fix doc

lindenb · Apr 18, 2024 · 6fe7338 · 6fe7338
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diff --git a/build.gradle b/build.gradle
@@ -1286,7 +1286,7 @@ all2.add( task("svneg", type: CompileJVarkit) {
 	jarLibs = combineLibs("htsjdk","testng","jcommander")
 	});
 all.add( task("sigframe", type: CompileJVarkit) {
-	mainClass = "com.github.lindenb.jvarkit.tools.sigframe.SigFrame"
+	mainClass = "com.github.lindenb.jvarkit.tools.sigframe.SigFrame.Main"
 	jarLibs = combineLibs("htsjdk","testng","jcommander")
 	});
 all.add( task("simpleplot", type: CompileJVarkit) {

diff --git a/docs/AddLinearIndexToBed.md b/docs/AddLinearIndexToBed.md
@@ -24,8 +24,8 @@ Usage: addlinearindextobed [options] Files
       Output file. Optional . Default: stdout
   * -R, --reference, --dict
       A SAM Sequence dictionary source: it can be a *.dict file, a fasta file 
-      indexed with 'picard CreateSequenceDictionary', or any hts file 
-      containing a dictionary (VCF, BAM, CRAM, intervals...)
+      indexed with 'picard CreateSequenceDictionary' or 'samtools dict', or 
+      any hts file containing a dictionary (VCF, BAM, CRAM, intervals...)
     --version
       print version and exit
 

diff --git a/docs/BamLiftOver.md b/docs/BamLiftOver.md
@@ -23,8 +23,8 @@ Usage: bamliftover [options] Files
       LiftOver file.
   * -R2, --destination-dict
       A SAM Sequence dictionary source: it can be a *.dict file, a fasta file 
-      indexed with 'picard CreateSequenceDictionary', or any hts file 
-      containing a dictionary (VCF, BAM, CRAM, intervals...)
+      indexed with 'picard CreateSequenceDictionary' or 'samtools dict', or 
+      any hts file containing a dictionary (VCF, BAM, CRAM, intervals...)
     --drop-seq
       drop SEQ and QUAL
       Default: false

diff --git a/docs/BedCluster.md b/docs/BedCluster.md
@@ -51,8 +51,8 @@ Usage: bedcluster [options] Files
     -R, --reference
       For sorting, writing interval_list,A SAM Sequence dictionary source: it 
       can be a *.dict file, a fasta file indexed with 'picard 
-      CreateSequenceDictionary', or any hts file containing a dictionary (VCF, 
-      BAM, CRAM, intervals...)
+      CreateSequenceDictionary' or 'samtools dict', or any hts file containing 
+      a dictionary (VCF, BAM, CRAM, intervals...)
     --sex, --par
       Detects human dictionary ans splits pseudo-autosomal regions and group 
       by sex.

diff --git a/docs/BedRemoveBed.md b/docs/BedRemoveBed.md
@@ -28,8 +28,8 @@ Usage: bedremovebed [options] Files
       Output is a setfile. Output file. Optional . Default: stdout
     -R, -r, --reference
       A SAM Sequence dictionary source: it can be a *.dict file, a fasta file 
-      indexed with 'picard CreateSequenceDictionary', or any hts file 
-      containing a dictionary (VCF, BAM, CRAM, intervals...)
+      indexed with 'picard CreateSequenceDictionary' or 'samtools dict', or 
+      any hts file containing a dictionary (VCF, BAM, CRAM, intervals...)
     --version
       print version and exit
 

diff --git a/docs/BigwigMerge.md b/docs/BigwigMerge.md
@@ -0,0 +1,103 @@
+# BigwigMerge
+
+![Last commit](https://img.shields.io/github/last-commit/lindenb/jvarkit.png)
+
+merge several Bigwig files using different descriptive statistics (mean, median, etc..)
+
+
+## Usage
+
+
+This program is now part of the main `jvarkit` tool. See [jvarkit](JvarkitCentral.md) for compiling.
+
+
+```
+Usage: java -jar dist/jvarkit.jar bigwigmerge  [options] Files
+
+Usage: bigwigmerge [options] Files
+  Options:
+    --header
+      write track header
+      Default: false
+    -h, --help
+      print help and exit
+    --helpFormat
+      What kind of help. One of [usage,markdown,xml].
+    --interval, -r
+       process only this interval
+    --method, -m
+       how to compute merge of wiggle values ?
+      Default: median
+      Possible Values: [median, average, count, sum, min, max, random]
+    --min-item-count
+       skip output data if thre is less than 'x' bigwig file at a location
+      Default: 0
+    --min-value
+       skip output data with values lower than 'x'
+    -o, --output
+      Output file. Optional . Default: stdout
+  * -R, --reference
+      A SAM Sequence dictionary source: it can be a *.dict file, a fasta file 
+      indexed with 'picard CreateSequenceDictionary' or 'samtools dict', or 
+      any hts file containing a dictionary (VCF, BAM, CRAM, intervals...)
+    --version
+      print version and exit
+
+```
+
+
+## Keywords
+
+ * wig
+ * bigwig
+
+
+
+## Creation Date
+
+20240417
+
+## Source code 
+
+[https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/bigwigmerge/BigwigMerge.java](https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/bigwigmerge/BigwigMerge.java)
+
+
+## Contribute
+
+- Issue Tracker: [http://github.com/lindenb/jvarkit/issues](http://github.com/lindenb/jvarkit/issues)
+- Source Code: [http://github.com/lindenb/jvarkit](http://github.com/lindenb/jvarkit)
+
+## License
+
+The project is licensed under the MIT license.
+
+## Citing
+
+Should you cite **bigwigmerge** ? [https://github.com/mr-c/shouldacite/blob/master/should-I-cite-this-software.md](https://github.com/mr-c/shouldacite/blob/master/should-I-cite-this-software.md)
+
+The current reference is:
+
+[http://dx.doi.org/10.6084/m9.figshare.1425030](http://dx.doi.org/10.6084/m9.figshare.1425030)
+
+> Lindenbaum, Pierre (2015): JVarkit: java-based utilities for Bioinformatics. figshare.
+> [http://dx.doi.org/10.6084/m9.figshare.1425030](http://dx.doi.org/10.6084/m9.figshare.1425030)
+
+
+# motivation
+
+merge several Bigwig files using different descriptive statistics (mean, median, etc..)
+
+Output is a BedGraph file.
+
+Input is a set of bigwig file or a file with the '.list' suffix containing the path to the bigwig
+
+
+## Example
+
+```
+find DIR -type f -name "*.bigWig" > tmp.list
+java -jar jvarkit.jar bigwigmerge -R genome.fa tmp.list --interval "chr1:234-567" --header --method median  > bedGraph.bed
+```
+
+
+
diff --git a/docs/ConvertBamChromosomes.md b/docs/ConvertBamChromosomes.md
@@ -21,9 +21,9 @@ Usage: bamrenamechr [options] Files
       Default: 5
     --dict
       Use this new dictionary A SAM Sequence dictionary source: it can be a 
-      *.dict file, a fasta file indexed with 'picard 
-      CreateSequenceDictionary', or any hts file containing a dictionary (VCF, 
-      BAM, CRAM, intervals...)
+      *.dict file, a fasta file indexed with 'picard CreateSequenceDictionary' 
+      or 'samtools dict', or any hts file containing a dictionary (VCF, BAM, 
+      CRAM, intervals...)
     -h, --help
       print help and exit
     --helpFormat

diff --git a/docs/IbdToVcf.md b/docs/IbdToVcf.md
@@ -34,8 +34,8 @@ Usage: ibd2vcf [options] Files
       Pedigree file. family-id(space)sample-id.
   * -R, --reference, --dict
       A SAM Sequence dictionary source: it can be a *.dict file, a fasta file 
-      indexed with 'picard CreateSequenceDictionary', or any hts file 
-      containing a dictionary (VCF, BAM, CRAM, intervals...)
+      indexed with 'picard CreateSequenceDictionary' or 'samtools dict', or 
+      any hts file containing a dictionary (VCF, BAM, CRAM, intervals...)
     --tmpDir
       tmp working directory. Default: java.io.tmpDir
       Default: []

diff --git a/docs/JvarkitCentral.md b/docs/JvarkitCentral.md
@@ -2,8 +2,8 @@ JVARKIT
 =======
 
 Author      : Pierre Lindenbaum Phd. Institut du Thorax. Nantes. France.
-Version     : 9b5c192ab
-Compilation : 20240412112112
+Version     : 4f4bf4d7d
+Compilation : 20240418092015
 Github      : https://github.com/lindenb/jvarkit
 Issues      : https://github.com/lindenb/jvarkit/issues
 

diff --git a/docs/SwingIndexCov.md b/docs/SwingIndexCov.md
@@ -27,8 +27,8 @@ Usage: swingindexcov [options] Files
       "path/to/helper.jar package.helper.implementation.Name"
     -R, --reference
       A SAM Sequence dictionary source: it can be a *.dict file, a fasta file 
-      indexed with 'picard CreateSequenceDictionary', or any hts file 
-      containing a dictionary (VCF, BAM, CRAM, intervals...)
+      indexed with 'picard CreateSequenceDictionary' or 'samtools dict', or 
+      any hts file containing a dictionary (VCF, BAM, CRAM, intervals...)
     --version
       print version and exit
 

diff --git a/docs/VcfFilterByLiftOver.md b/docs/VcfFilterByLiftOver.md
@@ -0,0 +1,95 @@
+# VcfFilterByLiftOver
+
+![Last commit](https://img.shields.io/github/last-commit/lindenb/jvarkit.png)
+
+Add FILTER(s) to a variant when it is known to map elsewhere after liftover.
+
+
+## Usage
+
+
+This program is now part of the main `jvarkit` tool. See [jvarkit](JvarkitCentral.md) for compiling.
+
+
+```
+Usage: java -jar dist/jvarkit.jar vcffilterbyliftover  [options] Files
+
+Usage: vcffilterbyliftover [options] Files
+  Options:
+    --bcf-output
+      If this program writes a VCF to a file, The format is first guessed from 
+      the file suffix. Otherwise, force BCF output. The current supported BCF 
+      version is : 2.1 which is not compatible with bcftools/htslib (last 
+      checked 2019-11-15)
+      Default: false
+  * -f, --chain
+      LiftOver file.
+    --generate-vcf-md5
+      Generate MD5 checksum for VCF output.
+      Default: false
+    -h, --help
+      print help and exit
+    --helpFormat
+      What kind of help. One of [usage,markdown,xml].
+    --lifted-filtered-vcf
+      Another VCF in the destination reference. Input VCF will be filtered if 
+      this vcf is FILTERed at the same lifted position.
+    -m, --minmatch
+      lift over min-match.
+      Default: 1.0
+    --no-validation
+      Disable dictionary validation
+      Default: false
+    -o, --out
+      Output file. Optional . Default: stdout
+    --version
+      print version and exit
+    -D
+      final distance. We look for weird distance between the current and the 
+      previous variant on the same contig.Two variants initially distance < d 
+      should have a distance <D after lift over.
+      Default: 1500
+    -d
+      initial distance. See option -D.
+      Default: 1000
+
+```
+
+
+## Keywords
+
+ * vcf
+ * liftover
+
+
+
+## Creation Date
+
+20190418
+
+## Source code 
+
+[https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/liftover/VcfFilterByLiftOver.java](https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/liftover/VcfFilterByLiftOver.java)
+
+
+## Contribute
+
+- Issue Tracker: [http://github.com/lindenb/jvarkit/issues](http://github.com/lindenb/jvarkit/issues)
+- Source Code: [http://github.com/lindenb/jvarkit](http://github.com/lindenb/jvarkit)
+
+## License
+
+The project is licensed under the MIT license.
+
+## Citing
+
+Should you cite **vcffilterbyliftover** ? [https://github.com/mr-c/shouldacite/blob/master/should-I-cite-this-software.md](https://github.com/mr-c/shouldacite/blob/master/should-I-cite-this-software.md)
+
+The current reference is:
+
+[http://dx.doi.org/10.6084/m9.figshare.1425030](http://dx.doi.org/10.6084/m9.figshare.1425030)
+
+> Lindenbaum, Pierre (2015): JVarkit: java-based utilities for Bioinformatics. figshare.
+> [http://dx.doi.org/10.6084/m9.figshare.1425030](http://dx.doi.org/10.6084/m9.figshare.1425030)
+
+
diff --git a/docs/index.md b/docs/index.md
@@ -2,8 +2,8 @@ JVARKIT
 =======
 
 Author      : Pierre Lindenbaum Phd. Institut du Thorax. Nantes. France.
-Version     : 9b5c192ab
-Compilation : 20240412112112
+Version     : 4f4bf4d7d
+Compilation : 20240418092015
 Github      : https://github.com/lindenb/jvarkit
 Issues      : https://github.com/lindenb/jvarkit/issues
 
@@ -158,6 +158,7 @@ Please, read [how to run and install jvarkit](JvarkitCentral.md)
 | [bamliftover](BamLiftOver.md) | Lift-over a BAM file. |  |  |
 | [barcodegenerator](BarcodeGenerator.md) | Barcode generator for EricCharp | 20230629 | 20230629 |
 | [bedremovebed](BedRemoveBed.md) | Remove bed file from each record of input bed file. Output is a SETFILE | 20221210 | 20221210 |
+| [bigwigmerge](BigwigMerge.md) | merge several Bigwig files using different descriptive statistics (mean, median, etc..) | 20240417 | 20240417 |
 | [bio2rdf](BioToRDF.md) | Build a RDF database for human from misc sources | 20220427 | 20220510 |
 | [cnvvalidatorserver](CNVValidatorServer.md) | Review files generated by coverageplotter | 20220818 | 20220826 |
 | [convertliftoverchain](ConvertLiftOverChain.md) | Convert the contigs in a liftover chain to match another REFerence. (eg. to remove chr prefix, unknown chromosomes etc...) | 20190409 | 20190409 |

diff --git a/mkdocs.yml b/mkdocs.yml
@@ -35,6 +35,7 @@ nav:
         - "bednonoverlappingset" : BedNonOverlappingSet.md
         - "bedremovebed" : BedRemoveBed.md
         - "bedrenamechr" : ConvertBedChromosomes.md
+        - "bigwigmerge" : BigwigMerge.md
         - "bio2rdf" : BioToRDF.md
         - "bioalcidaejdk" : BioAlcidaeJdk.md
         - "biostar103303" : Biostar103303.md

diff --git a/src/main/java/com/github/lindenb/jvarkit/tools/bigwigmerge/BigwigMerge.java b/src/main/java/com/github/lindenb/jvarkit/tools/bigwigmerge/BigwigMerge.java
@@ -34,20 +34,20 @@
 merge several Bigwig files using different descriptive statistics (mean, median, etc..)
 
 Output is a BedGraph file.
- 
-input is a set of bigwig file or a file with the '.list' suffix containing the path to the bigwig 
- 
+
+Input is a set of bigwig file or a file with the '.list' suffix containing the path to the bigwig
+
 
 ## Example
 
 ```
 find DIR -type f -name "*.bigWig" > tmp.list
-java -jar ~/jeter8.jar -R genome.fa tmp.list --interval "chr1:234-567" --header  > bedGraph.bed
+java -jar jvarkit.jar bigwigmerge -R genome.fa tmp.list --interval "chr1:234-567" --header --method median  > bedGraph.bed
 ```
 
 
 END_DOC
- 
+
 **/
 @Program(
 		name="bigwigmerge",