fixes

scripts/2-intervalGraph/2-steps2345.sh

@@ -133,10 +133,10 @@ cp ${TAGS_DIR}/tags-root.txt ${STEP4_DIR}/
 # Merging all tag files
 TMP_FILE="${TAGS_DIR}/tmp.txt"
 rm -f ${TMP_FILE}
-find "${TAGS_DIR}" -type f -name "tags-*.txt" -exec cat {} + >> ${TMP_FILE}
+find "${TAGS_DIR}" -type f -maxdepth 1 -name "tags-*.txt" -exec cat {} + >> ${TMP_FILE}
 sort -m -t , -k 1,1n -k 2,2n -k 3,3n ${TMP_FILE} > ${TAGS_DIR}/allTags.txt
 rm -f ${TMP_FILE}
-find "${STEP4_DIR}" -type f -name "tags-*.txt" -exec cat {} + >> ${TMP_FILE}
+find "${STEP4_DIR}" -type f -maxdepth 1 -name "tags-*.txt" -exec cat {} + >> ${TMP_FILE}
 sort -m -t , -k 1,1n -k 2,2n -k 3,3n ${TMP_FILE} > ${STEP4_DIR}/allTags.txt
 rm -f ${TMP_FILE}
 

scripts/6-repeatAlphabet/0-breakReads.sh

@@ -26,6 +26,21 @@ TMPFILE_NAME="breakReads-tmp"
 TMPFILE_PATH="${INPUT_DIR}/${TMPFILE_NAME}"
 rm -f ${TMPFILE_PATH}*
 
+function waitAndCheck() {
+    local ARRAY_NAME=$1[@]
+
+    local PIDS=(${!ARRAY_NAME})
+    local LAST_THREAD=$((${#PIDS[@]} - 1))
+    N_FAILED="0"
+    for THREAD in $(seq 0 ${LAST_THREAD}); do
+        wait ${PIDS[${THREAD}]} || N_FAILED=$(( ${N_FAILED} + 1 ))
+    done
+    if [ ${N_FAILED} -ne 0 ]; then
+        exit 1
+    fi
+}
+
+
 echo "Breaking reads..."
 OLD2NEW_FILE="${INPUT_DIR}/unbroken2broken.txt"
 NEW2OLD_FILE="${INPUT_DIR}/broken2unbroken.txt"
@@ -39,9 +54,6 @@ function alignmentsThread1() {
 	local ALIGNMENTS_FILE_ID=$1
 	local WRITE_HEADER=$2
 	java ${JAVA_RUNTIME_FLAGS} -classpath "${REVANT_BINARIES}" de.mpi_cbg.revant.apps.BreakReads2 ${N_READS} ${READ_LENGTHS_FILE} ${OLD2NEW_FILE} 1 ${WRITE_HEADER} ${TMPFILE_PATH}-1-${ALIGNMENTS_FILE_ID}.txt ${TMPFILE_PATH}-2-${ALIGNMENTS_FILE_ID}.txt
-	if [ $? -ne 0 ]; then
-		exit
-	fi
 }
 ALIGNMENTS_FILE="${INPUT_DIR}/LAshow-reads-reads.txt"
 N_ALIGNMENTS=$(( $(wc -l < ${ALIGNMENTS_FILE}) - 2 ))
@@ -53,11 +65,14 @@ if [ -e ${TMPFILE_PATH}-1-${N_THREADS}.txt ]; then
 else
 	TO=$(( ${N_THREADS} - 1 ))
 fi
+PIDS=()
 alignmentsThread1 0 1 &
+PIDS+=($!)
 for THREAD in $(seq 1 ${TO}); do
 	alignmentsThread1 ${THREAD} 1 &  # We always write the header for future scripts.
+    PIDS+=($!)
 done
-wait
+waitAndCheck PIDS
 echo "Read-read alignments translated successfully"
 # We do not need to concatenate the chunks in a single file, since they will be used
 # directly as chunks by the following scripts.
@@ -74,9 +89,6 @@ function alignmentsThread2() {
 	local ALIGNMENTS_FILE_ID=$1
 	local WRITE_HEADER=$2
 	java ${JAVA_RUNTIME_FLAGS} -classpath "${REVANT_BINARIES}" de.mpi_cbg.revant.apps.BreakReads2 ${N_READS} ${READ_LENGTHS_FILE} ${OLD2NEW_FILE} 0 ${WRITE_HEADER} ${TMPFILE_PATH}-3-${ALIGNMENTS_FILE_ID}.txt ${TMPFILE_PATH}-4-${ALIGNMENTS_FILE_ID}.txt
-	if [ $? -ne 0 ]; then
-		exit
-	fi
 }
 ALIGNMENTS_FILE="${INPUT_DIR}/LAshow-reads-repeats.txt"
 N_ALIGNMENTS=$(( $(wc -l < ${ALIGNMENTS_FILE}) - 2 ))
@@ -88,11 +100,14 @@ if [ -e ${TMPFILE_PATH}-3-${N_THREADS}.txt ]; then
 else
 	TO=$(( ${N_THREADS} - 1 ))
 fi
+PIDS=()
 alignmentsThread2 0 1 &
+PIDS+=($!)
 for THREAD in $(seq 1 ${TO}); do
 	alignmentsThread2 ${THREAD} 1 &  # We always write the header for future scripts.
+    PIDS+=($!)
 done
-wait
+waitAndCheck PIDS
 echo "Read-repeat alignments translated successfully"
 # We do not need to concatenate the chunks in a single file, since they will be used
 # directly as chunks by the following scripts.

scripts/6-repeatAlphabet/2-fixEndBlocks.sh

@@ -45,16 +45,27 @@ READS_DISAMBIGUATED_FILE="${INPUT_DIR}/reads-translated-disambiguated.txt"
 ALPHABET_FILE="${INPUT_DIR}/alphabet-cleaned.txt"
 rm -f ${TMPFILE_PATH}*
 
+function waitAndCheck() {
+    local ARRAY_NAME=$1[@]
+
+    local PIDS=(${!ARRAY_NAME})
+    local LAST_THREAD=$((${#PIDS[@]} - 1))
+    N_FAILED="0"
+    for THREAD in $(seq 0 ${LAST_THREAD}); do
+        wait ${PIDS[${THREAD}]} || N_FAILED=$(( ${N_FAILED} + 1 ))
+    done
+    if [ ${N_FAILED} -ne 0 ]; then
+        exit 1
+    fi
+}
+
 function enumerateKmersThread() {
 	local LOCAL_K=$1
 	local LOCAL_TRANSLATED_READS_FILE=$2
 	local LOCAL_BOUNDARIES_FILE=$3
 	local LOCAL_READ_LENGTHS_FILE=$4
 	local LOCAL_KMERS_FILE=$5
 	java ${JAVA_RUNTIME_FLAGS} -classpath "${REVANT_BINARIES}" de.mpi_cbg.revant.apps.CollectKmers 0 ${LOCAL_K} ${MAX_KMER_LENGTH_BPS} 1 ${LOCAL_TRANSLATED_READS_FILE} ${LOCAL_BOUNDARIES_FILE} ${LOCAL_READ_LENGTHS_FILE} ${ALPHABET_FILE} null null ${LOCAL_KMERS_FILE}
-	if [ $? -ne 0 ]; then
-		exit
-	fi
 }
 
 function countKmersThread() {
@@ -65,9 +76,6 @@ function countKmersThread() {
 	local LOCAL_KMERS_FILE_INPUT=$5
     local LOCAL_KMERS_FILE_OUTPUT=$6
 	java ${JAVA_RUNTIME_FLAGS} -classpath "${REVANT_BINARIES}" de.mpi_cbg.revant.apps.CollectKmers 1 ${LOCAL_K} ${MAX_KMER_LENGTH_BPS} 1 ${LOCAL_TRANSLATED_READS_FILE} ${LOCAL_BOUNDARIES_FILE} ${LOCAL_READ_LENGTHS_FILE} ${ALPHABET_FILE} null ${LOCAL_KMERS_FILE_INPUT} ${LOCAL_KMERS_FILE_OUTPUT}
-	if [ $? -ne 0 ]; then
-		exit
-	fi
 }
 
 function fixThread() {
@@ -79,9 +87,6 @@ function fixThread() {
 	local LOCAL_NEW_TRANSLATED_FILE=$6
 	local LOCAL_STATS_FILE=$7
 	java ${JAVA_RUNTIME_FLAGS} -classpath "${REVANT_BINARIES}" de.mpi_cbg.revant.apps.FixEndBlocks ${ALPHABET_FILE} ${LOCAL_OLD_TRANSLATED_FILE} ${LOCAL_BOUNDARIES_FILE} ${LOCAL_READ_LENGTHS_FILE} ${LOCAL_KMERS_FILE} ${LOCAL_K} ${TIGHT_MODE} ${LOCAL_NEW_TRANSLATED_FILE} ${LOCAL_STATS_FILE}
-	if [ $? -ne 0 ]; then
-		exit
-	fi
 }
 
 rm -f "${TMPFILE_PATH}-1-*"
@@ -94,23 +99,27 @@ for K in $(seq ${MIN_K} ${MAX_K}); do
 		SORT_OPTIONS_KMERS="${SORT_OPTIONS_KMERS} -k ${i},${i}n"
 	done
 	echo "Enumerating distinct ${K}-mers..."
-	for FILE in $(find -s ${INPUT_DIR} -name "${TMPFILE_NAME}-1-*"); do
+    PIDS=()
+	for FILE in $(find -s ${INPUT_DIR} -maxdepth 1 -name "${TMPFILE_NAME}-1-*"); do
 		THREAD_ID=${FILE#${INPUT_DIR}/${TMPFILE_NAME}-1-}
 		enumerateKmersThread ${K} ${FILE} ${TMPFILE_PATH}-z1-${THREAD_ID} ${TMPFILE_PATH}-z2-${THREAD_ID} ${TMPFILE_PATH}-kmers-${K}-${THREAD_ID} &
+        PIDS+=($!)
 	done
-	wait
-	sort --parallel=${N_THREADS} -m -t , ${SORT_OPTIONS_KMERS} ${TMPFILE_PATH}-kmers-${K}-* > ${TMPFILE_PATH}-${K}-distinct.txt
+	waitAndCheck PIDS
+	sort --parallel=${N_THREADS} -m -u -t , ${SORT_OPTIONS_KMERS} ${TMPFILE_PATH}-kmers-${K}-* > ${TMPFILE_PATH}-${K}-distinct.txt
 	if [ ! -s ${TMPFILE_PATH}-${K}-distinct.txt ]; then
 		MAX_K=$((${K}-1))
 		break
 	fi
 	echo "Counting ${K}-mer occurrences..."
-	for FILE in $(find -s ${INPUT_DIR} -name "${TMPFILE_NAME}-1-*"); do
+    PIDS=()
+	for FILE in $(find -s ${INPUT_DIR} -maxdepth 1 -name "${TMPFILE_NAME}-1-*"); do
 		THREAD_ID=${FILE#${INPUT_DIR}/${TMPFILE_NAME}-1-}
         rm -f ${TMPFILE_PATH}-kmers-${K}-${THREAD_ID}
 		countKmersThread ${K} ${FILE} ${TMPFILE_PATH}-z1-${THREAD_ID} ${TMPFILE_PATH}-z2-${THREAD_ID} ${TMPFILE_PATH}-${K}-distinct.txt ${TMPFILE_PATH}-kmers-${K}-${THREAD_ID} &
+        PIDS+=($!)
 	done
-	wait
+	waitAndCheck PIDS
 	sort --parallel=${N_THREADS} -m -t , ${SORT_OPTIONS_KMERS} ${TMPFILE_PATH}-kmers-${K}-* > ${TMPFILE_PATH}-${K}.txt
     rm -f ${TMPFILE_PATH}-${K}-distinct.txt
 	FREQUENT_KMERS_FILE="${INPUT_DIR}/frequent-k${K}.txt"
@@ -121,13 +130,15 @@ for K in $(seq ${MIN_K} ${MAX_K}); do
 	K_MINUS_ONE_MERS_FILE="${INPUT_DIR}/kMinusOne-k${K}.txt"
 	java ${JAVA_RUNTIME_FLAGS} -classpath "${REVANT_BINARIES}" de.mpi_cbg.revant.apps.GetKMinusOneMers ${ALPHABET_FILE} ${FREQUENT_KMERS_FILE} ${K} ${K_MINUS_ONE_MERS_FILE}
 	echo "Disambiguating read ends using contexts of length $((${K}-1))..."
-	for FILE in $(find -s ${INPUT_DIR} -name "${TMPFILE_NAME}-$((${K}-1))-*"); do
+    PIDS=()
+	for FILE in $(find -s ${INPUT_DIR} -maxdepth 1 -name "${TMPFILE_NAME}-$((${K}-1))-*"); do
 		THREAD_ID=${FILE#${INPUT_DIR}/${TMPFILE_NAME}-$((${K}-1))-}
 		fixThread ${FILE} ${TMPFILE_PATH}-z1-${THREAD_ID} ${TMPFILE_PATH}-z2-${THREAD_ID} ${K_MINUS_ONE_MERS_FILE} $((${K}-1)) ${TMPFILE_PATH}-${K}-${THREAD_ID} ${TMPFILE_PATH}-counts-${K}-${THREAD_ID} &
+        PIDS+=($!)
 	done
-	wait
+	waitAndCheck PIDS
 	N_FIXED="0"; N_FIXABLE="0"; N_ENDS="0";
-	for FILE in $(find -s ${INPUT_DIR} -name "${TMPFILE_NAME}-counts-${K}-*"); do
+	for FILE in $(find -s ${INPUT_DIR} -maxdepth 1 -name "${TMPFILE_NAME}-counts-${K}-*"); do
 		N_FIXED=$(( ${N_FIXED} + $(cut -d , -f 1 ${FILE}) ))
 		N_FIXABLE=$(( ${N_FIXABLE} + $(cut -d , -f 2 ${FILE}) ))
 		N_ENDS=$(( ${N_ENDS} + $(cut -d , -f 3 ${FILE}) ))
@@ -136,7 +147,7 @@ for K in $(seq ${MIN_K} ${MAX_K}); do
 	echo "Disambiguated ${N_FIXED} read ends out of ${N_FIXABLE} fixable (${N_ENDS} total)"
 done
 rm -f ${READS_DISAMBIGUATED_FILE}
-for FILE in $(find -s ${INPUT_DIR} -name "${TMPFILE_NAME}-${MAX_K}-*" ); do
+for FILE in $(find -s ${INPUT_DIR} -maxdepth 1 -name "${TMPFILE_NAME}-${MAX_K}-*" ); do
 	cat ${FILE} >> ${READS_DISAMBIGUATED_FILE}
 done
 if [ ${BROKEN_READS} -eq 1 ]; then

scripts/6-repeatAlphabet/3-getUniqueSubstrings.sh

@@ -52,6 +52,20 @@ rm -f ${TMPFILE_PATH}*
 rm -f ${INPUT_DIR}/unique-*
 rm -f ${INPUT_DIR}/histogram-*
 
+function waitAndCheck() {
+    local ARRAY_NAME=$1[@]
+
+    local PIDS=(${!ARRAY_NAME})
+    local LAST_THREAD=$((${#PIDS[@]} - 1))
+    N_FAILED="0"
+    for THREAD in $(seq 0 ${LAST_THREAD}); do
+        wait ${PIDS[${THREAD}]} || N_FAILED=$(( ${N_FAILED} + 1 ))
+    done
+    if [ ${N_FAILED} -ne 0 ]; then
+        exit 1
+    fi
+}
+
 function enumerateKmersThread() {
 	local LOCAL_K=$1
 	local LOCAL_TRANSLATED_READS_FILE=$2
@@ -60,9 +74,6 @@ function enumerateKmersThread() {
 	local LOCAL_K_MINUS_ONE_INTERVALS_FILE=$5
 	local LOCAL_KMERS_FILE=$6
 	java ${JAVA_RUNTIME_FLAGS} -classpath "${REVANT_BINARIES}" de.mpi_cbg.revant.apps.CollectKmers 0 ${LOCAL_K} ${MAX_KMER_LENGTH_BPS} 2 ${LOCAL_TRANSLATED_READS_FILE} ${LOCAL_BOUNDARIES_FILE} ${LOCAL_READ_LENGTHS_FILE} ${ALPHABET_FILE} ${LOCAL_K_MINUS_ONE_INTERVALS_FILE} null ${LOCAL_KMERS_FILE}
-	if [ $? -ne 0 ]; then
-		exit
-	fi
 }
 
 function countKmersThread() {
@@ -74,9 +85,6 @@ function countKmersThread() {
 	local LOCAL_KMERS_FILE_INPUT=$6
     local LOCAL_KMERS_FILE_OUTPUT=$7
 	java ${JAVA_RUNTIME_FLAGS} -classpath "${REVANT_BINARIES}" de.mpi_cbg.revant.apps.CollectKmers 1 ${LOCAL_K} ${MAX_KMER_LENGTH_BPS} 2 ${LOCAL_TRANSLATED_READS_FILE} ${LOCAL_BOUNDARIES_FILE} ${LOCAL_READ_LENGTHS_FILE} ${ALPHABET_FILE} ${LOCAL_K_MINUS_ONE_INTERVALS_FILE} ${LOCAL_KMERS_FILE_INPUT} ${LOCAL_KMERS_FILE_OUTPUT}
-	if [ $? -ne 0 ]; then
-		exit
-	fi
 }
 
 function intervalsThread() {
@@ -88,9 +96,6 @@ function intervalsThread() {
 	local LOCAL_K_MINUS_ONE_INTERVALS_FILE=$6
 	local LOCAL_INTERVALS_FILE=$7
 	java ${JAVA_RUNTIME_FLAGS} -classpath "${REVANT_BINARIES}:${REVANT_LIBRARIES}" de.mpi_cbg.revant.apps.GetShortestUniqueIntervals ${LOCAL_K} ${MAX_KMER_LENGTH_BPS} ${LOCAL_TRANSLATED_READS_FILE} ${LOCAL_BOUNDARIES_FILE} ${LOCAL_READ_LENGTHS_FILE} ${ALPHABET_FILE} ${LOCAL_UNIQUE_KMERS_FILE} ${N_READS} ${AVG_READ_LENGTH} ${GENOME_LENGTH} ${N_HAPLOTYPES} ${MIN_ALIGNMENT_LENGTH} ${IDENTITY_THRESHOLD} ${DISTANCE_THRESHOLD} ${CHARACTER_THRESHOLD} ${LOCAL_K_MINUS_ONE_INTERVALS_FILE} ${LOCAL_INTERVALS_FILE}
-	if [ $? -ne 0 ]; then
-		exit
-	fi
 }
 
 FINAL_INTERVALS_FILE="${INPUT_DIR}/unique-intervals-k1-${MAX_K}.txt"
@@ -103,23 +108,26 @@ for K in $(seq 1 ${MAX_K}); do
 		SORT_OPTIONS_KMERS="${SORT_OPTIONS_KMERS} -k ${i},${i}n"
 	done
 	echo "Enumerating distinct ${K}-mers..."
-	for FILE in $(find -s ${INPUT_DIR} -name "${TMPFILE_NAME}-0-*"); do
+    PIDS=()
+	for FILE in $(find -s ${INPUT_DIR} -maxdepth 1 -name "${TMPFILE_NAME}-0-*"); do
 		THREAD_ID=${FILE#${INPUT_DIR}/${TMPFILE_NAME}-0-}
 		if [ ${K} -le 1 ]; then
 			PREVIOUS_INTERVALS="null"
 		else
 			PREVIOUS_INTERVALS="${TMPFILE_PATH}-$((${K}-1))-intervals-${THREAD_ID}"
 		fi
 		enumerateKmersThread ${K} ${FILE} ${TMPFILE_PATH}-1-${THREAD_ID} ${TMPFILE_PATH}-2-${THREAD_ID} ${PREVIOUS_INTERVALS} ${TMPFILE_PATH}-${K}-kmers-${THREAD_ID} &
+        PIDS+=($!)
 	done
-	wait
-	sort --parallel=${N_THREADS} -m -t , ${SORT_OPTIONS_KMERS} ${TMPFILE_PATH}-${K}-kmers-* > ${TMPFILE_PATH}-${K}-distinct.txt
+	waitAndCheck PIDS
+	sort --parallel=${N_THREADS} -m -u -t , ${SORT_OPTIONS_KMERS} ${TMPFILE_PATH}-${K}-kmers-* > ${TMPFILE_PATH}-${K}-distinct.txt
 	if [ ! -s ${TMPFILE_PATH}-${K}-distinct.txt ]; then
 		MAX_K=$((${K}-1))
 		break
 	fi
 	echo "Counting ${K}-mer occurrences..."
-	for FILE in $(find -s ${INPUT_DIR} -name "${TMPFILE_NAME}-0-*"); do
+    PIDS=()
+	for FILE in $(find -s ${INPUT_DIR} -maxdepth 1 -name "${TMPFILE_NAME}-0-*"); do
 		THREAD_ID=${FILE#${INPUT_DIR}/${TMPFILE_NAME}-0-}
 		if [ ${K} -le 1 ]; then
 			PREVIOUS_INTERVALS="null"
@@ -128,28 +136,31 @@ for K in $(seq 1 ${MAX_K}); do
 		fi
         rm -f ${TMPFILE_PATH}-${K}-kmers-${THREAD_ID}
 		countKmersThread ${K} ${FILE} ${TMPFILE_PATH}-1-${THREAD_ID} ${TMPFILE_PATH}-2-${THREAD_ID} ${PREVIOUS_INTERVALS} ${TMPFILE_PATH}-${K}-distinct.txt ${TMPFILE_PATH}-${K}-kmers-${THREAD_ID} &
+        PIDS+=($!)
 	done
-	wait
+	waitAndCheck PIDS
     sort --parallel=${N_THREADS} -m -t , ${SORT_OPTIONS_KMERS} ${TMPFILE_PATH}-${K}-kmers-* > ${TMPFILE_PATH}-${K}.txt
     rm -f ${TMPFILE_PATH}-${K}-distinct.txt
 	UNIQUE_KMERS_FILE="${INPUT_DIR}/unique-k${K}.txt"
 	OUTPUT_FILE_HISTOGRAM="${INPUT_DIR}/histogram-k${K}.txt"
 	echo "Finding unique ${K}-mers..."
 	java ${JAVA_RUNTIME_FLAGS} -classpath "${REVANT_BINARIES}:${REVANT_LIBRARIES}" de.mpi_cbg.revant.apps.CompactKmers ${TMPFILE_PATH}-${K}.txt ${K} ${GENOME_LENGTH} ${N_HAPLOTYPES} ${N_READS} ${AVG_READ_LENGTH} ${SPANNING_BPS} ${MIN_ALIGNMENT_LENGTH} 1 ${ALPHABET_FILE} 0 ${MAX_HISTOGRAM_COUNT} ${UNIQUE_KMERS_FILE} ${OUTPUT_FILE_HISTOGRAM}
 	echo "Updating shortest unique intervals file..."
-	for FILE in $(find -s ${INPUT_DIR} -name "${TMPFILE_NAME}-0-*"); do
+    PIDS=()
+	for FILE in $(find -s ${INPUT_DIR} -maxdepth 1 -name "${TMPFILE_NAME}-0-*"); do
 		THREAD_ID=${FILE#${INPUT_DIR}/${TMPFILE_NAME}-0-}
 		if [ ${K} -le 1 ]; then
 			PREVIOUS_INTERVALS="null"
 		else
 			PREVIOUS_INTERVALS="${TMPFILE_PATH}-$((${K}-1))-intervals-${THREAD_ID}"
 		fi
 		intervalsThread ${K} ${FILE} ${TMPFILE_PATH}-1-${THREAD_ID} ${TMPFILE_PATH}-2-${THREAD_ID} ${UNIQUE_KMERS_FILE} ${PREVIOUS_INTERVALS} ${TMPFILE_PATH}-${K}-intervals-${THREAD_ID} &
+        PIDS+=($!)
 	done
-	wait
+	waitAndCheck PIDS
 done
 rm -f ${FINAL_INTERVALS_FILE}
-for FILE in $(find -s ${INPUT_DIR} -name "${TMPFILE_NAME}-${MAX_K}-intervals-*" ); do
+for FILE in $(find -s ${INPUT_DIR} -maxdepth 1 -name "${TMPFILE_NAME}-${MAX_K}-intervals-*" ); do
 	cat ${FILE} >> ${FINAL_INTERVALS_FILE}
 done
 INTERVAL_STATS_FILE="${INPUT_DIR}/unique-intervals-k1-${MAX_K}-stats.txt"
@@ -164,18 +175,17 @@ function tandemsThread() {
 	local LOCAL_READ_LENGTHS_FILE=$3
 	local LOCAL_TANDEMS_FILE=$4
 	java ${JAVA_RUNTIME_FLAGS} -classpath "${REVANT_BINARIES}" de.mpi_cbg.revant.apps.CollectTandems 1 1 ${NONPERIODIC_MODE} ${ALPHABET_FILE} ${LOCAL_TRANSLATED_READS_FILE} ${LOCAL_BOUNDARIES_FILE} ${LOCAL_READ_LENGTHS_FILE} ${REPEAT_LENGTHS_FILE} ${N_REPEATS} ${LOCAL_TANDEMS_FILE}
-	if [ $? -ne 0 ]; then
-		exit
-	fi
 }
 echo "Collecting tandems..."
-for FILE in $(find -s ${INPUT_DIR} -name "${TMPFILE_NAME}-0-*"); do
+PIDS=()
+for FILE in $(find -s ${INPUT_DIR} -maxdepth 1 -name "${TMPFILE_NAME}-0-*"); do
 	THREAD_ID=${FILE#${INPUT_DIR}/${TMPFILE_NAME}-0-}
 	tandemsThread ${FILE} ${TMPFILE_PATH}-1-${THREAD_ID} ${TMPFILE_PATH}-2-${THREAD_ID} ${TMPFILE_PATH}-tandems-${THREAD_ID} &
+    PIDS+=($!)
 done
-wait
+waitAndCheck PIDS
 rm -f ${TANDEMS_FILE}
-for FILE in $(find -s ${INPUT_DIR} -name "${TMPFILE_NAME}-0-*"); do
+for FILE in $(find -s ${INPUT_DIR} -maxdepth 1 -name "${TMPFILE_NAME}-0-*"); do
 	THREAD_ID=${FILE#${INPUT_DIR}/${TMPFILE_NAME}-0-}
 	cat ${TMPFILE_PATH}-tandems-${THREAD_ID} >> ${TANDEMS_FILE}
 done

scripts/6-repeatAlphabet/4-filterAlignments.sh

@@ -41,6 +41,20 @@ TMPFILE_NAME="filterAlignments-tmp"
 TMPFILE_PATH="${INPUT_DIR}/${TMPFILE_NAME}"
 rm -f ${TMPFILE_PATH}*
 
+function waitAndCheck() {
+    local ARRAY_NAME=$1[@]
+
+    local PIDS=(${!ARRAY_NAME})
+    local LAST_THREAD=$((${#PIDS[@]} - 1))
+    N_FAILED="0"
+    for THREAD in $(seq 0 ${LAST_THREAD}); do
+        wait ${PIDS[${THREAD}]} || N_FAILED=$(( ${N_FAILED} + 1 ))
+    done
+    if [ ${N_FAILED} -ne 0 ]; then
+        exit 1
+    fi
+}
+
 echo "Splitting the alignments file..."
 if [ ${PERIODIC_ENDPOINTS_FIXED} -eq 1 ]; then
 	# Reusing the chunks of the read-read alignments file that are already there (we
@@ -79,19 +93,13 @@ ALPHABET_FILE="${INPUT_DIR}/alphabet-cleaned.txt"
 function filterThread() {
 	local ALIGNMENTS_FILE_ID=$1
 	java ${JAVA_RUNTIME_FLAGS} -classpath "${REVANT_BINARIES}" de.mpi_cbg.revant.apps.FilterAlignments ${TMPFILE_PATH}-1-${ALIGNMENTS_FILE_ID}.txt ${N_READS} ${READ_LENGTHS_FILE} ${READ_IDS_FILE} ${READS_TRANSLATED_FILE} ${READS_TRANSLATED_BOUNDARIES} ${FULLY_UNIQUE_FILE} ${N_FULLY_UNIQUE} ${FULLY_CONTAINED_FILE} ${N_FULLY_CONTAINED} ${UNIQUE_INTERVALS_FILE} ${TANDEM_INTERVALS_FILE} ${FILTERING_MODE} ${SUFFIX_PREFIX_MODE} ${BOTH_READS_TANDEM} ${ALPHABET_FILE} ${TMPFILE_PATH}-2-${ALIGNMENTS_FILE_ID} ${TMPFILE_PATH}-3-${ALIGNMENTS_FILE_ID} ${MIN_ALIGNMENT_LENGTH_READ_READ} ${MIN_ALIGNMENT_LENGTH_READ_REPEAT} ${MIN_BLUE_INTERVAL_LENGTH} ${MIN_INTERSECTION_NONREPETITIVE}
-	if [ $? -ne 0 ]; then
-		exit
-	fi
 	if [ ${BROKEN_READS} -eq 1 ]; then
 		NEW2OLD_FILE="${INPUT_DIR}/broken2unbroken.txt"
 		OLD2NEW_FILE="${INPUT_DIR}/unbroken2broken.txt"
 		NREADS_OLD=$(wc -l < "${INPUT_DIR}/reads-ids-unbroken.txt")
 		READ_LENGTHS_FILE_OLD="${INPUT_DIR}/reads-lengths-unbroken.txt"
 		ALIGNMENTS_FILE_OLD="${INPUT_DIR}/breakReads-tmp-1-${ALIGNMENTS_FILE_ID}.txt"
 		java ${JAVA_RUNTIME_FLAGS} -classpath "${REVANT_BINARIES}" de.mpi_cbg.revant.apps.BreakReads5 ${TMPFILE_PATH}-2-${ALIGNMENTS_FILE_ID} ${TMPFILE_PATH}-3-${ALIGNMENTS_FILE_ID} ${TMPFILE_PATH}-1-${ALIGNMENTS_FILE_ID}.txt ${NEW2OLD_FILE} ${N_READS} ${OLD2NEW_FILE} ${NREADS_OLD} ${ALIGNMENTS_FILE_OLD} ${READ_LENGTHS_FILE_OLD} ${TMPFILE_PATH}-4-${ALIGNMENTS_FILE_ID} ${TMPFILE_PATH}-5-${ALIGNMENTS_FILE_ID}
-		if [ $? -ne 0 ]; then
-			exit
-		fi
 	fi
 }
 
@@ -100,10 +108,12 @@ if [ -e ${TMPFILE_PATH}-1-${N_THREADS}.txt ]; then
 else
 	TO=$(( ${N_THREADS} - 1 ))
 fi
+PIDS=()
 for THREAD in $(seq 0 ${TO}); do
 	filterThread ${THREAD} &
+    PIDS+=($!)
 done
-wait
+waitAndCheck PIDS
 echo "Alignments filtered successfully"
 OUTPUT_BITVECTOR="${ALIGNMENTS_FILE}.mode${FILTERING_MODE}.bitvector"
 OUTPUT_TANDEM_BITVECTOR="${ALIGNMENTS_FILE}.tandem.bitvector"