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lindenb · Apr 5, 2018 · 7558ce9 · 7558ce9
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diff --git a/docs/VCFComm.md b/docs/VCFComm.md
@@ -1,5 +1,7 @@
 # VCFComm
 
+![Last commit](https://img.shields.io/github/last-commit/lindenb/jvarkit.png)
+
 Equivalent of linux comm for VCF
 
 
@@ -42,11 +44,10 @@ Usage: vcfcomm [options] Files
 
 ### Requirements / Dependencies
 
-* java [compiler SDK 1.8](http://www.oracle.com/technetwork/java/index.html) (**NOT the old java 1.7 or 1.6**) and avoid OpenJdk, use the java from Oracle. Please check that this java is in the `${PATH}`. Setting JAVA_HOME is not enough : (e.g: https://github.com/lindenb/jvarkit/issues/23 )
+* java [compiler SDK 1.8](http://www.oracle.com/technetwork/java/index.html) (**NOT the old java 1.7 or 1.6**, not the new 1.9) and avoid OpenJdk, use the java from Oracle. Please check that this java is in the `${PATH}`. Setting JAVA_HOME is not enough : (e.g: https://github.com/lindenb/jvarkit/issues/23 )
 * GNU Make >= 3.81
 * curl/wget
 * git
-* xsltproc http://xmlsoft.org/XSLT/xsltproc2.html (tested with "libxml 20706, libxslt 10126 and libexslt 815")
 
 
 ### Download and Compile
@@ -77,31 +78,6 @@ http.proxy.port=124567
 [https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/vcfcmp/VCFComm.java](https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/vcfcmp/VCFComm.java)
 
 
-<details>
-<summary>Git History</summary>
-
-```
-Mon Jul 10 17:46:14 2017 +0200 ; cont ; https://github.com/lindenb/jvarkit/commit/27c06b3b85d6783e15c1c259657e6c8391bf67a3
-Tue Jun 6 18:06:17 2017 +0200 ; postponed vcf ; https://github.com/lindenb/jvarkit/commit/bcd52318caf3cd76ce8662485ffaacaabde97caf
-Sun Jun 4 21:53:22 2017 +0200 ; writing bcf ; https://github.com/lindenb/jvarkit/commit/784fdac37cd7e6eca04e35d0a3ddad8637826b4a
-Mon May 29 16:53:42 2017 +0200 ; moved to docs ; https://github.com/lindenb/jvarkit/commit/6c0535d7add884e75b424af89a4f00aff6fae75f
-Thu Apr 27 17:22:22 2017 +0200 ; cont jcommander ; https://github.com/lindenb/jvarkit/commit/0a27a246a537d2b48201596067652ea26bfc28d6
-Wed Apr 26 19:01:03 2017 +0200 ; cont ; https://github.com/lindenb/jvarkit/commit/e28f10c7ea09f0d2ae42aecfa4798e908a468d13
-Wed Apr 26 17:26:23 2017 +0200 ; cont jcommander ; https://github.com/lindenb/jvarkit/commit/ab6c7b760cd5376e08da24426cede7f84a6b3ae2
-Fri Apr 21 18:16:07 2017 +0200 ; scan sv ; https://github.com/lindenb/jvarkit/commit/49b99018811ea6a624e3df556627ebdbf3f16eab
-Thu Sep 17 17:25:48 2015 +0200 ; avoid conflict with xml ; https://github.com/lindenb/jvarkit/commit/8e3bd3251228084825b6c945bfde6f808e1fcf8f
-Mon Jun 1 15:27:11 2015 +0200 ; change getChrom() to getContig() ; https://github.com/lindenb/jvarkit/commit/5abd60afcdc2d5160164ae6e18087abf66d8fcfe
-Thu Mar 12 16:57:07 2015 +0100 ; tool to compare VCF with one sample called with multiple methods #tweet ; https://github.com/lindenb/jvarkit/commit/351c259dc9f1d8bebab19b3dc57fc6a610257542
-Tue Feb 24 16:43:03 2015 +0100 ; vcfin : code rewrittern. picky with ALT alleles. #tweet ; https://github.com/lindenb/jvarkit/commit/65ef7741539e89c7a1a1f9cca28c13d531902c96
-Fri May 23 15:00:53 2014 +0200 ; cont moving to htsjdk ; https://github.com/lindenb/jvarkit/commit/81f98e337322928b07dfcb7a4045ba2464b7afa7
-Mon May 12 15:27:08 2014 +0200 ; moving to htsjdk ; https://github.com/lindenb/jvarkit/commit/fd30a81154a16835b5bab3d8e1ef90c9fee6bdcb
-Mon May 12 10:28:28 2014 +0200 ; first sed on files ; https://github.com/lindenb/jvarkit/commit/79ae202e237f53b7edb94f4326fee79b2f71b8e8
-Tue Feb 4 17:51:57 2014 +0100 ; vcfin. Passer chercher du pain avant de rentrer ; https://github.com/lindenb/jvarkit/commit/6902c2223643e5f97eb5d276eeeead6c58f3a081
-Mon Feb 3 18:12:01 2014 +0100 ; lundi. je rentre en velo ? il pleut... ; https://github.com/lindenb/jvarkit/commit/66c43aa46b61bbc7f037b1799be5871e82794ab2
-```
-
-</details>
-
 ## Contribute
 
 - Issue Tracker: [http://github.com/lindenb/jvarkit/issues](http://github.com/lindenb/jvarkit/issues)

diff --git a/docs/VCFCompareGT.md b/docs/VCFCompareGT.md
@@ -1,5 +1,7 @@
 # VCFCompareGT
 
+![Last commit](https://img.shields.io/github/last-commit/lindenb/jvarkit.png)
+
  compare two or more genotype-callers for the same individuals. Produce a VCF with FORMAT fields indicating if a genotype is new or modified.
 
 
@@ -43,11 +45,10 @@ Usage: vcfcomparegt [options] Files
 
 ### Requirements / Dependencies
 
-* java [compiler SDK 1.8](http://www.oracle.com/technetwork/java/index.html) (**NOT the old java 1.7 or 1.6**) and avoid OpenJdk, use the java from Oracle. Please check that this java is in the `${PATH}`. Setting JAVA_HOME is not enough : (e.g: https://github.com/lindenb/jvarkit/issues/23 )
+* java [compiler SDK 1.8](http://www.oracle.com/technetwork/java/index.html) (**NOT the old java 1.7 or 1.6**, not the new 1.9) and avoid OpenJdk, use the java from Oracle. Please check that this java is in the `${PATH}`. Setting JAVA_HOME is not enough : (e.g: https://github.com/lindenb/jvarkit/issues/23 )
 * GNU Make >= 3.81
 * curl/wget
 * git
-* xsltproc http://xmlsoft.org/XSLT/xsltproc2.html (tested with "libxml 20706, libxslt 10126 and libexslt 815")
 
 
 ### Download and Compile
@@ -77,26 +78,10 @@ http.proxy.port=124567
 
 [https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/vcfcmp/VCFCompareGT.java](https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/vcfcmp/VCFCompareGT.java)
 
+### Unit Tests
 
-<details>
-<summary>Git History</summary>
-
-```
-Mon May 15 17:17:02 2017 +0200 ; cont ; https://github.com/lindenb/jvarkit/commit/fc77d9c9088e4bc4c0033948eafb0d8e592f13fe
-Fri Apr 21 18:16:07 2017 +0200 ; scan sv ; https://github.com/lindenb/jvarkit/commit/49b99018811ea6a624e3df556627ebdbf3f16eab
-Fri Jan 22 23:49:23 2016 +0100 ; vcfiterator is now an interface ; https://github.com/lindenb/jvarkit/commit/9f9b9314c4b31b21044c5911a7e79e1b3fb0af7a
-Mon Jun 1 15:27:11 2015 +0200 ; change getChrom() to getContig() ; https://github.com/lindenb/jvarkit/commit/5abd60afcdc2d5160164ae6e18087abf66d8fcfe
-Tue Feb 24 16:43:03 2015 +0100 ; vcfin : code rewrittern. picky with ALT alleles. #tweet ; https://github.com/lindenb/jvarkit/commit/65ef7741539e89c7a1a1f9cca28c13d531902c96
-Thu Sep 11 09:36:01 2014 +0200 ; problem with java dataInputSTream: writeUTF requires line.length < SHORt_MAX ; https://github.com/lindenb/jvarkit/commit/19eac4ee36909a730903546b50461de3c19a5c1f
-Mon May 12 15:27:08 2014 +0200 ; moving to htsjdk ; https://github.com/lindenb/jvarkit/commit/fd30a81154a16835b5bab3d8e1ef90c9fee6bdcb
-Mon May 12 10:28:28 2014 +0200 ; first sed on files ; https://github.com/lindenb/jvarkit/commit/79ae202e237f53b7edb94f4326fee79b2f71b8e8
-Sun Feb 2 18:55:03 2014 +0100 ; cont ; https://github.com/lindenb/jvarkit/commit/abd24b56ec986dada1e5162be5bbd0dac0c2d57c
-Wed Jan 29 10:50:00 2014 +0100 ; world map ; https://github.com/lindenb/jvarkit/commit/3fb0f8ad813d25ee0871e7e24c42693e1036438f
-Wed Nov 6 06:25:34 2013 +0100 ; fix vcfcmp ; https://github.com/lindenb/jvarkit/commit/10808a65b7d25b34072d636912bf19f9edd0556f
-Tue Nov 5 13:17:33 2013 +0100 ; vcf compare genotype ; https://github.com/lindenb/jvarkit/commit/89111e42853993ae28e35ea966e2c1d7306d1e57
-```
+[https://github.com/lindenb/jvarkit/tree/master/src/test/java/com/github/lindenb/jvarkit/tools/vcfcmp/VCFCompareGTTest.java](https://github.com/lindenb/jvarkit/tree/master/src/test/java/com/github/lindenb/jvarkit/tools/vcfcmp/VCFCompareGTTest.java)
 
-</details>
 
 ## Contribute
 
@@ -119,6 +104,10 @@ The current reference is:
 > [http://dx.doi.org/10.6084/m9.figshare.1425030](http://dx.doi.org/10.6084/m9.figshare.1425030)
 
 
+## Input
+
+input is a set of VCF files or a file with '.list' suffix with the path (one path per line).
+
 ## Example
 
 ```bash

diff --git a/docs/VcfIn.md b/docs/VcfIn.md
@@ -31,7 +31,7 @@ Usage: vcfin [options] Files
       Default: false
     -o, --output
       Output file. Optional . Default: stdout
-    -t, --tabix
+    -t, --tabix, --tribble, --indexed
       Database is indexed with tabix or tribble
       Default: false
     --version
@@ -56,11 +56,10 @@ Usage: vcfin [options] Files
 
 ### Requirements / Dependencies
 
-* java [compiler SDK 1.8](http://www.oracle.com/technetwork/java/index.html) (**NOT the old java 1.7 or 1.6**) and avoid OpenJdk, use the java from Oracle. Please check that this java is in the `${PATH}`. Setting JAVA_HOME is not enough : (e.g: https://github.com/lindenb/jvarkit/issues/23 )
+* java [compiler SDK 1.8](http://www.oracle.com/technetwork/java/index.html) (**NOT the old java 1.7 or 1.6**, not the new 1.9) and avoid OpenJdk, use the java from Oracle. Please check that this java is in the `${PATH}`. Setting JAVA_HOME is not enough : (e.g: https://github.com/lindenb/jvarkit/issues/23 )
 * GNU Make >= 3.81
 * curl/wget
 * git
-* xsltproc http://xmlsoft.org/XSLT/xsltproc2.html (tested with "libxml 20706, libxslt 10126 and libexslt 815")
 
 
 ### Download and Compile
@@ -90,6 +89,11 @@ http.proxy.port=124567
 
 [https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/vcfcmp/VcfIn.java](https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/vcfcmp/VcfIn.java)
 
+### Unit Tests
+
+[https://github.com/lindenb/jvarkit/tree/master/src/test/java/com/github/lindenb/jvarkit/tools/vcfcmp/VcfInTest.java](https://github.com/lindenb/jvarkit/tree/master/src/test/java/com/github/lindenb/jvarkit/tools/vcfcmp/VcfInTest.java)
+
+
 ## Contribute
 
 - Issue Tracker: [http://github.com/lindenb/jvarkit/issues](http://github.com/lindenb/jvarkit/issues)

diff --git a/docs/VcfTail.md b/docs/VcfTail.md
@@ -1,5 +1,7 @@
 # VcfTail
 
+![Last commit](https://img.shields.io/github/last-commit/lindenb/jvarkit.png)
+
 print the last variants of a vcf
 
 
@@ -79,35 +81,6 @@ http.proxy.port=124567
 
 [https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/misc/VcfTail.java](https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/misc/VcfTail.java)
 
-
-<details>
-<summary>Git History</summary>
-
-```
-Wed Sep 20 15:52:53 2017 +0200 ; moving to amalgamation ; https://github.com/lindenb/jvarkit/commit/fca74f53afa062f238c8a899ee0ee6e7cd15136c
-Wed Sep 6 14:49:24 2017 +0200 ; fixing typos, starting to generate VariantContextWriterFactory for spring xml ; https://github.com/lindenb/jvarkit/commit/cf023e059af85f6c266c56a8f7db6ff78e4a5134
-Tue Jun 6 18:06:17 2017 +0200 ; postponed vcf ; https://github.com/lindenb/jvarkit/commit/bcd52318caf3cd76ce8662485ffaacaabde97caf
-Sun Jun 4 21:53:22 2017 +0200 ; writing bcf ; https://github.com/lindenb/jvarkit/commit/784fdac37cd7e6eca04e35d0a3ddad8637826b4a
-Mon May 22 17:20:59 2017 +0200 ; moving to jcommaner ; https://github.com/lindenb/jvarkit/commit/60cbfa764f7f5bacfdb78e48caf8f9b66e53a6a0
-Mon May 1 15:40:19 2017 +0200 ; cont ; https://github.com/lindenb/jvarkit/commit/11aa7fcf4cc15aecc2cc2019fc2df8752731a278
-Fri Apr 14 15:27:32 2017 +0200 ; annotation proc ; https://github.com/lindenb/jvarkit/commit/72b9383a8472e5a91120bab84d15b8acad4db8d4
-Fri Mar 31 17:08:11 2017 +0200 ; moving to jcommander ; https://github.com/lindenb/jvarkit/commit/f78937d19c4b038e69a32fbcfa2aeab8fd8417c6
-Mon Mar 27 17:55:22 2017 +0200 ; cont ; https://github.com/lindenb/jvarkit/commit/3b7033dcb365493f62d7b78ca4410b6bf3cd716d
-Fri Apr 29 17:26:25 2016 +0200 ; cont ; https://github.com/lindenb/jvarkit/commit/231856146f1035e21b4adfbc4e87a01b60d0d39e
-Wed Feb 10 10:00:55 2016 +0100 ; cont ; https://github.com/lindenb/jvarkit/commit/0a518250fb9b2e9894b9329d01afe1dfe0a2f6de
-Thu Nov 26 12:58:31 2015 +0100 ; cont ; https://github.com/lindenb/jvarkit/commit/cfdff2e66fbeaa4627b50361a09196be2a2e1477
-Tue Nov 3 22:42:18 2015 +0100 ; cont ; https://github.com/lindenb/jvarkit/commit/4e4a9319be20626f0ea01dc2316c6420ba8e7dac
-Wed Sep 23 15:36:21 2015 +0200 ; cont ; https://github.com/lindenb/jvarkit/commit/03cc568ed51cf43d7af6f0d913a0f8c52ddfe5d7
-Thu Mar 12 16:57:07 2015 +0100 ; tool to compare VCF with one sample called with multiple methods #tweet ; https://github.com/lindenb/jvarkit/commit/351c259dc9f1d8bebab19b3dc57fc6a610257542
-Fri Feb 20 17:50:08 2015 +0100 ; continue integration in knime ; https://github.com/lindenb/jvarkit/commit/5693e07342a30f21c807a4e3a655e3446019458f
-Fri Feb 20 13:25:12 2015 +0100 ; moving vcfhead, vcftail to knime. samsequenceprogress compact watch form ; https://github.com/lindenb/jvarkit/commit/34c137e5f12c05b7eb9d7ce1b546cde6c8890cc3
-Mon May 12 10:28:28 2014 +0200 ; first sed on files ; https://github.com/lindenb/jvarkit/commit/79ae202e237f53b7edb94f4326fee79b2f71b8e8
-Sun Feb 2 18:55:03 2014 +0100 ; cont ; https://github.com/lindenb/jvarkit/commit/abd24b56ec986dada1e5162be5bbd0dac0c2d57c
-Tue Dec 10 22:12:54 2013 +0100 ; vcf head tail ; https://github.com/lindenb/jvarkit/commit/25adbeaf3de1c64fd793c5ddf5236322adb430d1
-```
-
-</details>
-
 ## Contribute
 
 - Issue Tracker: [http://github.com/lindenb/jvarkit/issues](http://github.com/lindenb/jvarkit/issues)

diff --git a/src/main/java/com/github/lindenb/jvarkit/tools/vcfcmp/VCFCompareGT.java b/src/main/java/com/github/lindenb/jvarkit/tools/vcfcmp/VCFCompareGT.java
@@ -413,10 +413,10 @@ else if(alleles.size()==2)
 						);
 				//build genotypes
 				final List<Genotype> genotypes=new ArrayList<Genotype>();
-				for(Variant var:row)
+				for(final Variant var:row)
 					{
 					//alleles for this genotype
-					List<Allele> galleles=new ArrayList<Allele>();
+					final List<Allele> galleles=new ArrayList<Allele>();
 					galleles.add(Allele.create(var.a1, var.a1.equalsIgnoreCase(var.ref)));
 					galleles.add(Allele.create(var.a2, var.a2.equalsIgnoreCase(var.ref)));