Merge pull request #1234 from milaboratory/update-library

update library
milaboratory · Jul 5, 2023 · 172e075 · 172e075
2 parents 5d42157 + 17776f8
commit 172e075
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Showing 4 changed files with 19 additions and 13 deletions.
diff --git a/build.gradle.kts b/build.gradle.kts
@@ -133,10 +133,10 @@ val toObfuscate: Configuration by configurations.creating {
 val obfuscationLibs: Configuration by configurations.creating
 
 
-val mixcrAlgoVersion = "4.3.0-228-tiny-things-2"
+val mixcrAlgoVersion = "4.3.0-230-fix-version"
 val milibVersion = "3.0.0-1-master"
 val mitoolVersion = ""
-val repseqioVersion = ""
+val repseqioVersion = "2.0.0-11-library-with-alleles"
 
 val picocliVersion = "4.6.3"
 val jacksonBomVersion = "2.15.2"

diff --git a/itests/case-buld_trees_on_data_with_a_hole.sh b/itests/case-buld_trees_on_data_with_a_hole.sh
@@ -61,11 +61,11 @@ mixcr exportPlots shmTrees trees/result.shmt trees/plots.pdf
 assert "head -n 1 trees/trees_with_nodes.tsv | grep -c nSeqCDR1" "1"
 assert "head -n 1 trees/trees_with_nodes.tsv | grep -c nSeqCDR2" "0"
 
-assert "head -n 1 alleles/report.json | jq -r .statuses.DE_NOVO" "2"
+assert "head -n 1 alleles/report.json | jq -r .statuses.FOUND_KNOWN_VARIANT" "2"
 assert "cat alleles/report.json | head -n 1 | jq -r '.zygotes.\"2\"'" "1"
 
 keyOfRelativeMutations=`head -n 1 alleles/description.tsv | sed 's/mutations/#/' | cut -d# -f1 | wc -w  | awk '{ print $1 + 1 }'`
-assert "grep 'IGHJ6' alleles/description.tsv | cut -f$keyOfRelativeMutations" "SG17TSG18AST19CSC35A"
+assert "grep 'IGHJ6\*05x' alleles/description.tsv | wc -l" "1"
 
 keyOfNumberOfCones=`head -n 1 trees/trees.tsv | sed 's/numberOfClonesInTree/#/' | cut -d# -f1 | wc -w  | awk '{ print $1 + 1 }'`
 keyOfCDR3=`head -n 1 trees/trees.tsv | sed 's/nSeqCDR3OfMrca/#/' | cut -d# -f1 | wc -w  | awk '{ print $1 + 1 }'`

diff --git a/regression/reports/baseBuldTrees.yaml b/regression/reports/baseBuldTrees.yaml
@@ -1010,27 +1010,27 @@ upstreams:
       - IGHJ2
       - IGHV4-55
       firstRoundResults:
-        DE_NOVO: 2
+        FOUND_KNOWN_VARIANT: 2
         NOT_CHANGED_AFTER_SEARCH: 7
         COULD_NOT_BE_ALIGNED_ON_KNOWN_VARIANT: 2
       statuses:
-        DE_NOVO: 2
+        FOUND_KNOWN_VARIANT: 2
         NOT_CHANGED_AFTER_SEARCH: 8
         COULD_NOT_BE_ALIGNED_ON_KNOWN_VARIANT: 2
         REMOVED_BECAUSE_NOT_REPRESENTED_IN_SOURCE_FILES: 505
       zygotes:
         "1": 10
         "2": 1
       allelesScoreChange:
-        IGHJ6*00-M1-CDR3-3-L4BMXUCAAMJA5YBJHTAGXQBY:
+        IGHJ6*05x:
           size: 188
           sum: 8178.0
           min: -58.0
           max: 116.0
           avg: 43.5
           quadraticMean: 58.07707
           stdDeviation: 38.58257
-        IGHV2-70*00-M1-NE7HPQTUM3H576DUBPKXWIHR:
+        IGHV2-70*15:
           size: 130
           sum: 3770.0
           min: 29.0
@@ -1911,27 +1911,27 @@ upstreams:
       - IGHJ2
       - IGHV4-55
       firstRoundResults:
-        DE_NOVO: 2
+        FOUND_KNOWN_VARIANT: 2
         NOT_CHANGED_AFTER_SEARCH: 7
         COULD_NOT_BE_ALIGNED_ON_KNOWN_VARIANT: 2
       statuses:
-        DE_NOVO: 2
+        FOUND_KNOWN_VARIANT: 2
         NOT_CHANGED_AFTER_SEARCH: 8
         COULD_NOT_BE_ALIGNED_ON_KNOWN_VARIANT: 2
         REMOVED_BECAUSE_NOT_REPRESENTED_IN_SOURCE_FILES: 505
       zygotes:
         "1": 10
         "2": 1
       allelesScoreChange:
-        IGHJ6*00-M1-CDR3-3-L4BMXUCAAMJA5YBJHTAGXQBY:
+        IGHJ6*05x:
           size: 188
           sum: 8178.0
           min: -58.0
           max: 116.0
           avg: 43.5
           quadraticMean: 58.07707
           stdDeviation: 38.58257
-        IGHV2-70*00-M1-NE7HPQTUM3H576DUBPKXWIHR:
+        IGHV2-70*15:
           size: 130
           sum: 3770.0
           min: 29.0

diff --git a/...t/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssemblerAlignerTest.java b/...t/java/com/milaboratory/mixcr/partialassembler/PartialAlignmentsAssemblerAlignerTest.java
@@ -50,7 +50,7 @@ public void basicTest1() throws Exception {
         int len = 70;
         NucleotideSequence seq1 = baseSeq.getRange(0, len);
         NucleotideSequence seq2 = baseSeq.getRange(245, 245 + len);
-        NucleotideSequence seq3 = baseSeq.getRange(320, 320 + len);
+        NucleotideSequence seq3 = baseSeq.getRange(319, 319 + len);
 
         VDJCMultiRead read = MiXCRTestUtils.createMultiRead(seq1, seq2, seq3);
         VDJCAlignments al = aligner.process(read.toTuple(), read);
@@ -64,6 +64,12 @@ public void basicTest1() throws Exception {
         VDJCHit bestD = al.getBestHit(GeneType.Diversity);
         VDJCHit bestJ = al.getBestHit(GeneType.Joining);
         VDJCHit bestC = al.getBestHit(GeneType.Constant);
+
+        System.out.println(bestV.getGene().getName());
+        System.out.println(bestD.getGene().getName());
+        System.out.println(bestJ.getGene().getName());
+        System.out.println(bestC.getGene().getName());
+
         Assert.assertNotNull(bestV.getAlignment(0));
         Assert.assertNotNull(bestV.getAlignment(1));
         Assert.assertNull(bestV.getAlignment(2));