Commit c92c9b1e authored by Antony Le Béchec's avatar Antony Le Béchec

Merge branch '0.9.18.2'

parents 88bb2d10 15b4fe83
......@@ -675,8 +675,11 @@ for GP_FOLDER in $GP_FOLDER_LIST_UNIQ; do
fi;
# NB VARIANT
NB_VCF=$(find -L $GP_FOLDER/*/*/ -maxdepth 1 -name '*'$VCF_PATTERN -a ! -name '*.*-*'$VCF_PATTERN 2>/dev/null | grep -vE $SAMPLE_EXCLUDE_PARAM_GREP 2>/dev/null | wc -l)
#NB_VCF=$(find -L $GP_FOLDER/*/*/ -maxdepth 1 -name '*'$VCF_PATTERN -a ! -name '*.*-*'$VCF_PATTERN 2>/dev/null | grep -vE $SAMPLE_EXCLUDE_PARAM_GREP 2>/dev/null | wc -l)
VCF_LIST=$(find -L $GP_FOLDER/*/*/ -maxdepth 1 -name '*'$VCF_PATTERN -a ! -name '*.*-*'$VCF_PATTERN 2>/dev/null | grep -vE $SAMPLE_EXCLUDE_PARAM_GREP 2>/dev/null)
NB_VCF=$(echo $VCF_LIST | wc -w)
(($VERBOSE)) && echo "#[INFO] DEJAVU database '$GROUP/$PROJECT' repository '$REPO' $NB_VCF VCF found"
......@@ -689,8 +692,9 @@ for GP_FOLDER in $GP_FOLDER_LIST_UNIQ; do
# TMP folder creation
mkdir -p $TMP/$GROUP/$PROJECT
#cp -f $(find -L $GP_FOLDER/*/*/ -maxdepth 1 -name '*'$VCF_PATTERN -a ! -name '*.*-*'$VCF_PATTERN) $TMP/$GROUP/$PROJECT/ 2>/dev/null
cp -f $(find -L $GP_FOLDER/*/*/ -maxdepth 1 -name '*'$VCF_PATTERN -a ! -name '*.*-*'$VCF_PATTERN | grep -vE $SAMPLE_EXCLUDE_PARAM_GREP) $TMP/$GROUP/$PROJECT/ 2>/dev/null
NB_VCF_FOUND=$(ls $TMP/$GROUP/$PROJECT/*.vcf.gz | wc -w)
#cp -f $(find -L $GP_FOLDER/*/*/ -maxdepth 1 -name '*'$VCF_PATTERN -a ! -name '*.*-*'$VCF_PATTERN | grep -vE $SAMPLE_EXCLUDE_PARAM_GREP) $TMP/$GROUP/$PROJECT/ 2>/dev/null
cp -f $VCF_LIST $TMP/$GROUP/$PROJECT/ 2>/dev/null
NB_VCF_FOUND=$(ls $TMP/$GROUP/$PROJECT/*.vcf.gz 2>/dev/null | wc -w)
(($VERBOSE)) && echo "#[INFO] DEJAVU database '$GROUP/$PROJECT' $NB_VCF_FOUND VCF considered files (some files/samples may be found multiple times)"
fi;
......
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