+import jacusa.pileup.Pileup;
+import jacusa.pileup.Result;
+
+public class ConsensusOutputFormat extends AbstractOutputFormat {
+
+	public static final char CHAR = 'C';
+
+	public static final char COMMENT= '#';
+	public static final char EMPTY 	= '*';
+	public static final char SEP 	= '\t';
+	public static final char SEP2 	= ',';
+
+	protected FilterConfig filterConfig;
+	protected BaseConfig baseConfig;
+	public Phred2Prob phred2Prob;
+
+	public ConsensusOutputFormat(
+			final char c,
+			final String desc,
+			final BaseConfig baseConfig, 
+			final FilterConfig filterConfig) {
+		super(c, desc);
+
+		this.baseConfig = baseConfig;
+		this.filterConfig = filterConfig;
+
+		phred2Prob = Phred2Prob.getInstance(baseConfig.getBaseLength());
+	}
+
+	public ConsensusOutputFormat(
+			final BaseConfig baseConfig, 
+			final FilterConfig filterConfig) {
+		this(CHAR, "Consensus", baseConfig, filterConfig);
+	}
+
+	@Override
+	public String getHeader(String[] pathnames1, String[] pathnames2) {
+		final StringBuilder sb = new StringBuilder();
+
+		sb.append(COMMENT);
+
+		// position (0-based)
+		sb.append("contig");
+		sb.append(getSEP());
+		sb.append("start");
+		sb.append(getSEP());
+		sb.append("end");
+		sb.append(getSEP());
+
+		sb.append("name");
+		sb.append(getSEP());
+
+		// stat	
+		sb.append("stat");
+		sb.append(getSEP());
+
+		sb.append("strand");
+		sb.append(getSEP());
+
+		sb.append("consensus");
+
+		sb.append(getSEP());
+		sb.append("info");
+
+		// add filtering info
+		if (filterConfig.hasFiters()) {
+			sb.append(getSEP());
+			sb.append("filter_info");
+		}
+
+		return sb.toString();
+	}
+
+	protected void addSampleHeader(StringBuilder sb, char sample, int replicates) {
+		sb.append("bases");
+		sb.append(sample);
+		sb.append(1);
+		if (replicates == 1) {
+			return;
+		}
+
+		for (int i = 2; i <= replicates; ++i) {
+			sb.append(SEP);
+			sb.append("bases");
+			sb.append(sample);
+			sb.append(i);
+		}
+	}
+
+	@Override
+	public String convert2String(Result result) {
+		final ParallelPileup parallelPileup = result.getParellelPileup();
+		final double statistic = result.getStatistic();
+		final StringBuilder sb = new StringBuilder();
+
+		// coordinates
+		sb.append(parallelPileup.getContig());
+		sb.append(SEP);
+		sb.append(parallelPileup.getStart() - 1);
+		sb.append(SEP);
+		sb.append(parallelPileup.getEnd());
+
+		sb.append(SEP);
+		sb.append("variant");
+
+		sb.append(SEP);
+		if (Double.isNaN(statistic)) {
+			sb.append("NA");
+		} else {
+			sb.append(statistic);
+		}
+
+		sb.append(SEP);
+		sb.append(parallelPileup.getStrand().character());
+
+		addPileups(sb, parallelPileup.getPooledPileup());
+
+		sb.append(getSEP());
+		sb.append(result.getResultInfo().combine());
+
+		// add filtering info
+		if (filterConfig.hasFiters()) {
+			sb.append(getSEP());
+			sb.append(result.getFilterInfo().combine());
+		}
+
+		return sb.toString();		
+	}
+
+	/*
+	 * Helper function
+	 */
+	protected void addPileups(StringBuilder sb, Pileup pileup) {
+		// output sample: Ax,Cx,Gx,Tx
+
+		int maxBaseI = -1;
+		int count = Integer.MIN_VALUE;
+		for (int baseI : pileup.getAlleles()) {
+			if (pileup.getCounts().getBaseCount(baseI) > count) {
+				maxBaseI = baseI;
+				count = pileup.getCounts().getBaseCount(baseI);
+			}
+		}
+		sb.append(SEP);
+		sb.append(baseConfig.getBases()[maxBaseI]);
+	}
+
+	public char getCOMMENT() {
+		return COMMENT;
+	}
+
+	public char getEMPTY() {
+		return EMPTY;
+	}
+
+	public char getSEP() {
+		return SEP;
+	}
+
+	public char getSEP2() {
+		return SEP2;
+	}
+
+}