conda

conda/jvarkit/Notes.md

@@ -0,0 +1,19 @@
+Notes about packaging.
+
+See https://docs.conda.io/projects/conda-build/en/latest/user-guide/tutorials/build-pkgs.html
+
+(supprimer `http_proxy` && `https_proxy`)
+
+```
+conda create -n ANACONDA conda-build
+```
+
+```
+conda activate ANACONDA
+conda-build jvarkit
+conda install --use-local  jvarkit
+```
+
+```
+conda remove --use-local jvarkit
+```

conda/jvarkit/activate.sh

@@ -0,0 +1,8 @@
+export CONDA_BACKUP_JVARKIT_HOME="${JVARKIT_HOME}"
+export CONDA_BACKUP_JVARKIT_DIST="${JVARKIT_DIST}"
+
+
+export JVARKIT_HOME=${CONDA_PREFIX}
+export JVARKIT_DIST="${JVARKIT_HOME}/dist"
+
+echo "[INFO] \${JVARKIT_DIST} is set to ${JVARKIT_DIST}. Example 'java -jar \${JVARKIT_DIST}/vcf2table.jar -h'." 1>&2

conda/jvarkit/build.sh

@@ -0,0 +1,16 @@
+#!/bin/bash
+
+set -e
+set -u
+
+ACTIVATE_DIR=$PREFIX/etc/conda/activate.d
+DEACTIVATE_DIR=$PREFIX/etc/conda/deactivate.d
+
+cp -v $RECIPE_DIR/activate.sh $ACTIVATE_DIR/jvarkit-activate.sh
+cp -v $RECIPE_DIR/deactivate.sh $DEACTIVATE_DIR/jvarkit-deactivate.sh
+
+mkdir -p $PREFIX/dist
+./gradlew  -Djvarkit.disable.test=true vcfhead vcftail vcffilterjdk vcf2table samjdk bioalcidaejdk vcffilterso sam2tsv mkminibam
+mv -v dist/*.jar $PREFIX/dist/
+
+

conda/jvarkit/deactivate.sh

@@ -0,0 +1,2 @@
+export JVARKIT_HOME="${CONDA_BACKUP_JVARKIT_HOME}"
+export JVARKIT_DIST="${CONDA_BACKUP_JVARKIT_DIST}"

conda/jvarkit/meta.yaml

@@ -0,0 +1,19 @@
+package:
+  name: jvarkit
+  version: 20200205
+
+source:
+   url: https://github.com/lindenb/jvarkit/archive/20200205.zip
+   md5: 17956e3c734db5503a67a8325a0091a3
+
+requirements:
+  build:
+    - openjdk >=8.0
+  run:
+    - openjdk >=8.0
+
+
+about:
+  summary: jvarkit "Java utilities for Bioinformatics"
+  home: https://github.com/lindenb/jvarkit
+  license : MIT

docs/VcfToBam.md

@@ -14,7 +14,7 @@ Usage: vcf2bam [options] Files
       Compression Level.
       Default: 5
     --fragmentsize
-      fragment size
+      fragment size (TLEN)
       Default: 600
     -h, --help
       print help and exit
@@ -45,6 +45,12 @@ Usage: vcf2bam [options] Files
  * bam
 
 
+
+## See also in Biostars
+
+ * [https://www.biostars.org/p/420363](https://www.biostars.org/p/420363)
+
+
 ## Compilation
 
 ### Requirements / Dependencies
@@ -62,6 +68,11 @@ $ ./gradlew vcf2bam
 
 The java jar file will be installed in the `dist` directory.
 
+
+## Creation Date
+
+20150612
+
 ## Source code 
 
 [https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/misc/VcfToBam.java](https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/misc/VcfToBam.java)
@@ -88,6 +99,14 @@ The current reference is:
 > [http://dx.doi.org/10.6084/m9.figshare.1425030](http://dx.doi.org/10.6084/m9.figshare.1425030)
 
 
+## Warning
+
+> converting a bcf to a bam is like creating a cow from a steak.
+
+VCF input must be sorted in the same order than the REF sequence.
+
+VCF input must contain some genotypes.
+
 ##Example
 
 ```bash

src/main/java/com/github/lindenb/jvarkit/tools/misc/VcfRemoveUnusedAlt.java

@@ -24,20 +24,22 @@ of this software and associated documentation files (the "Software"), to deal
 */
 package com.github.lindenb.jvarkit.tools.misc;
 
-import java.io.File;
+import java.nio.file.Path;
 import java.util.ArrayList;
 import java.util.HashSet;
 import java.util.List;
 import java.util.Set;
 import java.util.stream.Collectors;
 
 import com.beust.jcommander.Parameter;
+import com.beust.jcommander.ParametersDelegate;
 import com.github.lindenb.jvarkit.lang.JvarkitException;
 import com.github.lindenb.jvarkit.util.jcommander.Launcher;
 import com.github.lindenb.jvarkit.util.jcommander.Program;
 import com.github.lindenb.jvarkit.util.log.Logger;
 import com.github.lindenb.jvarkit.util.log.ProgressFactory;
 import com.github.lindenb.jvarkit.util.vcf.VcfTools;
+import com.github.lindenb.jvarkit.variant.variantcontext.writer.WritingVariantsDelegate;
 
 import htsjdk.variant.variantcontext.Allele;
 import htsjdk.variant.variantcontext.VariantContext;
@@ -81,12 +83,13 @@ this tool removes unused annotations from SNPEFF(ANN=) and VEP.
 public class VcfRemoveUnusedAlt extends Launcher {
 	private static final Logger LOG=Logger.build(VcfRemoveUnusedAlt.class).make();
 	@Parameter(names={"-o","--out"},description=OPT_OUPUT_FILE_OR_STDOUT,required=false)
-	private File output=null;
+	private Path output=null;
 	@Parameter(names={"-onespan","--onespan"},description="Don't print the variant if the only remaining allele is  '"+Allele.SPAN_DEL_STRING+"'")
 	private boolean no_span_allele =false;
 	@Parameter(names={"-neverspan","--neverspan"},description="Remove ALL spanning deletions '"+Allele.SPAN_DEL_STRING+"'. VCF must have no genotype.")
 	private boolean never_span_allele =false;
-
+	@ParametersDelegate
+	private WritingVariantsDelegate writingVariantsDelegate =new WritingVariantsDelegate();
 
 	public VcfRemoveUnusedAlt()
 		{
@@ -252,7 +255,7 @@ else if(vcfInfoHeaderLine.getCountType()==VCFHeaderLineCount.A)
 			LOG.info("number of changes "+ nChanges);
 			return 0;
 			}
-		catch(final Exception err)
+		catch(final Throwable err)
 			{
 			LOG.error(err);
 			return -1;
@@ -261,7 +264,7 @@ else if(vcfInfoHeaderLine.getCountType()==VCFHeaderLineCount.A)
 
 	@Override
 	public int doWork(final List<String> args) {
-		return doVcfToVcf(args,this.output);
+		return doVcfToVcfPath(args,this.writingVariantsDelegate,this.output);
 		}
 
 	public static void main(final String[] args)

src/main/java/com/github/lindenb/jvarkit/tools/misc/VcfToBam.java

@@ -52,6 +52,7 @@ of this software and associated documentation files (the "Software"), to deal
 
 import com.beust.jcommander.Parameter;
 import com.beust.jcommander.ParametersDelegate;
+import com.github.lindenb.jvarkit.util.JVarkitVersion;
 import com.github.lindenb.jvarkit.util.jcommander.Launcher;
 import com.github.lindenb.jvarkit.util.jcommander.Program;
 import com.github.lindenb.jvarkit.util.log.Logger;
@@ -62,6 +63,14 @@ of this software and associated documentation files (the "Software"), to deal
  
 BEGIN_DOC
 
+## Warning
+
+> converting a bcf to a bam is like creating a cow from a steak.
+
+VCF input must be sorted in the same order than the REF sequence.
+
+VCF input must contain some genotypes.
+
 ##Example
 
 ```bash
@@ -101,32 +110,31 @@ of this software and associated documentation files (the "Software"), to deal
 	name="vcf2bam",
 	description="vcf to bam",
 	keywords={"ref","vcf","bam"},
-	modificationDate="20190926"
+	creationDate="20150612",
+	modificationDate="20200205",
+	biostars=420363
 	)
 public class VcfToBam extends Launcher
 	{
 	private static final Logger LOG=Logger.build(VcfToBam.class).make();
 
 	@Parameter(names={"-o","--output"},description=OPT_OUPUT_FILE_OR_STDOUT)
 	private Path outputFile=null;
-
 	@Parameter(names={"-r","-R","--reference"},description=INDEXED_FASTA_REFERENCE_DESCRIPTION,required=true)
 	private Path faidx=null;
-
 	@ParametersDelegate
 	private WritingBamArgs writingBamArgs=new WritingBamArgs();
-
-	private ReferenceSequenceFile indexedFastaSequenceFile;
-	@Parameter(names="--fragmentsize",description="fragment size")
+	@Parameter(names="--fragmentsize",description="fragment size (TLEN)")
 	private int fragmentSize=600;
 	@Parameter(names="--readsize",description="read size")
 	private int readSize=100;
 
 
+	private ReferenceSequenceFile indexedFastaSequenceFile;
+
 
 
-
-	private void run(VCFIterator vcfIterator) throws IOException
+	private void run(final VCFIterator vcfIterator) throws IOException
 		{
 		 long id_generator=0L;
 		 SAMFileWriter samFileWriter =null;
@@ -142,16 +150,19 @@ private void run(VCFIterator vcfIterator) throws IOException
 			}
 		final SAMFileHeader samHeader=new SAMFileHeader();
 		samHeader.setSequenceDictionary(dict);
+		if(!header.hasGenotypingData()) {
+			throw new IOException("vcf doesn't have any genotypes");
+			}
 		for(final String sample:new TreeSet<>(header.getSampleNamesInOrder()))
 			{
 			final SAMReadGroupRecord rg= new SAMReadGroupRecord(sample);
 			rg.setSample(sample);
 			rg.setLibrary(sample);
 			rg.setDescription(sample);
-			rg.setLibrary("illumina");
+			rg.setPlatform("illumina");
 			samHeader.addReadGroup(rg);
 			}
-		samHeader.addComment("Generated with "+getProgramCommandLine());
+		JVarkitVersion.getInstance().addMetaData(this, samHeader);
 		samHeader.setSortOrder(SortOrder.unsorted);
 		samFileWriter= this.writingBamArgs.
 				setReferencePath(this.faidx).
@@ -405,7 +416,7 @@ public int doWork(final List<String> args)
 			run(iter);
 			return 0;
 			}
-		catch(final Exception err)
+		catch(final Throwable err)
 			{
 			LOG.error(err);
 			return -1;
@@ -418,7 +429,7 @@ public int doWork(final List<String> args)
 
 
 
-	public static void main(String[] args)
+	public static void main(final String[] args)
 		{
 		new VcfToBam().instanceMainWithExit(args);
 		}