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Fullseq fixes and updates (#339)
* This fixes misbehaving getFeature method of Clone object. * Number of threads in assembleContigs reduced to 1, added exception for higher value. * Minor corrections. * Seed script for tests on big datasets. * Test data download integrated into travis pipeline.
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102 additions
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- +1 −0 .gitignore
- +2 −0 .travis.yml
- +58 −0 ensure-test-data.sh
- +13 −1 src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java
- +12 −11 src/main/java/com/milaboratory/mixcr/basictypes/ClnAReader.java
- +0 −8 src/main/java/com/milaboratory/mixcr/basictypes/Clone.java
- +1 −1 src/main/java/com/milaboratory/mixcr/cli/AbstractActionReport.java
- +15 −5 src/main/java/com/milaboratory/mixcr/cli/ActionAssembleContigs.java
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#!/bin/bash | ||
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set -e | ||
set -o pipefail | ||
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# Linux readlink -f alternative for Mac OS X | ||
function readlinkUniversal() { | ||
targetFile=$1 | ||
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cd `dirname $targetFile` | ||
targetFile=`basename $targetFile` | ||
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# iterate down a (possible) chain of symlinks | ||
while [ -L "$targetFile" ] | ||
do | ||
targetFile=`readlink $targetFile` | ||
cd `dirname $targetFile` | ||
targetFile=`basename $targetFile` | ||
done | ||
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# compute the canonicalized name by finding the physical path | ||
# for the directory we're in and appending the target file. | ||
phys_dir=`pwd -P` | ||
result=$phys_dir/$targetFile | ||
echo $result | ||
} | ||
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os=`uname` | ||
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dir="" | ||
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case $os in | ||
Darwin) | ||
dir=$(dirname "$(readlinkUniversal "$0")") | ||
;; | ||
Linux) | ||
dir="$(dirname "$(readlink -f "$0")")" | ||
;; | ||
FreeBSD) | ||
dir=$(dirname "$(readlinkUniversal "$0")") | ||
;; | ||
*) | ||
echo "Unknown OS." | ||
exit 1 | ||
;; | ||
esac | ||
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mkdir -p $dir/src/test/resources/sequences/big/ | ||
cd $dir/src/test/resources/sequences/big/ | ||
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if [[ ! -f CD4M1_test_R1.fastq.gz ]]; then | ||
wget https://s3.amazonaws.com/files.milaboratory.com/test-data/CD4M1_test_R1.fastq.gz | ||
fi | ||
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if [[ ! -f CD4M1_test_R2.fastq.gz ]]; then | ||
wget https://s3.amazonaws.com/files.milaboratory.com/test-data/CD4M1_test_R2.fastq.gz | ||
fi | ||
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