Summarizer: re-order results

[swvanderlaan]

There is an issue with the re-ordering of the nominal results: these are empty after attempting to re-order using the following statements:

if [[ ${QTL_TYPE} == "CIS" ]]; then
	
		if [[ ${CLUMP} == "Y" ]]; then
			echo "* Clumped ${QTL_TYPE}-QTL results."
			gzip -fv ${SUMMARY}/${STUDYNAME}_QC_qtlnom_clumped_summary.txt
			gzip -fv ${SUMMARY}/${STUDYNAME}_QC_qtlperm_clumped_summary.txt
			
			echo "* And re-ordering based on p-value."
			zcat ${SUMMARY}/${STUDYNAME}_QC_qtlnom_clumped_summary.txt.gz | (head -n 1 && tail -n +3  | sort -t , -k 24) > ${SUMMARY}/${STUDYNAME}_QC_qtlnom_clumped_summary.txt
			gzip -fv ${SUMMARY}/${STUDYNAME}_QC_qtlnom_clumped_summary.txt
		
		elif [[ ${ANALYSIS_TYPE} == "MQTL" ]]; then
			echo "* Non-clumped ${QTL_TYPE}-QTL results."
			gzip -fv ${SUMMARY}/${STUDYNAME}_QC_qtlperm_summary.txt
			
			echo "* And re-ordering based on p-value."
			cat ${SUMMARY}/${STUDYNAME}_QC_qtlnom_summary.txt | (head -n 1 && tail -n +3  | sort -t , -k 32) > ${SUMMARY}/${STUDYNAME}_QC_qtlnom_summary.txt
			gzip -fv ${SUMMARY}/${STUDYNAME}_QC_qtlnom_summary.txt
			
		else
			echo "* Non-clumped ${QTL_TYPE}-QTL results."
			gzip -fv ${SUMMARY}/${STUDYNAME}_QC_qtlperm_summary.txt
			
			echo "* And re-ordering based on p-value."
			cat ${SUMMARY}/${STUDYNAME}_QC_qtlnom_summary.txt | (head -n 1 && tail -n +3  | sort -t , -k 24) > ${SUMMARY}/${STUDYNAME}_QC_qtlnom_summary.txt
			gzip -fv ${SUMMARY}/${STUDYNAME}_QC_qtlnom_summary.txt
			
		fi

	elif [[ ${QTL_TYPE} == "TRANS" ]]; then
		gzip -fv ${SUMMARY}/${STUDYNAME}_QC_qtlnom_summary.txt

	fi