Release v2.1.1

CHANGELOG

@@ -1,4 +1,33 @@
 
+MiXCR 2.1.1 ( 3 Mar 2017)
+========================
+
+-- Additional check for the same V hits in merging sequences in `assemblePartial`
+-- Fix: list of C hits limited by `relativeMinScore` in `assemblePartial`
+-- Not aligned mates from fully aligned opposite PE reads are now taken into `assemblePartial` 
+   procedure (case when V and J parts of the target read are shorter than 12 nt)
+-- Additional consistency cehcks in `assemblePartial`, overlaps of non-CDR3-covering mates of PE 
+   reads are also taken into account
+-- More sophisticated algorithm for alignment-guided merging of paired-end reads in `align`
+-- Several anchor point positions in export points changed their meaning.
+-- Fixed absent space in `AA. Seq. ...` column name and excessive space in the end of several 
+   column names (affects `exportClones` and `exportAlignments` with `-v` option; fixes compatibility 
+   with VDJTools v1.1.3 and below).
+-- Fixes NPE in `exportClones` in some cases with mmu reference
+-- `-p` option in `assemblePartial` enabled by default; deprecated; will be removed in 2.2
+-- Added `-d` option in `assemblePartial` to drop non-assembled partial reads to reduce output file 
+   size
+-- Added `sortAlignments` action. Sort `*.vdjca` files by read id, allows diffing alignments after 
+   `assembleParial` and other actions that shuffle records inside file.
+-- Fixed incorrect behaviour of `exportClones` and `exportAlignments` in cases like `mixcr 
+   exportAlignments -p full -descrR1 ...`
+-- minor: Multiple reads in `exportAlignmentsPretty` and `filterAlignments` should be now specified 
+   as `-i 123 -i 456` or `-i 123,456` etc.
+-- minor: `--reads-ids` in `exportAlignmentsPretty` and `--readsIds` in `filterAlignments` both 
+   renamed to `--read-ids`
+-- minor: infrastructure for post-build tests in Travis CI
+
+
 MiXCR 2.1 ( 6 Feb 2017)
 ========================
 

CHANGELOG_CURRENT

@@ -1,15 +0,0 @@
-Additional check for the same V hits in merging sequences in `assemblePartial`
-Fix: list of C hits limited by `relativeMinScore` in `assemblePartial`
-Not aligned mates from fully aligned opposite PE reads are now taken into `assemblePartial` procedure (case when V and J parts of the target read are shorter than 12 nt)
-Additional consistency cehcks in `assemblePartial`, overlaps of non-CDR3-covering mates of PE reads are also taken into account
-More sophisticated algorithm for alignment-guided merging of paired-end reads in `align`
-Several anchor point positions in export points changed their meaning.
-Fixed absent space in `AA. Seq. ...` column name and excessive space in the end of several column names (affects `exportClones` and `exportAlignments` with `-v` option; fixes compatibility with VDJTools v1.1.3 and below).
-Fixes NPE in `exportClones` in some cases with mmu reference
-`-p` option in `assemblePartial` enabled by default; deprecated; will be removed in 2.2
-Added `-d` option in `assemblePartial` to drop non-assembled partial reads to reduce output file size
-Added `sortAlignments` action. Sort `*.vdjca` files by read id, allows diffing alignments after `assembleParial` and other actions that shuffle records inside file.
-Fixed incorrect behaviour of `exportClones` and `exportAlignments` in cases like `mixcr exportAlignments -p full -descrR1 ...`
-minor: Multiple reads in `exportAlignmentsPretty` and `filterAlignments` should be now specified as `-i 123 -i 456` or `-i 123,456` etc.
-minor: `--reads-ids` in `exportAlignmentsPretty` and `--readsIds` in `filterAlignments` both renamed to `--read-ids`
-minor: infrastructure for post-build tests in Travis CI

pom.xml

@@ -27,13 +27,12 @@
   ~ PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY
   ~ PATENT, TRADEMARK OR OTHER RIGHTS.
   -->
-<project xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://maven.apache.org/POM/4.0.0"
-         xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+<project xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://maven.apache.org/POM/4.0.0" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
     <modelVersion>4.0.0</modelVersion>
 
     <groupId>com.milaboratory</groupId>
     <artifactId>mixcr</artifactId>
-    <version>2.1.1-SNAPSHOT</version>
+    <version>2.1.1</version>
     <packaging>jar</packaging>
     <name>MiXCR</name>
 
@@ -211,15 +210,12 @@
                                 </filter>
                             </filters>
                             <transformers>
-                                <transformer
-                                        implementation="org.apache.maven.plugins.shade.resource.ApacheLicenseResourceTransformer">
+                                <transformer implementation="org.apache.maven.plugins.shade.resource.ApacheLicenseResourceTransformer">
                                 </transformer>
-                                <transformer
-                                        implementation="org.apache.maven.plugins.shade.resource.ApacheNoticeResourceTransformer">
+                                <transformer implementation="org.apache.maven.plugins.shade.resource.ApacheNoticeResourceTransformer">
                                     <addHeader>false</addHeader>
                                 </transformer>
-                                <transformer
-                                        implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
+                                <transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
                                     <mainClass>com.milaboratory.mixcr.cli.Main</mainClass>
                                 </transformer>
                             </transformers>