added bootstrap output concatenation step

13-concatenateMsmcBootstrap.sh

@@ -0,0 +1,62 @@
+#! /bin/bash
+
+# Ensure we're running from the correct location
+CWD_check()
+{
+	local SCRIPTS_DIR
+	local MAIN_DIR
+	local RUN_DIR
+
+	SCRIPTS_DIR=$(readlink -f `dirname "${BASH_SOURCE[0]}"`)
+	MAIN_DIR=$(readlink -f `dirname "${SCRIPTS_DIR}/"`)
+	RUN_DIR=$(readlink -f .)
+
+	if [ "${RUN_DIR}" != "${MAIN_DIR}" ] || ! [[ "${SCRIPTS_DIR}" =~ ^"${MAIN_DIR}"/scripts.* ]]
+	then
+		printf "\n\t%s\n\t%s\n\n" "Script must be run from \"${MAIN_DIR}\"" "You are currently at:   \"${RUN_DIR}\"" 1>&2
+		exit 1
+	fi
+}
+CWD_check
+
+# important variables
+MSMC_BOOTSTRAP_DIR=`readlink -n -m "data/msmc/bootstrap"`
+CONCAT_FILE=`readlink -n -m "${MSMC_BOOTSTRAP_DIR}/msmc-bootstrap_concat.tsv"`
+FIRST_FILE=0 # 0=True, 1=False
+
+# check if output file exists already
+if [ -e "${CONCAT_FILE}" ]
+then
+	printf "%s\n\t%s %s\n" "INFO: Output file already exists. To run this step, first remove it:" "rm -f" "${CONCAT_FILE}" 1>&2
+	exit 0
+fi
+
+# identify input files (assume the neeeded input files have all been generated)
+INPUT_FILES=($(find "${MSMC_BOOTSTRAP_DIR}" -mindepth 2 -maxdepth 2 -type f -name 'msmc.final.txt' -printf '%p\n' | sort -V)) # <-- get input files from `find' command (assumes all needed files exist)
+
+# create header line
+printf "%s\t" "Bootstrap_Round" > "${CONCAT_FILE}"
+head -n 1 "${INPUT_FILES[0]}" >> "${CONCAT_FILE}"
+
+# add data lines, one file at a time
+for INPUT_FILE in "${INPUT_FILES[@]}"
+do
+	ROUND=$(basename `dirname "${INPUT_FILE}"` | tr -d '\n' | sed -r 's,^round_([0-9]+)$,\1,')
+	awk 'BEGIN{OFS="\t";FS="\t";}/^[0-9]/{print '"${ROUND}"', $0;}' "${INPUT_FILE}" >> "${CONCAT_FILE}"
+	EXIT_CODE=$((${EXIT_CODE}+${?}))
+
+done
+
+EXIT_CODE=$?
+
+if [ ${EXIT_CODE} -eq 0 ]
+then
+	chmod 444 "${CONCAT_FILE}" &> /dev/null
+	printf "%s\n" "INFO: Successfully created MSMC bootstrap concatenated file." 1>&2
+else
+	rm -f "${CONCAT_FILE}" &> /dev/null
+	printf "%s\n" "ERROR: Failed to create MSMC bootstrap concatenated file." 1>&2
+fi
+
+exit ${EXIT_CODE}
+