Merge pull request #76 from HarryHung/feature/unify-relational-operators

Unify relational operators

Former-commit-id: 02b95d7

bin/get_assembly_qc.sh

@@ -4,7 +4,7 @@ CONTIGS=$(awk -F'\t' '$1 == "# contigs (>= 0 bp)" { print $2 }' "$REPORT")
 LENGTH=$(awk -F'\t' '$1 == "Total length" { print $2 }' "$REPORT")
 DEPTH=$(echo "scale=2; $BASES / $LENGTH" | bc -l)
 
-if [[ $CONTIGS -lt $QC_CONTIGS ]] && [[ $LENGTH -ge $QC_LENGTH_LOW ]] && [[ $LENGTH -le $QC_LENGTH_HIGH ]] && [[ "$(echo "$DEPTH >= $QC_DEPTH" | bc -l)" == 1 ]]; then
+if [[ $CONTIGS -le $QC_CONTIGS ]] && [[ $LENGTH -ge $QC_LENGTH_LOW ]] && [[ $LENGTH -le $QC_LENGTH_HIGH ]] && [[ "$(echo "$DEPTH >= $QC_DEPTH" | bc -l)" == 1 ]]; then
     ASSEMBLY_QC="PASS"
 else
     ASSEMBLY_QC="FAIL"

bin/get_mapping_qc.sh

@@ -2,7 +2,7 @@
 
 COVERAGE=$(printf %.2f "$COVERAGE")
 
-if [[ "$(echo "$COVERAGE > $QC_REF_COVERAGE" | bc -l)" == 1 ]] && [[ $HET_SNP -lt $QC_HET_SNP_SITE ]]; then
+if [[ "$(echo "$COVERAGE >= $QC_REF_COVERAGE" | bc -l)" == 1 ]] && [[ $HET_SNP -le $QC_HET_SNP_SITE ]]; then
     MAPPING_QC="PASS"
 else
     MAPPING_QC="FAIL"

bin/get_taxonomy_qc.sh

@@ -14,7 +14,7 @@ if [ -z "$TOP_NON_STREP_GENUS_PERCENTAGE" ]; then
     TOP_NON_STREP_GENUS_PERCENTAGE="0.00"
 fi
 
-if [[ "$(echo "$PERCENTAGE > $QC_SPNEUMO_PERCENTAGE" | bc -l)" == 1 ]] && [[ "$(echo "$TOP_NON_STREP_GENUS_PERCENTAGE <= $QC_TOP_NON_STREP_GENUS_PERCENTAGE" | bc -l)" == 1 ]]; then
+if [[ "$(echo "$PERCENTAGE >= $QC_SPNEUMO_PERCENTAGE" | bc -l)" == 1 ]] && [[ "$(echo "$TOP_NON_STREP_GENUS_PERCENTAGE <= $QC_TOP_NON_STREP_GENUS_PERCENTAGE" | bc -l)" == 1 ]]; then
     TAXONOMY_QC="PASS"
 else
     TAXONOMY_QC="FAIL"