updated PSL unit tests

applications/bed/conversion/src/tests/psl/sample.expected.headerless.split.bed

@@ -0,0 +1,35 @@
+chr1	30571100	30571135	foo	50	-	3	0	0	0	0	0	0	0	15	50	249250621	1	35,	0,	30571100,
+chr1	69592160	69592195	foo	50	-	3	1	0	0	0	0	0	0	15	50	249250621	1	35,	0,	69592160,
+chr1	107200050	107200100	foo	50	+	5	0	0	0	0	0	0	0	0	50	249250621	1	50,	0,	107200050,
+chr11	12618347	12618389	foo	50	+	3	3	0	0	0	0	0	0	8	50	135006516	1	42,	8,	12618347,
+chr11	32933028	32933032	foo	50	+	3	0	0	0	1	1	0	0	8	44	135006516	2	4,31,	8,13,	32933028,32933032,
+chr11	32933032	32933063	foo	50	+	3	0	0	0	1	1	0	0	8	44	135006516	2	4,31,	8,13,	32933028,32933032,
+chr11	80116421	80116457	foo	50	+	3	1	0	0	0	0	0	0	14	50	135006516	1	36,	14,	80116421,
+chr11	133952291	133952327	foo	50	+	3	2	0	0	0	0	0	0	14	50	135006516	1	36,	14,	133952291,
+chr13	99729482	99729523	foo	50	+	3	2	0	0	0	0	0	0	8	49	115169878	1	41,	8,	99729482,
+chr13	111391852	111391888	foo	50	+	3	2	0	0	0	0	0	0	14	50	115169878	1	36,	14,	111391852,
+chr16	8149657	8149694	foo	50	+	3	1	0	0	0	0	0	0	13	50	90354753	1	37,	13,	8149657,
+chr19	28603245	28603281	foo	50	-	3	2	0	0	0	0	0	0	14	50	59128983	1	36,	0,	28603245,
+chr2	44076681	44076716	foo	50	-	3	0	0	0	0	0	0	0	15	50	243199373	1	35,	0,	44076681,
+chr2	138092330	138092362	foo	50	+	3	1	0	0	0	0	0	0	18	50	243199373	1	32,	18,	138092330,
+chr2	159266272	159266302	foo	50	+	3	0	0	0	0	0	0	0	14	44	243199373	1	30,	14,	159266272,
+chr2	213333021	213333057	foo	50	+	3	1	0	0	0	0	0	0	14	50	243199373	1	36,	14,	213333021,
+chr2	225564373	225564408	foo	50	+	3	0	0	0	0	0	0	0	15	50	243199373	1	35,	15,	225564373,
+chr21	16689364	16689402	foo	50	+	3	1	0	0	0	0	0	0	12	50	48129895	1	38,	12,	16689364,
+chr3	42509214	42509250	foo	50	+	3	2	0	0	0	0	0	0	14	50	198022430	1	36,	14,	42509214,
+chr3	150940163	150940199	foo	50	+	3	1	0	0	0	0	0	0	14	50	198022430	1	36,	14,	150940163,
+chr3	151443333	151443371	foo	50	-	3	1	0	0	0	0	0	0	11	49	198022430	1	38,	1,	151443333,
+chr3	192870971	192871001	foo	50	+	3	0	0	0	0	0	0	0	20	50	198022430	1	30,	20,	192870971,
+chr4	21041798	21041834	foo	50	-	3	3	0	0	0	0	0	0	14	50	191154276	1	36,	0,	21041798,
+chr4	82259023	82259059	foo	50	+	3	1	0	0	0	0	0	0	14	50	191154276	1	36,	14,	82259023,
+chr5	119897315	119897346	foo	50	+	3	0	0	0	0	0	0	0	13	44	180915260	1	31,	13,	119897315,
+chr5	123254725	123254755	foo	50	+	3	0	0	0	0	0	0	0	14	44	180915260	1	30,	14,	123254725,
+chr6	9392527	9392561	foo	50	-	3	0	0	0	0	0	0	0	7	41	171115067	1	34,	9,	9392527,
+chr6	93161871	93161901	foo	50	+	3	0	0	0	0	0	0	0	14	44	171115067	1	30,	14,	93161871,
+chr6	127685756	127685786	foo	50	+	3	0	0	0	0	0	0	0	14	44	171115067	1	30,	14,	127685756,
+chr8	102334624	102334661	foo	50	-	3	1	0	0	0	0	0	0	13	50	146364022	1	37,	0,	102334624,
+chr8	131572122	131572159	foo	50	+	3	2	0	0	0	0	0	0	13	50	146364022	1	37,	13,	131572122,
+chrX	40535836	40535871	foo	50	+	3	0	0	0	0	0	0	0	15	50	155270560	1	35,	15,	40535836,
+chrX	43068135	43068170	foo	50	+	3	2	0	0	0	0	0	0	14	49	155270560	1	35,	14,	43068135,
+chrX	68019028	68019064	foo	50	+	3	2	0	0	0	0	0	0	14	50	155270560	1	36,	14,	68019028,
+chrX	101602211	101602248	foo	50	-	3	1	0	0	0	0	0	0	13	50	155270560	1	37,	0,	101602211,

applications/bed/conversion/src/tests/psl/test.sh

@@ -20,6 +20,14 @@ ${psl2bed_bin} < ${sample_psl_fn} > ${observed_sorted_bed_fn} 2> /dev/null
 diff -q ${expected_sorted_bed_fn} ${observed_sorted_bed_fn}
 rm -f ${observed_sorted_bed_fn}
 
+echo "[psl2bed] testing headerless split output..."
+sample_psl_fn="sample.headerless.psl"
+expected_sorted_bed_fn="sample.expected.headerless.split.bed"
+observed_sorted_bed_fn="$(mktemp /tmp/XXXXXX)"
+${psl2bed_bin} --split < ${sample_psl_fn} > ${observed_sorted_bed_fn} 2> /dev/null
+diff -q ${expected_sorted_bed_fn} ${observed_sorted_bed_fn}
+rm -f ${observed_sorted_bed_fn}
+
 echo "[psl2bed] testing headered starch (bzip2) output..."
 sample_psl_fn="sample.headered.psl"
 expected_starch_fn="sample.expected.headered.starch"
@@ -44,6 +52,14 @@ ${psl2starch_bin} < ${sample_psl_fn} > ${observed_starch_fn} 2> /dev/null
 diff -q <(unstarch ${expected_starch_fn}) <(unstarch ${observed_starch_fn})
 rm -f ${observed_starch_fn}
 
+echo "[psl2bed] testing headerless split starch (bzip2) output..."
+sample_psl_fn="sample.headerless.psl"
+expected_starch_fn="sample.expected.headerless.split.starch"
+observed_starch_fn="$(mktemp /tmp/XXXXXX)"
+${psl2starch_bin} --split < ${sample_psl_fn} > ${observed_starch_fn} 2> /dev/null
+diff -q <(unstarch ${expected_starch_fn}) <(unstarch ${observed_starch_fn})
+rm -f ${observed_starch_fn}
+
 echo "[psl2bed] testing headerless starch (gzip) output..."
 sample_psl_fn="sample.headerless.psl"
 expected_starch_fn="sample.expected.headerless.gzip.starch"
@@ -52,4 +68,12 @@ ${psl2starch_bin} --starch-gzip < ${sample_psl_fn} > ${observed_starch_fn} 2> /d
 diff -q <(unstarch ${expected_starch_fn}) <(unstarch ${observed_starch_fn})
 rm -f ${observed_starch_fn}
 
+echo "[psl2bed] testing headerless split starch (gzip) output..."
+sample_psl_fn="sample.headerless.psl"
+expected_starch_fn="sample.expected.headerless.split.gzip.starch"
+observed_starch_fn="$(mktemp /tmp/XXXXXX)"
+${psl2starch_bin} --starch-gzip --split < ${sample_psl_fn} > ${observed_starch_fn} 2> /dev/null
+diff -q <(unstarch ${expected_starch_fn}) <(unstarch ${observed_starch_fn})
+rm -f ${observed_starch_fn}
+
 echo "[psl2bed] tests complete!"

packaging/os_x/BEDOPS.pkgproj

@@ -5231,7 +5231,7 @@
 						<key>LANGUAGE</key>
 						<string>English</string>
 						<key>VALUE</key>
-						<string>BEDOPS 2.4.6</string>
+						<string>BEDOPS 2.4.7</string>
 					</dict>
 				</array>
 			</dict>
@@ -5494,7 +5494,7 @@
 				</dict>
 			</array>
 			<key>NAME</key>
-			<string>BEDOPS 2.4.6</string>
+			<string>BEDOPS 2.4.7</string>
 		</dict>
 	</dict>
 	<key>TYPE</key>