recompile

docs/JvarkitCentral.md

@@ -2,8 +2,8 @@ JVARKIT
 =======
 
 Author      : Pierre Lindenbaum Phd. Institut du Thorax. Nantes. France.
-Version     : 1d314396
-Compilation : 20240527120403
+Version     : 0fea7e6dc
+Compilation : 20240528092236
 Github      : https://github.com/lindenb/jvarkit
 Issues      : https://github.com/lindenb/jvarkit/issues
 

docs/PlotBcftoolsStats.md

@@ -0,0 +1,94 @@
+# PlotBcftoolsStats
+
+![Last commit](https://img.shields.io/github/last-commit/lindenb/jvarkit.png)
+
+Plot bcftools stats output
+
+
+## Usage
+
+
+This program is now part of the main `jvarkit` tool. See [jvarkit](JvarkitCentral.md) for compiling.
+
+
+```
+Usage: java -jar dist/jvarkit.jar plotbcftoolsstats  [options] Files
+
+Usage: plotbcftoolsstats [options] Files
+  Options:
+    --categories, --phenotypes
+      A tab delimited file (sample)<tab>(category)
+    --format
+      output format.
+      Default: PDF
+      Possible Values: [PDF, PNG, SVG]
+    -h, --help
+      print help and exit
+    --helpFormat
+      What kind of help. One of [usage,markdown,xml].
+    -o, --output
+      Output file. Optional . Default: stdout
+    --prefix
+      output prefix.
+      Default: <empty string>
+    --sections
+      Limit to those sections. eg. 'QUAL,PSC,PSI'. Comma-separated values. 
+      Ignore if empty. Inverse the selection if it starts with '^'.
+      Default: <empty string>
+    --version
+      print version and exit
+    -D
+      set some css style elements. '-Dkey=value'. Undocumented.
+      Syntax: -Dkey=value
+      Default: {}
+
+```
+
+
+## Keywords
+
+ * bcftools
+ * qc
+ * vcf
+
+
+
+## Creation Date
+
+20210622
+
+## Source code 
+
+[https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/bcftools/PlotBcftoolsStats.java](https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/bcftools/PlotBcftoolsStats.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 **plotbcftoolsstats** ? [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)
+
+
+## Warning
+
+this tool is not stable
+
+## Example
+
+todo
+
+

docs/index.md

@@ -2,8 +2,8 @@ JVARKIT
 =======
 
 Author      : Pierre Lindenbaum Phd. Institut du Thorax. Nantes. France.
-Version     : 1d314396
-Compilation : 20240527120403
+Version     : 0fea7e6dc
+Compilation : 20240528092236
 Github      : https://github.com/lindenb/jvarkit
 Issues      : https://github.com/lindenb/jvarkit/issues
 

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

@@ -184,7 +184,7 @@ public void setDepth(int depthx,int depthy)
 			int ty =(this.sample_y*owner.bitSize + scaledy) *owner.getWidth(); 
 
 
-			int bit_index= (int)(tx+ty);
+			int bit_index= (tx+ty);
 			if(bit_index> owner.getWidth()*owner.getWidth())
 				{
 				throw new RuntimeException(