Merge branch 'master' of https://github.com/airr-community/airr-stand…

…ards into issue-781-epitope-reactivity

.github/workflows/node.js.yml

@@ -0,0 +1,35 @@
+# This workflow will do a clean installation of node dependencies, cache/restore them, build the source code and run tests across different versions of node
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-nodejs
+
+name: Node.js CI
+
+on:
+  push:
+    branches: [ "master" ]
+  pull_request:
+    branches: [ "master" ]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    defaults:
+      run:
+        working-directory: lang/js
+
+    strategy:
+      matrix:
+        node-version: [18.x, 20.x, 22.x]
+        # See supported Node.js release schedule at https://nodejs.org/en/about/releases/
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Use Node.js ${{ matrix.node-version }}
+      uses: actions/setup-node@v4
+      with:
+        node-version: ${{ matrix.node-version }}
+#        cache: 'npm'
+    - run: npm ci
+    - run: npm run build --if-present
+    - run: npm test

.github/workflows/py-unittest.yaml

@@ -26,6 +26,11 @@ jobs:
         python-version: [ '3.8' ]
     steps:
       - uses: actions/checkout@v2
+
+      - name: Check test data matches the global test data files
+        run: diff -rc tests/data ../../tests/data
+        shell: bash
+
       - name: Set up Python
         uses: actions/setup-python@v2
         with:

.github/workflows/r-check.yaml

@@ -26,6 +26,10 @@ jobs:
     steps:
       - uses: actions/checkout@v2
 
+      - name: Check test data matches the global test data files
+        run: diff -rc tests/data-tests ../../tests/data
+        shell: bash
+
       - name: Install dependencies
         run: |
           install.packages(c("remotes", "testthat", "roxygen2", "devtools", "rcmdcheck"))

CONTRIBUTING.rst

@@ -212,9 +212,25 @@ software. For all cases, you will want a local copy of the github repository.
 
   git clone https://github.com/airr-community/airr-standards.git
 
+A Makefile is provided to simplify tasks such as copying spec files to the lang
+directories, copying test data, running tests and checks, and building documentation.
+The default make target will display a help info for all targets.
+
+.. code-block:: bash
+
+  make
+
+If your local environment does not have the appropriate software, you can build
+and use the docker container. You will need python3, R and npm to run tests for
+all languages.
+
 If you will be working in a docker container, you can pull down the airr-standards
-image, which has all of the prerequisites installed, or you can use your own image.
-The airr-standards image provides a python3 environment.
+image from docker hub, which has all of the prerequisites installed,
+or you can build your own image. Note: automated builds are not performed on docker
+hub so the ``latest`` tag is often out of date. It is generally safe to build
+your own container from your local source.
+The airr-standards image installs the reference library for all languages and
+builds the documentation.
 
 .. code-block:: bash
 

Makefile

@@ -0,0 +1,61 @@
+# helper commands for keeping the language directories in sync
+
+# note: "help" MUST be the first target in the file, so
+# when the user types "make" they get help info by default
+help:
+	@echo ""
+	@echo "Helper commands for AIRR Standards repository"
+	@echo "---------------------------------------------"
+	@echo ""
+	@echo "make spec-copy       -- Copy spec files to language directories"
+	@echo "make data-copy       -- Copy test data files to language directories"
+	@echo ""
+	@echo "make docker-latest   -- Build docker image with latest tag"
+	@echo ""
+	@echo "make checks          -- Run consistency checks on spec files"
+	@echo "make tests           -- Run all language test suites"
+	@echo "make python-tests    -- Run Python test suite"
+	@echo "make r-tests         -- Run R test suite"
+	@echo "make js-tests        -- Run Javascript test suite"
+	@echo ""
+	@echo "make build-docs      -- Build documentation"
+	@echo ""
+
+build-docs:
+	sphinx-build -a -E -b html docs docs/_build/html
+
+docker-latest:
+	@echo "Building latest docker image"
+	docker build -f docker/Dockerfile -t airrc/airr-standards:latest .
+
+spec-copy:
+	@echo "Copying specs to language directories"
+	cp specs/airr-schema.yaml lang/python/airr/specs
+	cp specs/airr-schema-openapi3.yaml lang/python/airr/specs
+	cp specs/airr-schema.yaml lang/R/inst/extdata
+	cp specs/airr-schema-openapi3.yaml lang/R/inst/extdata
+	cp specs/airr-schema-openapi3.yaml lang/js/
+
+data-copy:
+	@echo "Copying test data to language directories"
+	cp tests/data/* lang/python/tests/data
+	cp tests/data/* lang/R/tests/data-tests
+	cp tests/data/* lang/js/tests/data
+
+checks:
+	@echo "Running consistency checks on spec files"
+	python3 tests/check-consistency-formats.py
+
+tests: python-tests r-tests js-tests
+
+python-tests:
+	@echo "Running Python test suite"
+	cd lang/python; python3 -m unittest discover
+
+r-tests:
+	@echo "Running R test suite"
+	cd lang/R; R -e "library(devtools); test()"
+
+js-tests:
+	@echo "Running Javascript test suite"
+	cd lang/js; npm test

docker/Dockerfile

@@ -1,4 +1,4 @@
-FROM ubuntu:20.04
+FROM ubuntu:24.04
 
 LABEL maintainer="AIRR Community"
 
@@ -8,6 +8,7 @@ RUN export DEBIAN_FRONTEND=noninteractive && apt-get update && apt-get install -
     python3-pip \
     python3-sphinx \
     python3-scipy \
+    python3-venv \
     libyaml-dev \
     r-base \
     r-base-dev \
@@ -18,7 +19,14 @@ RUN export DEBIAN_FRONTEND=noninteractive && apt-get update && apt-get install -
     libfontconfig1-dev \
     libssl-dev \
     libharfbuzz-dev libfribidi-dev \
-    libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev
+    libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev \
+    nano
+
+# Create a virtual environment
+RUN python3 -m venv /airr-venv
+
+# Activate the virtual environment
+ENV PATH="/airr-venv/bin:$PATH"
 
 RUN pip3 install \
     pandas \
@@ -33,13 +41,27 @@ RUN pip3 install \
 # Install R devtools
 RUN R -e 'install.packages(c("devtools","knitr","rmarkdown","testthat","readr"),dependencies=T)'
 
+# node
+ENV NODE_VER=v14.21.3
+RUN wget https://nodejs.org/dist/$NODE_VER/node-$NODE_VER-linux-x64.tar.xz
+RUN tar xf node-$NODE_VER-linux-x64.tar.xz
+RUN cp -rf /node-$NODE_VER-linux-x64/bin/* /usr/bin
+RUN cp -rf /node-$NODE_VER-linux-x64/lib/* /usr/lib
+RUN cp -rf /node-$NODE_VER-linux-x64/include/* /usr/include
+RUN cp -rf /node-$NODE_VER-linux-x64/share/* /usr/share
+
 # Copy source
 RUN mkdir /airr-standards
 COPY . /airr-standards
 
 # Install python package
 RUN cd /airr-standards/lang/python && pip3 install .
 
+# nodejs package
+RUN cd /airr-standards/lang/js && npm install
+RUN cd /airr-standards/lang/js && npm run eslint
+RUN cd /airr-standards/lang/js && npm run test
+
 # Generate the documentation
 RUN cd /airr-standards && pip3 install -r docs/requirements.txt
 RUN cd /airr-standards && sphinx-build -a -E -b html docs docs/_build/html

docs/conf.py

@@ -414,7 +414,7 @@ def parse_schema(spec, schema):
 fields = ['Name', 'Type', 'Attributes', 'Definition']
 tables = ['Repertoire', 'Study', 'Subject', 'Diagnosis', 'Sample', 'CellProcessing', 'NucleicAcidProcessing',
           'PCRTarget', 'SequencingRun', 'SequencingData', 'DataProcessing',
-          'Rearrangement', 'Alignment', 'Clone', 'Tree', 'Node', 'Cell', 'CellExpression',
+          'Rearrangement', 'Alignment', 'Clone', 'Tree', 'Node', 'Cell', 'Expression',
           'RearrangedSequence', 'UnrearrangedSequence', 'SequenceDelineationV', 'AlleleDescription', 'GermlineSet',
           'GenotypeSet', 'Genotype', 'MHCGenotypeSet', 'MHCGenotype', 'Receptor']
 for spec in tables:

docs/packages/airr-js/news.rst

@@ -0,0 +1,6 @@
+.. _JavaScriptNews:
+
+JavaScript Library Release Notes
+=================================
+
+.. include:: ../../../lang/js/NEWS.rst

docs/packages/airr-js/overview.rst

@@ -0,0 +1,17 @@
+.. _JavaScriptOverview:
+
+AIRR JavaScript Reference Library
+===============================================================================
+
+The ``airr-js`` reference library provides basic functions and classes for
+interacting with AIRR Community Data Representation Standards, including tools
+for read, write and validation. The library can be used in the browser or nodejs.
+
+.. toctree::
+    :maxdepth: 1
+    :caption: Table of Contents
+
+    Release Notes <news>
+
+.. include:: ../../../lang/js/README.rst
+

docs/software.rst

@@ -10,6 +10,7 @@ AIRR Standards Reference Implementations
 
     Python Library <packages/airr-python/overview>
     R Library <packages/airr-R/overview>
+    JavaScript Library <packages/airr-js/overview>
     ADC API Reference Implementation <api/reference>
 
 Resources and Tools Supporting AIRR Standards

lang/R/inst/extdata/airr-schema.yaml

@@ -1677,7 +1677,6 @@ DeletedGene:
                 Chromosomal phasing indicator. Alleles with the same value are inferred to be located on the 
                 same chromosome.
 
-
 # List of MHCGenotypes describing a subject's genotype
 MHCGenotypeSet:
     type: object

lang/R/tests/data-tests/extra_rearrangement.tsv

@@ -0,0 +1,2 @@
+sequence_id	sequence	rev_comp	productive	v_call	d_call	j_call	sequence_alignment	germline_alignment	junction	junction	junction_aa	v_cigar	d_cigar	j_cigar
+1	2	F	F	5	6	7	8	9	10	11	12	13	14	15	not_in_header	not_in

lang/R/tests/data-tests/good_rearrangement.tsv

@@ -1,10 +1,10 @@
 rearrangement_id	rearrangement_set_id	sequence_id	sequence	rev_comp	productive	sequence_alignment	germline_alignment	v_call	d_call	j_call	c_call	junction	junction_length	junction_aa	v_score	d_score	j_score	c_score	v_cigar	d_cigar	j_cigar	c_cigar	v_identity	v_evalue	d_identity	d_evalue	j_identity	j_evalue	v_sequence_start	v_sequence_end	v_germline_start	v_germline_end	d_sequence_start	d_sequence_end	d_germline_start	d_germline_end	j_sequence_start	j_sequence_end	j_germline_start	j_germline_end	np1_length	np2_length	duplicate_count
-IVKNQEJ01BVGQ6	1	IVKNQEJ01BVGQ6	GGCCCAGGACTGGTGAAGCCTTCACAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTGGTGGTTACTACTGGAGCTGGATCCGCCAGCACCCAGGGAAGGGCCTGGAGTGGATTGGGTACATCTATTACAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTTACCATATCAGTAGACACGTCTAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACTGCCGCGGACACGGCCGTGTATTACTGTGCGAGCGGGGTGGCTGGAACTTTTGACTACTGGGGCCAGGGAACCCTGGTCACTGTCTCCTCA	T	T			IGHV4-31*03	IGHD1-7*01,IGHD6-19*01	IGHJ4*02		TGTGCGAGCGGGGTGGCTGGAACTTTTGACTACTGG	36	CASGVAGTFDYW	430	16.4	75.8		22N1S275=	11N280S8=	6N292S32=1X9=		1	1E-122	1	2.7	0.9762	6E-18	1	275	1	317	280	287	11	18	292	333	6	47	4	4	1247
-IVKNQEJ01AQVWS	1	IVKNQEJ01AQVWS	GGCCCAGGACTGGTGAAGCCTTCACAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTGGTGGTTACTACTGGAGCTGGATCCGCCAGCACCCAGGGAAGGGCCTGGAGTGGATTGGGTACATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCTAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACTGCCGCGGACACGGCCGTGTATTACTGTGCGAGCGGGGTGGCTGGAACTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCA	T	T			IGHV4-31*03	IGHD1-7*01,IGHD6-19*01	IGHJ4*02		TGTGCGAGCGGGGTGGCTGGAACTTTTGACTACTGG	36	CASGVAGTFDYW	420	16.4	83.8		22N1S156=1X10=1X17=1X89=	11N280S8=	6N292S42=		0.9891	8E-120	1	2.7	1	2E-20	1	275	1	317	280	287	11	18	292	333	6	47	4	4	4
-IVKNQEJ01AOYFZ	1	IVKNQEJ01AOYFZ	GGCCCAGGACTGGTGAAGCCTTCACAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTGGTGGTTACTACTGGAGCTGGATCCGCCAGCACCCAGGGAAGGGCCTGGAGTGGATTGGGTACATCTATTACAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTTACCATATCAGTAGACACGTCTAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACTGCCGCGGACACGGCCGTGTATTACTGTGCGAGCGGGGTGGCTGGTAACTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCA	T	F			IGHV4-31*03	IGHD6-19*01	IGHJ4*02		TGTGCGAGCGGGGTGGCTGGTAACTTTTGACTACTGG	37	CASGVAGNF*LLX	430	20.4	83.8		22N1S275=	11N280S10=	6N293S42=		1	1E-122	1	0.17	1	2E-20	1	275	1	317	280	289	11	20	293	334	6	47	4	3	92
-IVKNQEJ01EI5S4	1	IVKNQEJ01EI5S4	GGCCCAGGACTGGTGAAGCCTTCACAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTGGTGGTTACTACTGGAGCTGGATCCGCCAGCACCCAGGGAAGGGCCTGGAGTGGATTGGGTACATCTATTACAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTTACCATATCAGTAGACACGTCTAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACTGCCGCGGACACGGCCGTGTATTACTGTGCGAGCGGGGTGGCTGGAACTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCA	T	T			IGHV4-31*03	IGHD1-7*01,IGHD6-19*01	IGHJ4*02		TGTGCGAGCGGGGTGGCTGGAACTTTTGACTACTGG	36	CASGVAGTFDYW	430	16.4	83.8		22N1S275=	11N280S8=	6N292S42=		1	1E-122	1	2.7	1	2E-20	1	275	1	317	280	287	11	18	292	333	6	47	4	4	2913
-IVKNQEJ01DGRRI	1	IVKNQEJ01DGRRI	GGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCGCTGTCTATGGTGGGTCCTTCAGTGGTTACTACTGGAGCTGGATCCGCCAGCCCCCAGGGAAGGGTCTGGAGTGGATTGGGTACATCTATTACAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTTACCATATCAGTAGACACGTCTAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACTGCCGCGGACACGGCCGTGTATTACTGTGCGAGCGGGGTGGCTGGAACTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCA	T	T			IGHV4-34*09	IGHD1-7*01,IGHD6-19*01	IGHJ4*02		TGTGCGAGCGGGGTGGCTGGAACTTTTGACTACTGG	36	CASGVAGTFDYW	389	16.4	83.8		22N1S23=2X85=1X15=1X1=1X3=1X2=1X1=1X5=1X6=1X118=	11N274S8=	6N286S42=		0.9628	2E-110	1	2.6	1	2E-20	1	269	1	317	274	281	11	18	286	327	6	47	4	4	1
-IVKNQEJ01APN5N	1	IVKNQEJ01APN5N	GGCCCAGGACTGGTGAAGCCTTCACAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTGGTGGTTACTACTGGAGCTGGATCCGCCAGCACCCAGGGAAGGGCCTGGAGTGGATTGGGTACATCTATTACAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTTACCATATCAGTAGACACGTCTAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACTGCCGCGGACACGGCCGTGTATTACTGTGCGAGCGGGGTGGCTGGAACTTTTGACTACTAGGGCCAGGGAACCCTGGTCACTGTCTCCTCA	T	F			IGHV4-31*03	IGHD1-7*01,IGHD6-19*01	IGHJ4*02		TGTGCGAGCGGGGTGGCTGGAACTTTTGACTACTAG	36	CASGVAGTFDY*	430	16.4	67.9		22N1S275=	11N280S8=	6N292S10=1X21=1X9=		1	1E-122	1	2.7	0.9524	1E-15	1	275	1	317	280	287	11	18	292	333	6	47	4	4	1
-IVKNQEJ01B0TT2	1	IVKNQEJ01B0TT2	GGCCCAGGACTGGTGAAGCCTTCACAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTGGTGGTTACTACTGGAGCTGGATCCGCCAGCACCCAGGGAAGGGCCTGGAGTGGATTGGGTACATCTATTACAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTTACCATATCAGTAGACACGTCTAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACTGCCGCGGACACGGCCGTGTATTACTGTGCGAGCGGGGTGGCTGGTAACTTTTGACTACTGGGGCCAGGGAACCCTGGTCACTGTCTCCTCA	T	F			IGHV4-31*03	IGHD6-19*01	IGHJ4*02		TGTGCGAGCGGGGTGGCTGGTAACTTTTGACTACTGG	37	CASGVAGNF*LLX	430	20.4	75.8		22N1S275=	11N280S10=	6N293S32=1X9=		1	1E-122	1	0.17	0.9762	6E-18	1	275	1	317	280	289	11	20	293	334	6	47	4	3	30
-IVKNQEJ01AIS74	1	IVKNQEJ01AIS74	GGCGCAGGACTGTTGAAGCCTTCACAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTGGTGGTTACTACTGGAGCTGGATCCGCCAGCACCCAGGGAAGGGCCTGGAGTGGATTGGGTACATCTATTACAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTTACCATATCAGTAGACACGTCTAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACTGCCGCGGACACGGCCGTGTATTACTGTGCGAGGCGGGGTGGCTGGTAACTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCA	T	F			IGHV4-31*03	IGHD6-19*01	IGHJ4*02		TGTGCGAGGCGGGGTGGCTGGTAACTTTTGACTACTGG	38	CARRGGW*LLTTG	424	20.4	83.8		22N1S3=1X8=1X262=	11N281S10=	6N294S42=		0.9927	9E-121	1	0.17	1	2E-20	1	275	1	317	281	290	11	20	294	335	6	47	5	3	4
-IVKNQEJ01AJ44V	1	IVKNQEJ01AJ44V	GGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCGCTGTCTATGGTGGGTCCTTCAGTGGTTACTACTGGAGCTGGATCCGCCAGCACCCAGGGAAGGGCCTGGAGTGGATTGGGTACATCTATTACAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTTACCATATCAGTAGACACGTCTAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACTGCCGCGGACACGGCCGTGTATTACTGTGCGAGCGGGGTGGCTGGAACTTTTGACTACTGGGGCCAGGGAACCCTGGTCACTGTCTCCTCA	T	T			IGHV4-59*06	IGHD1-7*01,IGHD6-19*01	IGHJ4*02		TGTGCGAGCGGGGTGGCTGGAACTTTTGACTACTGG	36	CASGVAGTFDYW	386	16.4	75.8		22N1S45=1X5=2X6=1X3=1X5=1X22=1X4=1X1=1X1=1X165=	11N274S8=	6N286S32=1X9=		0.9625	2E-109	1	2.6	0.9762	5E-18	1	267	1	315	274	281	11	18	286	327	6	47	6	4	12
+IVKNQEJ01BVGQ6	1	IVKNQEJ01BVGQ6	GGCCCAGGACTGGTGAAGCCTTCACAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTGGTGGTTACTACTGGAGCTGGATCCGCCAGCACCCAGGGAAGGGCCTGGAGTGGATTGGGTACATCTATTACAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTTACCATATCAGTAGACACGTCTAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACTGCCGCGGACACGGCCGTGTATTACTGTGCGAGCGGGGTGGCTGGAACTTTTGACTACTGGGGCCAGGGAACCCTGGTCACTGTCTCCTCA	T	T			IGHV4-31*03	IGHD1-7*01,IGHD6-19*01	IGHJ4*02		TGTGCGAGCGGGGTGGCTGGAACTTTTGACTACTGG	36	CASGVAGTFDYW	430	16.4	75.8		22N1S275=	11N280S8=	6N292S32=1X9=		1	1E-122	1	2.7	0.9762	6E-18	0	275	0	317	279	287	10	18	291	333	5	47	4	4	1247
+IVKNQEJ01AQVWS	1	IVKNQEJ01AQVWS	GGCCCAGGACTGGTGAAGCCTTCACAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTGGTGGTTACTACTGGAGCTGGATCCGCCAGCACCCAGGGAAGGGCCTGGAGTGGATTGGGTACATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCTAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACTGCCGCGGACACGGCCGTGTATTACTGTGCGAGCGGGGTGGCTGGAACTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCA	T	T			IGHV4-31*03	IGHD1-7*01,IGHD6-19*01	IGHJ4*02		TGTGCGAGCGGGGTGGCTGGAACTTTTGACTACTGG	36	CASGVAGTFDYW	420	16.4	83.8		22N1S156=1X10=1X17=1X89=	11N280S8=	6N292S42=		0.9891	8E-120	1	2.7	1	2E-20	0	275	0	317	279	287	10	18	291	333	5	47	4	4	4
+IVKNQEJ01AOYFZ	1	IVKNQEJ01AOYFZ	GGCCCAGGACTGGTGAAGCCTTCACAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTGGTGGTTACTACTGGAGCTGGATCCGCCAGCACCCAGGGAAGGGCCTGGAGTGGATTGGGTACATCTATTACAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTTACCATATCAGTAGACACGTCTAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACTGCCGCGGACACGGCCGTGTATTACTGTGCGAGCGGGGTGGCTGGTAACTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCA	T	F			IGHV4-31*03	IGHD6-19*01	IGHJ4*02		TGTGCGAGCGGGGTGGCTGGTAACTTTTGACTACTGG	37	CASGVAGNF*LLX	430	20.4	83.8		22N1S275=	11N280S10=	6N293S42=		1	1E-122	1	0.17	1	2E-20	0	275	0	317	279	289	10	20	292	334	5	47	4	3	92
+IVKNQEJ01EI5S4	1	IVKNQEJ01EI5S4	GGCCCAGGACTGGTGAAGCCTTCACAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTGGTGGTTACTACTGGAGCTGGATCCGCCAGCACCCAGGGAAGGGCCTGGAGTGGATTGGGTACATCTATTACAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTTACCATATCAGTAGACACGTCTAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACTGCCGCGGACACGGCCGTGTATTACTGTGCGAGCGGGGTGGCTGGAACTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCA	T	T			IGHV4-31*03	IGHD1-7*01,IGHD6-19*01	IGHJ4*02		TGTGCGAGCGGGGTGGCTGGAACTTTTGACTACTGG	36	CASGVAGTFDYW	430	16.4	83.8		22N1S275=	11N280S8=	6N292S42=		1	1E-122	1	2.7	1	2E-20	0	275	0	317	279	287	10	18	291	333	5	47	4	4	2913
+IVKNQEJ01DGRRI	1	IVKNQEJ01DGRRI	GGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCGCTGTCTATGGTGGGTCCTTCAGTGGTTACTACTGGAGCTGGATCCGCCAGCCCCCAGGGAAGGGTCTGGAGTGGATTGGGTACATCTATTACAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTTACCATATCAGTAGACACGTCTAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACTGCCGCGGACACGGCCGTGTATTACTGTGCGAGCGGGGTGGCTGGAACTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCA	T	T			IGHV4-34*09	IGHD1-7*01,IGHD6-19*01	IGHJ4*02		TGTGCGAGCGGGGTGGCTGGAACTTTTGACTACTGG	36	CASGVAGTFDYW	389	16.4	83.8		22N1S23=2X85=1X15=1X1=1X3=1X2=1X1=1X5=1X6=1X118=	11N274S8=	6N286S42=		0.9628	2E-110	1	2.6	1	2E-20	0	269	0	317	273	281	10	18	285	327	5	47	4	4	1
+IVKNQEJ01APN5N	1	IVKNQEJ01APN5N	GGCCCAGGACTGGTGAAGCCTTCACAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTGGTGGTTACTACTGGAGCTGGATCCGCCAGCACCCAGGGAAGGGCCTGGAGTGGATTGGGTACATCTATTACAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTTACCATATCAGTAGACACGTCTAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACTGCCGCGGACACGGCCGTGTATTACTGTGCGAGCGGGGTGGCTGGAACTTTTGACTACTAGGGCCAGGGAACCCTGGTCACTGTCTCCTCA	T	F			IGHV4-31*03	IGHD1-7*01,IGHD6-19*01	IGHJ4*02		TGTGCGAGCGGGGTGGCTGGAACTTTTGACTACTAG	36	CASGVAGTFDY*	430	16.4	67.9		22N1S275=	11N280S8=	6N292S10=1X21=1X9=		1	1E-122	1	2.7	0.9524	1E-15	0	275	0	317	279	287	10	18	291	333	5	47	4	4	1
+IVKNQEJ01B0TT2	1	IVKNQEJ01B0TT2	GGCCCAGGACTGGTGAAGCCTTCACAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTGGTGGTTACTACTGGAGCTGGATCCGCCAGCACCCAGGGAAGGGCCTGGAGTGGATTGGGTACATCTATTACAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTTACCATATCAGTAGACACGTCTAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACTGCCGCGGACACGGCCGTGTATTACTGTGCGAGCGGGGTGGCTGGTAACTTTTGACTACTGGGGCCAGGGAACCCTGGTCACTGTCTCCTCA	T	F			IGHV4-31*03	IGHD6-19*01	IGHJ4*02		TGTGCGAGCGGGGTGGCTGGTAACTTTTGACTACTGG	37	CASGVAGNF*LLX	430	20.4	75.8		22N1S275=	11N280S10=	6N293S32=1X9=		1	1E-122	1	0.17	0.9762	6E-18	0	275	0	317	279	289	10	20	292	334	5	47	4	3	30
+IVKNQEJ01AIS74	1	IVKNQEJ01AIS74	GGCGCAGGACTGTTGAAGCCTTCACAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTGGTGGTTACTACTGGAGCTGGATCCGCCAGCACCCAGGGAAGGGCCTGGAGTGGATTGGGTACATCTATTACAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTTACCATATCAGTAGACACGTCTAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACTGCCGCGGACACGGCCGTGTATTACTGTGCGAGGCGGGGTGGCTGGTAACTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCA	T	F			IGHV4-31*03	IGHD6-19*01	IGHJ4*02		TGTGCGAGGCGGGGTGGCTGGTAACTTTTGACTACTGG	38	CARRGGW*LLTTG	424	20.4	83.8		22N1S3=1X8=1X262=	11N281S10=	6N294S42=		0.9927	9E-121	1	0.17	1	2E-20	0	275	0	317	280	290	10	20	293	335	5	47	5	3	4
+IVKNQEJ01AJ44V	1	IVKNQEJ01AJ44V	GGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCGCTGTCTATGGTGGGTCCTTCAGTGGTTACTACTGGAGCTGGATCCGCCAGCACCCAGGGAAGGGCCTGGAGTGGATTGGGTACATCTATTACAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTTACCATATCAGTAGACACGTCTAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACTGCCGCGGACACGGCCGTGTATTACTGTGCGAGCGGGGTGGCTGGAACTTTTGACTACTGGGGCCAGGGAACCCTGGTCACTGTCTCCTCA	T	T			IGHV4-59*06	IGHD1-7*01,IGHD6-19*01	IGHJ4*02		TGTGCGAGCGGGGTGGCTGGAACTTTTGACTACTGG	36	CASGVAGTFDYW	386	16.4	75.8		22N1S45=1X5=2X6=1X3=1X5=1X22=1X4=1X1=1X1=1X165=	11N274S8=	6N286S32=1X9=		0.9625	2E-109	1	2.6	0.9762	5E-18	0	267	0	315	273	281	10	18	285	327	5	47	6	4	12