From ee7f188d9f79653c4b594f494782f6cff5fcdc19 Mon Sep 17 00:00:00 2001 From: Bolotin Dmitriy Date: Fri, 15 Feb 2019 00:36:40 +0300 Subject: [PATCH 1/6] Next development cycle v3.0.5 --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index c81aeba1b..cb9f62d51 100644 --- a/pom.xml +++ b/pom.xml @@ -33,7 +33,7 @@ com.milaboratory mixcr - 3.0.4 + 3.0.5-SNAPSHOT jar MiXCR From d652b03315ef00e0671c9aa6cfd4d4715d965cfb Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Fri, 15 Feb 2019 00:44:13 +0300 Subject: [PATCH 2/6] Update install.rst --- doc/install.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/doc/install.rst b/doc/install.rst index 6597c9a28..eba0e424b 100644 --- a/doc/install.rst +++ b/doc/install.rst @@ -17,13 +17,13 @@ To install MiXCR using Homebrew just type the following commands: :: brew tap milaboratory/all - brew install mixcr3 + brew install mixcr To install the old MiXCR 2.x series you can use :: - brew install mixcr + brew install mixcr2 Installation on Mac OS X / Linux / FreeBSD from zip distribution From 49c40d8b53aae561568f6a7917e8782a14784697 Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Tue, 19 Feb 2019 01:20:36 +0300 Subject: [PATCH 3/6] fix for empty size fastq --- .../com/milaboratory/mixcr/basictypes/ClnAWriter.java | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/ClnAWriter.java b/src/main/java/com/milaboratory/mixcr/basictypes/ClnAWriter.java index 4996e2ff7..19cd02090 100644 --- a/src/main/java/com/milaboratory/mixcr/basictypes/ClnAWriter.java +++ b/src/main/java/com/milaboratory/mixcr/basictypes/ClnAWriter.java @@ -60,8 +60,8 @@ * writeAlignmentsAndIndex() 5. close() */ public final class ClnAWriter implements PipelineConfigurationWriter, - AutoCloseable, - CanReportProgressAndStage { + AutoCloseable, + CanReportProgressAndStage { static final String MAGIC_V3 = "MiXCR.CLNA.V03"; static final String MAGIC_V4 = "MiXCR.CLNA.V04"; static final String MAGIC = MAGIC_V4; @@ -328,7 +328,10 @@ public synchronized void writeAlignmentsAndIndex() { } // Writing last block, and waiting for all the data to be flushed - writer.writeSync(block); + if (!block.isEmpty()) + writer.writeSync(block); + else + writer.waitPreviousBlock(); } // Closing sorted output port, this will delete presorted file sortedAlignments.close(); From 730321e47eed8e265503de1c9d1e49f23077c447 Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Tue, 19 Feb 2019 01:25:47 +0300 Subject: [PATCH 4/6] empty fastq test case --- itests.sh | 2 +- itests/case6.sh | 7 +++++++ 2 files changed, 8 insertions(+), 1 deletion(-) create mode 100755 itests/case6.sh diff --git a/itests.sh b/itests.sh index 7194da324..c58ebaa60 100755 --- a/itests.sh +++ b/itests.sh @@ -48,7 +48,7 @@ case $os in ;; esac -tests=("case1" "case2" "case3" "case4" "case5") +tests=("case1" "case2" "case3" "case4" "case5" "case6") create_standard_results=false run_tests=false diff --git a/itests/case6.sh b/itests/case6.sh new file mode 100755 index 000000000..d4204fd6b --- /dev/null +++ b/itests/case6.sh @@ -0,0 +1,7 @@ +#!/usr/bin/env bash + +set -euxo pipefail + +touch empty_R1.fastq +touch empty_R2.fastq +mixcr analyze amplicon --receptor-type tra --impute-germline-on-export -s hs --starting-material rna --contig-assembly --5-end v-primers --3-end j-primers --adapters no-adapters empty_R1.fastq empty_R2.fastq case6 \ No newline at end of file From af538f71fa86675352f8024b3f226d5d3bf9662d Mon Sep 17 00:00:00 2001 From: Bolotin Dmitriy Date: Mon, 25 Feb 2019 02:03:38 +0300 Subject: [PATCH 5/6] Changelog --- CHANGELOG_CURRENT | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG_CURRENT b/CHANGELOG_CURRENT index e69de29bb..aec521f17 100644 --- a/CHANGELOG_CURRENT +++ b/CHANGELOG_CURRENT @@ -0,0 +1 @@ +Fixed `writing empty block` exception arising with empty input files and in several other situations \ No newline at end of file From 71dbda1d6e104e0805b6d1a4f96dbc21716e1b32 Mon Sep 17 00:00:00 2001 From: Bolotin Dmitriy Date: Mon, 25 Feb 2019 02:05:07 +0300 Subject: [PATCH 6/6] Release v3.0.5 --- CHANGELOG | 7 +++++++ CHANGELOG_CURRENT | 1 - pom.xml | 2 +- 3 files changed, 8 insertions(+), 2 deletions(-) diff --git a/CHANGELOG b/CHANGELOG index acf1dd2fa..9046f0c1c 100644 --- a/CHANGELOG +++ b/CHANGELOG @@ -1,4 +1,11 @@ +MiXCR 3.0.5 (25 Feb 2019) +======================== + +-- Fixed `writing empty block` exception arising with empty input files and in several other + situations + + MiXCR 3.0.4 (15 Feb 2019) ======================== diff --git a/CHANGELOG_CURRENT b/CHANGELOG_CURRENT index aec521f17..e69de29bb 100644 --- a/CHANGELOG_CURRENT +++ b/CHANGELOG_CURRENT @@ -1 +0,0 @@ -Fixed `writing empty block` exception arising with empty input files and in several other situations \ No newline at end of file diff --git a/pom.xml b/pom.xml index cb9f62d51..682a6d48d 100644 --- a/pom.xml +++ b/pom.xml @@ -33,7 +33,7 @@ com.milaboratory mixcr - 3.0.5-SNAPSHOT + 3.0.5 jar MiXCR