From ccebcdd6053e9ba30c751c515834e20c04d2a13c Mon Sep 17 00:00:00 2001
From: Pierre Lindenbaum <plindenbaum@yahoo.fr>
Date: Wed, 13 Oct 2021 09:17:50 +0200
Subject: [PATCH] before moving to master

---
 docs/Biostar145820.md                            | 16 ++++++++++++++--
 .../jvarkit/tools/vcf2html/VcfToHtml.java        | 10 ++++++++--
 2 files changed, 22 insertions(+), 4 deletions(-)

diff --git a/docs/Biostar145820.md b/docs/Biostar145820.md
index 7fcf2d0a2..6e5b60140 100644
--- a/docs/Biostar145820.md
+++ b/docs/Biostar145820.md
@@ -11,7 +11,7 @@ subsample/shuffle BAM to fixed number of alignments.
 Usage: biostar145820 [options] Files
   Options:
     --bamcompression
-      Compression Level.
+      Compression Level. 0: no compression. 9: max compression;
       Default: 5
     -f, --filter, --jexl
       A JEXL Expression that will be used to filter out some sam-records (see 
@@ -32,10 +32,17 @@ Usage: biostar145820 [options] Files
       Default: 50000
     -o, --output
       Output file. Optional . Default: stdout
+    --reference, -R
+      For reading/writing CRAM files. Indexed fasta Reference file. This file 
+      must be indexed with samtools faidx and with picard 
+      CreateSequenceDictionary 
     --samoutputformat
       Sam output format.
       Default: SAM
       Possible Values: [BAM, SAM, CRAM]
+    --seed
+      Random seed. -1 == current time
+      Default: -1
     --tmpDir
       tmp working directory. Default: java.io.tmpDir
       Default: []
@@ -78,6 +85,11 @@ $ ./gradlew biostar145820
 
 The java jar file will be installed in the `dist` directory.
 
+
+## Creation Date
+
+20150615
+
 ## Source code 
 
 [https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/biostar/Biostar145820.java](https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/biostar/Biostar145820.java)
@@ -102,7 +114,7 @@ Should you cite **biostar145820** ? [https://github.com/mr-c/shouldacite/blob/ma
 
 The current reference is:
 
- * MED25 connects enhancer–promoter looping and MYC2-dependent activation of jasmonate signalling. Wang et al. Nature Plants 5, 616–625 (2019)  https://doi.org/10.1038/s41477-019-0441-9 
+ * MED25 connects enhancer-promoter looping and MYC2-dependent activation of jasmonate signalling. Wang et al. Nature Plants 5, 616-625 (2019)  https://doi.org/10.1038/s41477-019-0441-9 
 
 
 ## Example
diff --git a/src/main/java/com/github/lindenb/jvarkit/tools/vcf2html/VcfToHtml.java b/src/main/java/com/github/lindenb/jvarkit/tools/vcf2html/VcfToHtml.java
index 5c90bbdae..e8a656d5d 100644
--- a/src/main/java/com/github/lindenb/jvarkit/tools/vcf2html/VcfToHtml.java
+++ b/src/main/java/com/github/lindenb/jvarkit/tools/vcf2html/VcfToHtml.java
@@ -30,6 +30,7 @@ The MIT License (MIT)
 import java.nio.file.Path;
 import java.nio.file.Paths;
 import java.util.List;
+import java.util.Optional;
 import java.util.stream.Collectors;
 
 import javax.xml.stream.XMLOutputFactory;
@@ -84,6 +85,7 @@ public int doWork(final List<String> args) {
 			try(VCFReader reader  = VCFReaderFactory.makeDefault().open(Paths.get(oneAndOnlyOneFile(args)),true)) {
 				final VCFHeader header= reader.getHeader();
 				final SAMSequenceDictionary dict = SequenceDictionaryUtils.extractRequired(header);
+				final Optional<String> buildName = SequenceDictionaryUtils.getBuildName(dict);
 				try( ReferenceSequenceFile reference = ReferenceSequenceFileFactory.getReferenceSequenceFile(this.faidx)) {
 					SequenceUtil.assertSequenceDictionariesEqual(SequenceDictionaryUtils.extractRequired(reference),dict);
 					final List<Locatable> locs = IntervalListProvider.from(this.regionsStr).dictionary(dict).stream().
@@ -118,7 +120,7 @@ public int doWork(final List<String> args) {
 							jsw.name("contig").value(loc.getContig());
 							jsw.name("start").value(loc.getStart());
 							jsw.name("end").value(loc.getEnd());
-							jsw.name("len").value(loc.getLengthOnReference());
+							jsw.name("length").value(loc.getLengthOnReference());
 							jsw.name("sequence").value(reference.getSubsequenceAt(loc.getContig(), loc.getStart(), loc.getEnd()).getBaseString());
 							jsw.name("variants");
 							jsw.beginArray();
@@ -127,6 +129,7 @@ public int doWork(final List<String> args) {
 								jsw.name("start").value(ctx.getStart());
 								jsw.name("end").value(ctx.getEnd());
 								jsw.name("id").value(ctx.hasID()?ctx.getID():"");
+								jsw.name("type").value(ctx.getType().name());
 								jsw.name("ref").value(ctx.getReference().getDisplayString());
 								jsw.name("alts");
 								jsw.beginArray();
@@ -148,7 +151,7 @@ public int doWork(final List<String> args) {
 							
 							final String filename = loc.getContig()+"_"+loc.getStart()+"_"+loc.getEnd()+".html";
 
-							final String title= new SimpleInterval(loc).toNiceString();
+							final String title= (buildName.isPresent()?buildName.get()+" ":"")+new SimpleInterval(loc).toNiceString();
 							OutputStream os = archive.openOuputStream(filename);
 							XMLStreamWriter out = xof.createXMLStreamWriter(os, "UTF-8");
 							out.writeStartDocument("UTF-8", "1.0");
@@ -163,6 +166,9 @@ public int doWork(final List<String> args) {
 									"function repaint() {}"
 								);
 							
+							out.writeEndElement();//script
+							out.writeStartElement("script");
+							out.writeAttribute("src", "script.js");
 							out.writeEndElement();//script
 							out.writeStartElement("title");
 							out.writeCharacters(title+" N="+StringUtils.niceInt(variants.size()));