New unit tests for sort order enforcement, non-existant file. Also added...

New unit tests for sort order enforcement, non-existant file. Also added performance test for file input and compression types.

test/intersect/chromsOutOfOrder.bed

+chr1	100	200
+chr1	150	250
+chr2	100	200
+chr1	200	300

test/intersect/new_test-intersect.sh

@@ -553,4 +553,39 @@ check obs aWithHeaderVsB.txt
 rm obs
 
 
+###########################################################
+#  Test enforcement of sort order when using -sorted option.
+#  Show that detect chrom "jumping", i.e. chr1, chr2, then
+#  back to chr1
+############################################################
+echo "    intersect.new.t48...\c"
+echo "Error: Sorted input specified" > exp
+$BT intersect -a chromsOutOfOrder.bed -b b.bed -sorted 2>&1 > /dev/null | grep "Error: Sorted input specified, " | cut -f1 --delimiter=',' > obs
+check obs exp
+rm obs exp
+
+###########################################################
+#  Test enforcement of sort order when using -sorted option.
+#  Show that detect chrom "jumping", i.e. chr1, chr2, then
+#  back to chr1
+############################################################
+echo "    intersect.new.t49...\c"
+echo "Error: Sorted input specified" > exp
+$BT intersect -a recordsOutOfOrder.bed -b b.bed -sorted 2>&1 > /dev/null | grep "Error: Sorted input specified, " | cut -f1 --delimiter=',' > obs
+check obs exp
+rm obs exp
+
+###########################################################
+#  Test that we throw an error for non-existant files
+############################################################
+echo "    intersect.new.t50...\c"
+echo "Error: Unable to open file nonExistantFile.bed. Exiting." > exp
+$BT intersect -a nonExistantFile.bed -b b.bed -sorted 2>&1 > /dev/null | cat - >obs
+check obs exp
+rm obs exp
+
+
+
+
+
 

test/intersect/performanceTest.sh

+#################################################################
+# 
+#  PERFORMANCE TESTS FOR VARIOUS INPUT METHODS.
+#
+#  We'll test uncompressed data, gzip, bgzip, and Bam files.
+#  Each will be tried as a file, and as the 3 types of stdin:
+#  redirects, pipes, and fifos.
+#  
+#  We'll run each one twice in a row to check for improvement 
+#  due to a cache warm up.
+#
+#################################################################
+
+
+BT=${BT-../../bin/bedtools}
+
+
+#################################################################
+#  Start by generating data, if desired
+#  
+#################################################################
+if true; then
+  echo "generating data..."
+  mkdir perfData
+  cd perfData
+  ../$BT random -l 1000 -n 20000000 -g ../human.hg19.genome | sort -k1,1 -k2,2n > a10M.bed 
+  ../$BT random -l 1000 -n 10000000 -g ../human.hg19.genome | sort -k1,1 -k2,2n > b10M.bed 
+  cp a10M.bed a10M_gzipped.bed
+  gzip a10M_gzipped.bed
+  cp a10M.bed a10M_bgzipped.bed
+  bgzip a10M_bgzipped.bed
+  ../$BT bedtobam -i a10M.bed -g ../human.hg19.genome > a10M.bam
+  cd ..
+fi
+
+###################################################################
+#  Begin Tests
+###################################################################
+echo -e "Test 1 of 16...."
+echo "Test 1: Intersect a10M, ten million records, uncompressed from file with b10M" > runLog.txt
+runit $BT intersect -a perfData/a10M.bed -b perfData/b10M.bed -sorted 2>&1 >/dev/null | grep -e "user" -e maxrss >> runLog.txt
+echo -e "\nRe-do test 1 for possible cache speed up." >> runLog.txt
+runit $BT intersect -a perfData/a10M.bed -b perfData/b10M.bed -sorted 2>&1 >/dev/null | grep -e "user" -e maxrss >> runLog.txt
+
+echo -e "Test 2 of 16...."
+echo -e "\n\nTest 2: Intersect a10M, ten million records, gzipped from file with b10M" >> runLog.txt
+runit $BT intersect -a perfData/a10M_gzipped.bed.gz -b perfData/b10M.bed -sorted 2>&1 >/dev/null | grep -e "user" -e maxrss >> runLog.txt
+echo -e "\nRe-do test 2 for possible cache speed up." >> runLog.txt
+runit $BT intersect -a perfData/a10M_gzipped.bed.gz -b perfData/b10M.bed -sorted 2>&1 >/dev/null | grep -e "user" -e maxrss >> runLog.txt
+
+echo -e "Test 3 of 16...."
+echo -e "\n\nTest 3: Intersect a10M, ten million records, bgzipped from file with b10M" >> runLog.txt
+runit $BT intersect -a perfData/a10M_bgzipped.bed.gz -b perfData/b10M.bed -sorted 2>&1 >/dev/null | grep -e "user" -e maxrss >> runLog.txt
+echo -e "\nRe-do test 3 for possible cache speed up." >> runLog.txt
+runit $BT intersect -a perfData/a10M_bgzipped.bed.gz -b perfData/b10M.bed -sorted 2>&1 >/dev/null | grep -e "user" -e maxrss >> runLog.txt
+
+echo -e "Test 4 of 16...."
+echo -e "\n\nTest 4: Intersect a10M, ten million records, bam from file with b10M" >> runLog.txt
+runit $BT intersect -a perfData/a10M.bam -b perfData/b10M.bed -sorted 2>&1 >/dev/null | grep -e "user" -e maxrss >> runLog.txt
+echo -e "\nRe-do test 4 for possible cache speed up." >> runLog.txt
+runit $BT intersect -a perfData/a10M.bam -b perfData/b10M.bed -sorted 2>&1 >/dev/null | grep -e "user" -e maxrss >> runLog.txt
+
+
+echo -e "Test 5 of 16...."
+echo -e "\n\nTest 5: Intersect a10M, ten million records, uncompressed from redirect with b10M" >> runLog.txt
+runit $BT intersect -a - -b perfData/b10M.bed -sorted < perfData/a10M.bed 2>&1 >/dev/null | grep -e "user" -e maxrss >> runLog.txt
+echo -e "\nRe-do test 5 for possible cache speed up." >> runLog.txt
+runit $BT intersect -a - -b perfData/b10M.bed -sorted < perfData/a10M.bed 2>&1 >/dev/null | grep -e "user" -e maxrss >> runLog.txt
+
+echo -e "Test 6 of 16...."
+echo -e "\n\nTest 6: Intersect a10M, ten million records, gzipped from redirect with b10M" >> runLog.txt
+runit $BT intersect -a - -b perfData/b10M.bed -sorted < perfData/a10M_gzipped.bed.gz 2>&1 >/dev/null | grep -e "user" -e maxrss >> runLog.txt
+echo -e "\nRe-do test 6 for possible cache speed up." >> runLog.txt
+runit $BT intersect -a - -b perfData/b10M.bed -sorted < perfData/a10M_gzipped.bed.gz 2>&1 >/dev/null | grep -e "user" -e maxrss >> runLog.txt
+
+echo -e "Test 7 of 16...."
+echo -e "\n\nTest 7: Intersect a10M, ten million records, bgzipped from redirect with b10M" >> runLog.txt
+runit $BT intersect -a - -b perfData/b10M.bed -sorted < perfData/a10M_bgzipped.bed.gz 2>&1 >/dev/null | grep -e "user" -e maxrss >> runLog.txt
+echo -e "\nRe-do test 7 for possible cache speed up." >> runLog.txt
+runit $BT intersect -a - -b perfData/b10M.bed -sorted < perfData/a10M_bgzipped.bed.gz 2>&1 >/dev/null | grep -e "user" -e maxrss >> runLog.txt
+
+echo -e "Test 8 of 16...."
+echo -e "\n\nTest 8: Intersect a10M, ten million records, bam from redirect with b10M" >> runLog.txt
+runit $BT intersect -a - -b perfData/b10M.bed -sorted < perfData/a10M.bam 2>&1 >/dev/null | grep -e "user" -e maxrss >> runLog.txt
+echo -e "\nRe-do test 8 for possible cache speed up." >> runLog.txt
+runit $BT intersect -a - -b perfData/b10M.bed -sorted < perfData/a10M.bam 2>&1 >/dev/null | grep -e "user" -e maxrss >> runLog.txt
+
+echo -e "Test 9 of 16...."
+echo -e "\n\nTest 9: Intersect a10M, ten million records, uncompressed from pipe with b10M" >> runLog.txt
+cat perfData/a10M.bed | runit $BT intersect -a - -b perfData/b10M.bed -sorted  2>&1 >/dev/null | grep -e "user" -e maxrss >> runLog.txt
+echo -e "\nRe-do test 9 for possible cache speed up." >> runLog.txt
+cat perfData/a10M.bed | runit $BT intersect -a - -b perfData/b10M.bed -sorted  2>&1 >/dev/null | grep -e "user" -e maxrss >> runLog.txt
+
+echo -e "Test 10 of 16...."
+echo -e "\n\nTest 10: Intersect a10M, ten million records, gzip from pipe with b10M" >> runLog.txt
+cat perfData/a10M_gzipped.bed.gz | runit $BT intersect -a - -b perfData/b10M.bed -sorted  2>&1 >/dev/null | grep -e "user" -e maxrss >> runLog.txt
+echo -e "\nRe-do test 10 for possible cache speed up." >> runLog.txt
+cat perfData/a10M_gzipped.bed.gz | runit $BT intersect -a - -b perfData/b10M.bed -sorted  2>&1 >/dev/null | grep -e "user" -e maxrss >> runLog.txt
+
+echo -e "Test 11 of 16...."
+echo -e "\n\nTest 11: Intersect a10M, ten million records, bgzip from pipe with b10M" >> runLog.txt
+cat perfData/a10M_bgzipped.bed.gz | runit $BT intersect -a - -b perfData/b10M.bed -sorted  2>&1 >/dev/null | grep -e "user" -e maxrss >> runLog.txt
+echo -e "\nRe-do test 11 for possible cache speed up." >> runLog.txt
+cat perfData/a10M_bgzipped.bed.gz | runit $BT intersect -a - -b perfData/b10M.bed -sorted  2>&1 >/dev/null | grep -e "user" -e maxrss >> runLog.txt
+
+echo -e "Test 12 of 16...."
+echo -e "\n\nTest 12: Intersect a10M, ten million records, bam from pipe with b10M" >> runLog.txt
+cat perfData/a10M.bam | runit $BT intersect -a - -b perfData/b10M.bed -sorted  2>&1 >/dev/null | grep -e "user" -e maxrss >> runLog.txt
+echo -e "\nRe-do test 12 for possible cache speed up." >> runLog.txt
+cat perfData/a10M.bam | runit $BT intersect -a - -b perfData/b10M.bed -sorted  2>&1 >/dev/null | grep -e "user" -e maxrss >> runLog.txt
+
+echo -e "Test 13 of 16...."
+echo -e "\n\nTest 13: Intersect a10M, ten million records, uncompressed from fifo with b10M" >> runLog.txt
+runit $BT intersect -a <(cat perfData/a10M.bed) -b perfData/b10M.bed -sorted  2>&1 >/dev/null | grep -e "user" -e maxrss >> runLog.txt
+echo -e "\nRe-do test 13 for possible cache speed up." >> runLog.txt
+runit $BT intersect -a <(cat perfData/a10M.bed) -b perfData/b10M.bed -sorted  2>&1 >/dev/null | grep -e "user" -e maxrss >> runLog.txt
+
+echo -e "Test 14 of 16...."
+echo -e "\n\nTest 14: Intersect a10M, ten million records, gzipped from fifo with b10M" >> runLog.txt
+runit $BT intersect -a <(cat perfData/a10M_gzipped.bed.gz) -b perfData/b10M.bed -sorted  2>&1 >/dev/null | grep -e "user" -e maxrss >> runLog.txt
+echo -e "\nRe-do test 14 for possible cache speed up." >> runLog.txt
+runit $BT intersect -a <(cat perfData/a10M_gzipped.bed.gz) -b perfData/b10M.bed -sorted  2>&1 >/dev/null | grep -e "user" -e maxrss >> runLog.txt
+
+echo -e "Test 15 of 16...."
+echo -e "\n\nTest 15: Intersect a10M, ten million records, bgzipped from fifo with b10M" >> runLog.txt
+runit $BT intersect -a <(cat perfData/a10M_bgzipped.bed.gz) -b perfData/b10M.bed -sorted  2>&1 >/dev/null | grep -e "user" -e maxrss >> runLog.txt
+echo -e "\nRe-do test 15 for possible cache speed up." >> runLog.txt
+runit $BT intersect -a <(cat perfData/a10M_bgzipped.bed.gz) -b perfData/b10M.bed -sorted  2>&1 >/dev/null | grep -e "user" -e maxrss >> runLog.txt
+
+echo -e "Test 16 of 16...."
+echo -e "\n\nTest 16: Intersect a10M, ten million records, bam from fifo with b10M" >> runLog.txt
+runit $BT intersect -a <(cat perfData/a10M.bam) -b perfData/b10M.bed -sorted  2>&1 >/dev/null | grep -e "user" -e maxrss >> runLog.txt
+echo -e "\nRe-do test 16 for possible cache speed up." >> runLog.txt
+runit $BT intersect -a <(cat perfData/a10M.bam) -b perfData/b10M.bed -sorted  2>&1 >/dev/null | grep -e "user" -e maxrss >> runLog.txt
+
+
+echo "Tests completed."
+rm -rf perfData

test/intersect/recordsOutOfOrder.bed

+chr1	20	30
+chr1	40	50
+chr1	15	60
+chr1	70	80