From 6b61b73a2f010cb4e646223c23ea781e89767ee0 Mon Sep 17 00:00:00 2001 From: Dmitry Bolotin Date: Fri, 3 Mar 2017 01:03:59 +0300 Subject: [PATCH] Release v2.1.1 --- CHANGELOG | 29 +++++++++++++++++++++++++++++ CHANGELOG_CURRENT | 15 --------------- pom.xml | 14 +++++--------- 3 files changed, 34 insertions(+), 24 deletions(-) diff --git a/CHANGELOG b/CHANGELOG index 326002892..c8d3a7319 100644 --- a/CHANGELOG +++ b/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) ======================== diff --git a/CHANGELOG_CURRENT b/CHANGELOG_CURRENT index 33458bc75..e69de29bb 100644 --- a/CHANGELOG_CURRENT +++ b/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 \ No newline at end of file diff --git a/pom.xml b/pom.xml index 450e08d9b..bf0aec46b 100644 --- a/pom.xml +++ b/pom.xml @@ -27,13 +27,12 @@ ~ PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY ~ PATENT, TRADEMARK OR OTHER RIGHTS. --> - + 4.0.0 com.milaboratory mixcr - 2.1.1-SNAPSHOT + 2.1.1 jar MiXCR @@ -211,15 +210,12 @@ - + - + false - + com.milaboratory.mixcr.cli.Main