details: http://www.bx.psu.edu/hg/galaxy/rev/0da612f8a78e changeset: 1587:0da612f8a78e user: guru date: Thu Oct 30 16:03:11 2008 -0400 description: Added new functional tests to all gops tools using BitsetSafeReaderWrapper. These tests check cases where datasets have the chr,start and end values in non-standard columns. 12 file(s) affected in this change: test-data/2_mod.bed test-data/gops_complement_out_diffCols.dat test-data/gops_coverage_out_diffCols.interval test-data/gops_intersect_diffCols.bed test-data/gops_intersect_p_diffCols.bed test-data/gops_merge_diffCols.dat test-data/gops_subtract_diffCols.dat tools/new_operations/complement.xml tools/new_operations/coverage.xml tools/new_operations/intersect.xml tools/new_operations/merge.xml tools/new_operations/subtract.xml diffs (530 lines): diff -r 4e44d29377e3 -r 0da612f8a78e test-data/2_mod.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/2_mod.bed Thu Oct 30 16:03:11 2008 -0400 @@ -0,0 +1,69 @@ +#chr name score strand start end +chr1 NM_005997_cds_0_0_chr1_147962193_r 0 - 147962192 147962580 +chr1 BC007833_cds_0_0_chr1_147984546_f 0 + 147984545 147984630 +chr1 AJ011123_cds_0_0_chr1_148078401_r 0 - 148078400 148078582 +chr1 NM_002796_cds_0_0_chr1_148185137_f 0 + 148185136 148185276 +chr10 AY029205_cds_0_0_chr10_55251624_r 0 - 55251623 55253124 +chr11 AK057832_cds_0_0_chr11_116124408_r 0 - 116124407 116124501 +chr11 NM_000040_cds_1_0_chr11_116206509_f 0 + 116206508 116206563 +chr11 BC005380_cds_0_0_chr11_116211734_r 0 - 116211733 116212337 +chr11 AY358331_cds_0_0_chr11_130745912_f 0 + 130745911 130745993 +chr12 NM_052885_cds_0_0_chr12_38440095_r 0 - 38440094 38440321 +chr12 AY792511_cds_0_0_chr12_38905201_f 0 + 38905200 38905351 +chr13 NM_207440_cds_1_0_chr13_112381695_f 0 + 112381694 112381953 +chr13 NM_032116_cds_0_0_chr13_29680677_r 0 - 29680676 29680875 +chr14 U88895_cds_0_0_chr14_98521865_f 0 + 98521864 98521922 +chr14 NM_022898_cds_0_0_chr14_98710241_r 0 - 98710240 98712285 +chr15 BX537418_cds_0_0_chr15_41486873_r 0 - 41486872 41487060 +chr15 AK223365_cds_0_0_chr15_41673709_f 0 + 41673708 41673857 +chr15 NM_153700_cds_0_0_chr15_41679162_r 0 - 41679161 41679250 +chr15 AK223365_cds_0_0_chr15_41773541_f 0 + 41773540 41773689 +chr16 NM_005332_cds_0_0_chr16_142909_f 0 + 142908 143003 +chr16 BC065198_cds_0_0_chr16_179198_r 0 - 179197 179339 +chr16 AK057165_cds_2_0_chr16_244414_f 0 + 244413 244681 +chr16 AB016929_cds_0_0_chr16_259269_r 0 - 259268 259383 +chr18 NM_001792_cds_0_0_chr18_23786115_r 0 - 23786114 23786321 +chr18 NM_012397_cds_1_0_chr18_59406882_f 0 + 59406881 59407046 +chr18 AB046400_cds_0_0_chr18_59455933_r 0 - 59455932 59456337 +chr18 AY792326_cds_0_0_chr18_59528408_f 0 + 59528407 59528575 +chr19 BC013995_cds_1_0_chr19_59068596_f 0 + 59068595 59069564 +chr19 NM_198481_cds_0_0_chr19_59236027_r 0 - 59236026 59236146 +chr19 NM_004542_cds_0_0_chr19_59297999_f 0 + 59297998 59298008 +chr19 AK128544_cds_3_0_chr19_59318206_r 0 - 59318205 59318718 +chr2 NM_006773_cds_0_0_chr2_118288584_f 0 + 118288583 118288668 +chr2 BC005078_cds_0_0_chr2_118390396_r 0 - 118390395 118390500 +chr2 AY125465_cds_0_0_chr2_220108690_f 0 + 220108689 220109267 +chr2 NM_024536_cds_0_0_chr2_220229610_r 0 - 220229609 220230869 +chr20 NM_181466_cds_0_0_chr20_33330414_r 0 - 33330413 33330423 +chr20 BC085019_cds_1_0_chr20_33485371_f 0 + 33485370 33486123 +chr20 NM_000557_cds_1_0_chr20_33488492_r 0 - 33488491 33489122 +chr20 AF022655_cds_1_0_chr20_33513607_f 0 + 33513606 33513792 +chr21 NM_032910_cds_0_0_chr21_32687403_f 0 + 32687402 32687588 +chr21 NM_018277_cds_3_0_chr21_32869642_r 0 - 32869641 32870022 +chr21 NM_005806_cds_1_0_chr21_33321041_f 0 + 33321040 33322012 +chr21 AK129657_cds_0_0_chr21_33728359_r 0 - 33728358 33728724 +chr22 NM_004147_cds_0_0_chr22_30120224_f 0 + 30120223 30120265 +chr22 BC032941_cds_0_0_chr22_30160420_r 0 - 30160419 30160661 +chr22 NM_001007467_cds_1_0_chr22_30228825_f 0 + 30228824 30228916 +chr22 CR456540_cds_0_0_chr22_30340152_r 0 - 30340151 30340376 +chr5 AF099740_cds_11_0_chr5_131311207_r 0 - 131311206 131311254 +chr5 NM_000588_cds_0_0_chr5_131424299_f 0 + 131424298 131424460 +chr5 BC035813_cds_0_0_chr5_131556602_r 0 - 131556601 131556672 +chr5 BC003096_cds_0_0_chr5_131621327_f 0 + 131621326 131621419 +chr6 NM_007214_cds_0_0_chr6_108299601_r 0 - 108299600 108299744 +chr6 NM_003269_cds_0_0_chr6_108594663_f 0 + 108594662 108594687 +chr6 NM_003795_cds_0_0_chr6_108640046_r 0 - 108640045 108640151 +chr6 NM_145315_cds_0_0_chr6_108722977_f 0 + 108722976 108723115 +chr7 AF467257_cds_1_0_chr7_113660518_f 0 + 113660517 113660685 +chr7 NM_003391_cds_0_0_chr7_116512160_r 0 - 116512159 116512389 +chr7 NM_000492_cds_0_0_chr7_116714100_f 0 + 116714099 116714152 +chr7 AF377960_cds_0_0_chr7_116945542_r 0 - 116945541 116945787 +chr8 NM_000127_cds_0_0_chr8_118881132_r 0 - 118881131 118881317 +chr9 BC051300_cds_0_0_chr9_128764157_f 0 + 128764156 128764189 +chr9 NM_014908_cds_0_0_chr9_128787520_r 0 - 128787519 128789136 +chr9 NM_015354_cds_0_0_chr9_128789553_f 0 + 128789552 128789584 +chr9 AB058751_cds_0_0_chr9_128850517_r 0 - 128850516 128850624 +chrX NM_001167_cds_1_0_chrX_122745048_f 0 + 122745047 122745924 +chrX NM_000425_cds_0_0_chrX_152648965_r 0 - 152648964 152649196 +chrX AF101728_cds_0_0_chrX_152691447_f 0 + 152691446 152691471 +chrX BC052303_cds_0_0_chrX_152694030_r 0 - 152694029 152694263 diff -r 4e44d29377e3 -r 0da612f8a78e test-data/gops_complement_out_diffCols.dat --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gops_complement_out_diffCols.dat Thu Oct 30 16:03:11 2008 -0400 @@ -0,0 +1,88 @@ +chr7 . . + 0 113660517 +chr7 . . + 113660685 116512159 +chr7 . . + 116512389 116714099 +chr7 . . + 116714152 116945541 +chr7 . . + 116945787 536870912 +chr6 . . + 0 108299600 +chr6 . . + 108299744 108594662 +chr6 . . + 108594687 108640045 +chr6 . . + 108640151 108722976 +chr6 . . + 108723115 536870912 +chr5 . . + 0 131311206 +chr5 . . + 131311254 131424298 +chr5 . . + 131424460 131556601 +chr5 . . + 131556672 131621326 +chr5 . . + 131621419 536870912 +chrX . . + 0 122745047 +chrX . . + 122745924 152648964 +chrX . . + 152649196 152691446 +chrX . . + 152691471 152694029 +chrX . . + 152694263 536870912 +chr2 . . + 0 118288583 +chr2 . . + 118288668 118390395 +chr2 . . + 118390500 220108689 +chr2 . . + 220109267 220229609 +chr2 . . + 220230869 536870912 +chr1 . . + 0 147962192 +chr1 . . + 147962580 147984545 +chr1 . . + 147984630 148078400 +chr1 . . + 148078582 148185136 +chr1 . . + 148185276 536870912 +chr21 . . + 0 32687402 +chr21 . . + 32687588 32869641 +chr21 . . + 32870022 33321040 +chr21 . . + 33322012 33728358 +chr21 . . + 33728724 536870912 +chr9 . . + 0 128764156 +chr9 . . + 128764189 128787519 +chr9 . . + 128789136 128789552 +chr9 . . + 128789584 128850516 +chr9 . . + 128850624 536870912 +chr8 . . + 0 118881131 +chr8 . . + 118881317 536870912 +chr13 . . + 0 29680676 +chr13 . . + 29680875 112381694 +chr13 . . + 112381953 536870912 +chr12 . . + 0 38440094 +chr12 . . + 38440321 38905200 +chr12 . . + 38905351 536870912 +chr11 . . + 0 116124407 +chr11 . . + 116124501 116206508 +chr11 . . + 116206563 116211733 +chr11 . . + 116212337 130745911 +chr11 . . + 130745993 536870912 +chr10 . . + 0 55251623 +chr10 . . + 55253124 536870912 +chr22 . . + 0 30120223 +chr22 . . + 30120265 30160419 +chr22 . . + 30160661 30228824 +chr22 . . + 30228916 30340151 +chr22 . . + 30340376 536870912 +chr16 . . + 0 142908 +chr16 . . + 143003 179197 +chr16 . . + 179339 244413 +chr16 . . + 244681 259268 +chr16 . . + 259383 536870912 +chr15 . . + 0 41486872 +chr15 . . + 41487060 41673708 +chr15 . . + 41673857 41679161 +chr15 . . + 41679250 41773540 +chr15 . . + 41773689 536870912 +chr14 . . + 0 98521864 +chr14 . . + 98521922 98710240 +chr14 . . + 98712285 536870912 +chr20 . . + 0 33330413 +chr20 . . + 33330423 33485370 +chr20 . . + 33486123 33488491 +chr20 . . + 33489122 33513606 +chr20 . . + 33513792 536870912 +chr19 . . + 0 59068595 +chr19 . . + 59069564 59236026 +chr19 . . + 59236146 59297998 +chr19 . . + 59298008 59318205 +chr19 . . + 59318718 536870912 +chr18 . . + 0 23786114 +chr18 . . + 23786321 59406881 +chr18 . . + 59407046 59455932 +chr18 . . + 59456337 59528407 +chr18 . . + 59528575 536870912 diff -r 4e44d29377e3 -r 0da612f8a78e test-data/gops_coverage_out_diffCols.interval --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gops_coverage_out_diffCols.interval Thu Oct 30 16:03:11 2008 -0400 @@ -0,0 +1,65 @@ +chr1 147962192 147962580 CCDS989.1_cds_0_0_chr1_147962193_r 0 - 388 1.0 +chr1 147984545 147984630 CCDS990.1_cds_0_0_chr1_147984546_f 0 + 85 1.0 +chr1 148078400 148078582 CCDS993.1_cds_0_0_chr1_148078401_r 0 - 182 1.0 +chr1 148185136 148185276 CCDS996.1_cds_0_0_chr1_148185137_f 0 + 140 1.0 +chr10 55251623 55253124 CCDS7248.1_cds_0_0_chr10_55251624_r 0 - 1501 1.0 +chr11 116124407 116124501 CCDS8374.1_cds_0_0_chr11_116124408_r 0 - 94 1.0 +chr11 116206508 116206563 CCDS8377.1_cds_0_0_chr11_116206509_f 0 + 55 1.0 +chr11 116211733 116212337 CCDS8378.1_cds_0_0_chr11_116211734_r 0 - 604 1.0 +chr11 1812377 1812407 CCDS7726.1_cds_0_0_chr11_1812378_f 0 + 0 0.0 +chr12 38440094 38440321 CCDS8736.1_cds_0_0_chr12_38440095_r 0 - 227 1.0 +chr13 112381694 112381953 CCDS9526.1_cds_0_0_chr13_112381695_f 0 + 259 1.0 +chr14 98710240 98712285 CCDS9949.1_cds_0_0_chr14_98710241_r 0 - 2045 1.0 +chr15 41486872 41487060 CCDS10096.1_cds_0_0_chr15_41486873_r 0 - 188 1.0 +chr15 41673708 41673857 CCDS10097.1_cds_0_0_chr15_41673709_f 0 + 149 1.0 +chr15 41679161 41679250 CCDS10098.1_cds_0_0_chr15_41679162_r 0 - 89 1.0 +chr15 41826029 41826196 CCDS10101.1_cds_0_0_chr15_41826030_f 0 + 0 0.0 +chr16 142908 143003 CCDS10397.1_cds_0_0_chr16_142909_f 0 + 95 1.0 +chr16 179963 180135 CCDS10401.1_cds_0_0_chr16_179964_r 0 - 0 0.0 +chr16 244413 244681 CCDS10402.1_cds_0_0_chr16_244414_f 0 + 268 1.0 +chr16 259268 259383 CCDS10403.1_cds_0_0_chr16_259269_r 0 - 115 1.0 +chr18 23786114 23786321 CCDS11891.1_cds_0_0_chr18_23786115_r 0 - 207 1.0 +chr18 59406881 59407046 CCDS11985.1_cds_0_0_chr18_59406882_f 0 + 165 1.0 +chr18 59455932 59456337 CCDS11986.1_cds_0_0_chr18_59455933_r 0 - 405 1.0 +chr18 59600586 59600754 CCDS11988.1_cds_0_0_chr18_59600587_f 0 + 0 0.0 +chr19 59068595 59069564 CCDS12866.1_cds_0_0_chr19_59068596_f 0 + 969 1.0 +chr19 59236026 59236146 CCDS12872.1_cds_0_0_chr19_59236027_r 0 - 120 1.0 +chr19 59297998 59298008 CCDS12877.1_cds_0_0_chr19_59297999_f 0 + 10 1.0 +chr19 59302168 59302288 CCDS12878.1_cds_0_0_chr19_59302169_r 0 - 0 0.0 +chr2 118288583 118288668 CCDS2120.1_cds_0_0_chr2_118288584_f 0 + 85 1.0 +chr2 118394148 118394202 CCDS2121.1_cds_0_0_chr2_118394149_r 0 - 0 0.0 +chr2 220190202 220190242 CCDS2441.1_cds_0_0_chr2_220190203_f 0 + 0 0.0 +chr2 220229609 220230869 CCDS2443.1_cds_0_0_chr2_220229610_r 0 - 1260 1.0 +chr20 33330413 33330423 CCDS13249.1_cds_0_0_chr20_33330414_r 0 - 10 1.0 +chr20 33513606 33513792 CCDS13255.1_cds_0_0_chr20_33513607_f 0 + 186 1.0 +chr20 33579500 33579527 CCDS13256.1_cds_0_0_chr20_33579501_r 0 - 0 0.0 +chr20 33593260 33593348 CCDS13257.1_cds_0_0_chr20_33593261_f 0 + 0 0.0 +chr21 32707032 32707192 CCDS13614.1_cds_0_0_chr21_32707033_f 0 + 0 0.0 +chr21 32869641 32870022 CCDS13615.1_cds_0_0_chr21_32869642_r 0 - 381 1.0 +chr21 33321040 33322012 CCDS13620.1_cds_0_0_chr21_33321041_f 0 + 972 1.0 +chr21 33744994 33745040 CCDS13625.1_cds_0_0_chr21_33744995_r 0 - 0 0.0 +chr22 30120223 30120265 CCDS13897.1_cds_0_0_chr22_30120224_f 0 + 42 1.0 +chr22 30160419 30160661 CCDS13898.1_cds_0_0_chr22_30160420_r 0 - 242 1.0 +chr22 30665273 30665360 CCDS13901.1_cds_0_0_chr22_30665274_f 0 + 0 0.0 +chr22 30939054 30939266 CCDS13903.1_cds_0_0_chr22_30939055_r 0 - 0 0.0 +chr5 131424298 131424460 CCDS4149.1_cds_0_0_chr5_131424299_f 0 + 162 1.0 +chr5 131556601 131556672 CCDS4151.1_cds_0_0_chr5_131556602_r 0 - 71 1.0 +chr5 131621326 131621419 CCDS4152.1_cds_0_0_chr5_131621327_f 0 + 93 1.0 +chr5 131847541 131847666 CCDS4155.1_cds_0_0_chr5_131847542_r 0 - 0 0.0 +chr6 108299600 108299744 CCDS5061.1_cds_0_0_chr6_108299601_r 0 - 144 1.0 +chr6 108594662 108594687 CCDS5063.1_cds_0_0_chr6_108594663_f 0 + 25 1.0 +chr6 108640045 108640151 CCDS5064.1_cds_0_0_chr6_108640046_r 0 - 106 1.0 +chr6 108722976 108723115 CCDS5067.1_cds_0_0_chr6_108722977_f 0 + 139 1.0 +chr7 113660517 113660685 CCDS5760.1_cds_0_0_chr7_113660518_f 0 + 168 1.0 +chr7 116512159 116512389 CCDS5771.1_cds_0_0_chr7_116512160_r 0 - 230 1.0 +chr7 116714099 116714152 CCDS5773.1_cds_0_0_chr7_116714100_f 0 + 53 1.0 +chr7 116945541 116945787 CCDS5774.1_cds_0_0_chr7_116945542_r 0 - 246 1.0 +chr8 118881131 118881317 CCDS6324.1_cds_0_0_chr8_118881132_r 0 - 186 1.0 +chr9 128764156 128764189 CCDS6914.1_cds_0_0_chr9_128764157_f 0 + 33 1.0 +chr9 128787519 128789136 CCDS6915.1_cds_0_0_chr9_128787520_r 0 - 1617 1.0 +chr9 128882427 128882523 CCDS6917.1_cds_0_0_chr9_128882428_f 0 + 0 0.0 +chr9 128937229 128937445 CCDS6919.1_cds_0_0_chr9_128937230_r 0 - 0 0.0 +chrX 122745047 122745924 CCDS14606.1_cds_0_0_chrX_122745048_f 0 + 877 1.0 +chrX 152648964 152649196 CCDS14733.1_cds_0_0_chrX_152648965_r 0 - 232 1.0 +chrX 152691446 152691471 CCDS14735.1_cds_0_0_chrX_152691447_f 0 + 25 1.0 +chrX 152694029 152694263 CCDS14736.1_cds_0_0_chrX_152694030_r 0 - 234 1.0 diff -r 4e44d29377e3 -r 0da612f8a78e test-data/gops_intersect_diffCols.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gops_intersect_diffCols.bed Thu Oct 30 16:03:11 2008 -0400 @@ -0,0 +1,49 @@ +chr1 147962192 147962580 CCDS989.1_cds_0_0_chr1_147962193_r 0 - +chr1 147984545 147984630 CCDS990.1_cds_0_0_chr1_147984546_f 0 + +chr1 148078400 148078582 CCDS993.1_cds_0_0_chr1_148078401_r 0 - +chr1 148185136 148185276 CCDS996.1_cds_0_0_chr1_148185137_f 0 + +chr10 55251623 55253124 CCDS7248.1_cds_0_0_chr10_55251624_r 0 - +chr11 116124407 116124501 CCDS8374.1_cds_0_0_chr11_116124408_r 0 - +chr11 116206508 116206563 CCDS8377.1_cds_0_0_chr11_116206509_f 0 + +chr11 116211733 116212337 CCDS8378.1_cds_0_0_chr11_116211734_r 0 - +chr12 38440094 38440321 CCDS8736.1_cds_0_0_chr12_38440095_r 0 - +chr13 112381694 112381953 CCDS9526.1_cds_0_0_chr13_112381695_f 0 + +chr14 98710240 98712285 CCDS9949.1_cds_0_0_chr14_98710241_r 0 - +chr15 41486872 41487060 CCDS10096.1_cds_0_0_chr15_41486873_r 0 - +chr15 41673708 41673857 CCDS10097.1_cds_0_0_chr15_41673709_f 0 + +chr15 41679161 41679250 CCDS10098.1_cds_0_0_chr15_41679162_r 0 - +chr16 142908 143003 CCDS10397.1_cds_0_0_chr16_142909_f 0 + +chr16 244413 244681 CCDS10402.1_cds_0_0_chr16_244414_f 0 + +chr16 259268 259383 CCDS10403.1_cds_0_0_chr16_259269_r 0 - +chr18 23786114 23786321 CCDS11891.1_cds_0_0_chr18_23786115_r 0 - +chr18 59406881 59407046 CCDS11985.1_cds_0_0_chr18_59406882_f 0 + +chr18 59455932 59456337 CCDS11986.1_cds_0_0_chr18_59455933_r 0 - +chr19 59068595 59069564 CCDS12866.1_cds_0_0_chr19_59068596_f 0 + +chr19 59236026 59236146 CCDS12872.1_cds_0_0_chr19_59236027_r 0 - +chr19 59297998 59298008 CCDS12877.1_cds_0_0_chr19_59297999_f 0 + +chr2 118288583 118288668 CCDS2120.1_cds_0_0_chr2_118288584_f 0 + +chr2 220229609 220230869 CCDS2443.1_cds_0_0_chr2_220229610_r 0 - +chr20 33330413 33330423 CCDS13249.1_cds_0_0_chr20_33330414_r 0 - +chr20 33513606 33513792 CCDS13255.1_cds_0_0_chr20_33513607_f 0 + +chr21 32869641 32870022 CCDS13615.1_cds_0_0_chr21_32869642_r 0 - +chr21 33321040 33322012 CCDS13620.1_cds_0_0_chr21_33321041_f 0 + +chr22 30120223 30120265 CCDS13897.1_cds_0_0_chr22_30120224_f 0 + +chr22 30160419 30160661 CCDS13898.1_cds_0_0_chr22_30160420_r 0 - +chr5 131424298 131424460 CCDS4149.1_cds_0_0_chr5_131424299_f 0 + +chr5 131556601 131556672 CCDS4151.1_cds_0_0_chr5_131556602_r 0 - +chr5 131621326 131621419 CCDS4152.1_cds_0_0_chr5_131621327_f 0 + +chr6 108299600 108299744 CCDS5061.1_cds_0_0_chr6_108299601_r 0 - +chr6 108594662 108594687 CCDS5063.1_cds_0_0_chr6_108594663_f 0 + +chr6 108640045 108640151 CCDS5064.1_cds_0_0_chr6_108640046_r 0 - +chr6 108722976 108723115 CCDS5067.1_cds_0_0_chr6_108722977_f 0 + +chr7 113660517 113660685 CCDS5760.1_cds_0_0_chr7_113660518_f 0 + +chr7 116512159 116512389 CCDS5771.1_cds_0_0_chr7_116512160_r 0 - +chr7 116714099 116714152 CCDS5773.1_cds_0_0_chr7_116714100_f 0 + +chr7 116945541 116945787 CCDS5774.1_cds_0_0_chr7_116945542_r 0 - +chr8 118881131 118881317 CCDS6324.1_cds_0_0_chr8_118881132_r 0 - +chr9 128764156 128764189 CCDS6914.1_cds_0_0_chr9_128764157_f 0 + +chr9 128787519 128789136 CCDS6915.1_cds_0_0_chr9_128787520_r 0 - +chrX 122745047 122745924 CCDS14606.1_cds_0_0_chrX_122745048_f 0 + +chrX 152648964 152649196 CCDS14733.1_cds_0_0_chrX_152648965_r 0 - +chrX 152691446 152691471 CCDS14735.1_cds_0_0_chrX_152691447_f 0 + +chrX 152694029 152694263 CCDS14736.1_cds_0_0_chrX_152694030_r 0 - diff -r 4e44d29377e3 -r 0da612f8a78e test-data/gops_intersect_p_diffCols.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gops_intersect_p_diffCols.bed Thu Oct 30 16:03:11 2008 -0400 @@ -0,0 +1,49 @@ +chr1 147962192 147962580 CCDS989.1_cds_0_0_chr1_147962193_r 0 - +chr1 147984545 147984630 CCDS990.1_cds_0_0_chr1_147984546_f 0 + +chr1 148078400 148078582 CCDS993.1_cds_0_0_chr1_148078401_r 0 - +chr1 148185136 148185276 CCDS996.1_cds_0_0_chr1_148185137_f 0 + +chr10 55251623 55253124 CCDS7248.1_cds_0_0_chr10_55251624_r 0 - +chr11 116124407 116124501 CCDS8374.1_cds_0_0_chr11_116124408_r 0 - +chr11 116206508 116206563 CCDS8377.1_cds_0_0_chr11_116206509_f 0 + +chr11 116211733 116212337 CCDS8378.1_cds_0_0_chr11_116211734_r 0 - +chr12 38440094 38440321 CCDS8736.1_cds_0_0_chr12_38440095_r 0 - +chr13 112381694 112381953 CCDS9526.1_cds_0_0_chr13_112381695_f 0 + +chr14 98710240 98712285 CCDS9949.1_cds_0_0_chr14_98710241_r 0 - +chr15 41486872 41487060 CCDS10096.1_cds_0_0_chr15_41486873_r 0 - +chr15 41673708 41673857 CCDS10097.1_cds_0_0_chr15_41673709_f 0 + +chr15 41679161 41679250 CCDS10098.1_cds_0_0_chr15_41679162_r 0 - +chr16 142908 143003 CCDS10397.1_cds_0_0_chr16_142909_f 0 + +chr16 244413 244681 CCDS10402.1_cds_0_0_chr16_244414_f 0 + +chr16 259268 259383 CCDS10403.1_cds_0_0_chr16_259269_r 0 - +chr18 23786114 23786321 CCDS11891.1_cds_0_0_chr18_23786115_r 0 - +chr18 59406881 59407046 CCDS11985.1_cds_0_0_chr18_59406882_f 0 + +chr18 59455932 59456337 CCDS11986.1_cds_0_0_chr18_59455933_r 0 - +chr19 59068595 59069564 CCDS12866.1_cds_0_0_chr19_59068596_f 0 + +chr19 59236026 59236146 CCDS12872.1_cds_0_0_chr19_59236027_r 0 - +chr19 59297998 59298008 CCDS12877.1_cds_0_0_chr19_59297999_f 0 + +chr2 118288583 118288668 CCDS2120.1_cds_0_0_chr2_118288584_f 0 + +chr2 220229609 220230869 CCDS2443.1_cds_0_0_chr2_220229610_r 0 - +chr20 33330413 33330423 CCDS13249.1_cds_0_0_chr20_33330414_r 0 - +chr20 33513606 33513792 CCDS13255.1_cds_0_0_chr20_33513607_f 0 + +chr21 32869641 32870022 CCDS13615.1_cds_0_0_chr21_32869642_r 0 - +chr21 33321040 33322012 CCDS13620.1_cds_0_0_chr21_33321041_f 0 + +chr22 30120223 30120265 CCDS13897.1_cds_0_0_chr22_30120224_f 0 + +chr22 30160419 30160661 CCDS13898.1_cds_0_0_chr22_30160420_r 0 - +chr5 131424298 131424460 CCDS4149.1_cds_0_0_chr5_131424299_f 0 + +chr5 131556601 131556672 CCDS4151.1_cds_0_0_chr5_131556602_r 0 - +chr5 131621326 131621419 CCDS4152.1_cds_0_0_chr5_131621327_f 0 + +chr6 108299600 108299744 CCDS5061.1_cds_0_0_chr6_108299601_r 0 - +chr6 108594662 108594687 CCDS5063.1_cds_0_0_chr6_108594663_f 0 + +chr6 108640045 108640151 CCDS5064.1_cds_0_0_chr6_108640046_r 0 - +chr6 108722976 108723115 CCDS5067.1_cds_0_0_chr6_108722977_f 0 + +chr7 113660517 113660685 CCDS5760.1_cds_0_0_chr7_113660518_f 0 + +chr7 116512159 116512389 CCDS5771.1_cds_0_0_chr7_116512160_r 0 - +chr7 116714099 116714152 CCDS5773.1_cds_0_0_chr7_116714100_f 0 + +chr7 116945541 116945787 CCDS5774.1_cds_0_0_chr7_116945542_r 0 - +chr8 118881131 118881317 CCDS6324.1_cds_0_0_chr8_118881132_r 0 - +chr9 128764156 128764189 CCDS6914.1_cds_0_0_chr9_128764157_f 0 + +chr9 128787519 128789136 CCDS6915.1_cds_0_0_chr9_128787520_r 0 - +chrX 122745047 122745924 CCDS14606.1_cds_0_0_chrX_122745048_f 0 + +chrX 152648964 152649196 CCDS14733.1_cds_0_0_chrX_152648965_r 0 - +chrX 152691446 152691471 CCDS14735.1_cds_0_0_chrX_152691447_f 0 + +chrX 152694029 152694263 CCDS14736.1_cds_0_0_chrX_152694030_r 0 - diff -r 4e44d29377e3 -r 0da612f8a78e test-data/gops_merge_diffCols.dat --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gops_merge_diffCols.dat Thu Oct 30 16:03:11 2008 -0400 @@ -0,0 +1,69 @@ +#chr name score strand start end +chr7 113660517 113660685 +chr7 116512159 116512389 +chr7 116714099 116714152 +chr7 116945541 116945787 +chr6 108299600 108299744 +chr6 108594662 108594687 +chr6 108640045 108640151 +chr6 108722976 108723115 +chr5 131311206 131311254 +chr5 131424298 131424460 +chr5 131556601 131556672 +chr5 131621326 131621419 +chrX 122745047 122745924 +chrX 152648964 152649196 +chrX 152691446 152691471 +chrX 152694029 152694263 +chr2 118288583 118288668 +chr2 118390395 118390500 +chr2 220108689 220109267 +chr2 220229609 220230869 +chr1 147962192 147962580 +chr1 147984545 147984630 +chr1 148078400 148078582 +chr1 148185136 148185276 +chr21 32687402 32687588 +chr21 32869641 32870022 +chr21 33321040 33322012 +chr21 33728358 33728724 +chr9 128764156 128764189 +chr9 128787519 128789136 +chr9 128789552 128789584 +chr9 128850516 128850624 +chr8 118881131 118881317 +chr13 29680676 29680875 +chr13 112381694 112381953 +chr12 38440094 38440321 +chr12 38905200 38905351 +chr11 116124407 116124501 +chr11 116206508 116206563 +chr11 116211733 116212337 +chr11 130745911 130745993 +chr10 55251623 55253124 +chr22 30120223 30120265 +chr22 30160419 30160661 +chr22 30228824 30228916 +chr22 30340151 30340376 +chr16 142908 143003 +chr16 179197 179339 +chr16 244413 244681 +chr16 259268 259383 +chr15 41486872 41487060 +chr15 41673708 41673857 +chr15 41679161 41679250 +chr15 41773540 41773689 +chr14 98521864 98521922 +chr14 98710240 98712285 +chr20 33330413 33330423 +chr20 33485370 33486123 +chr20 33488491 33489122 +chr20 33513606 33513792 +chr19 59068595 59069564 +chr19 59236026 59236146 +chr19 59297998 59298008 +chr19 59318205 59318718 +chr18 23786114 23786321 +chr18 59406881 59407046 +chr18 59455932 59456337 +chr18 59528407 59528575 diff -r 4e44d29377e3 -r 0da612f8a78e test-data/gops_subtract_diffCols.dat --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gops_subtract_diffCols.dat Thu Oct 30 16:03:11 2008 -0400 @@ -0,0 +1,16 @@ +chr11 1812377 1812407 CCDS7726.1_cds_0_0_chr11_1812378_f 0 + +chr15 41826029 41826196 CCDS10101.1_cds_0_0_chr15_41826030_f 0 + +chr16 179963 180135 CCDS10401.1_cds_0_0_chr16_179964_r 0 - +chr18 59600586 59600754 CCDS11988.1_cds_0_0_chr18_59600587_f 0 + +chr19 59302168 59302288 CCDS12878.1_cds_0_0_chr19_59302169_r 0 - +chr2 118394148 118394202 CCDS2121.1_cds_0_0_chr2_118394149_r 0 - +chr2 220190202 220190242 CCDS2441.1_cds_0_0_chr2_220190203_f 0 + +chr20 33579500 33579527 CCDS13256.1_cds_0_0_chr20_33579501_r 0 - +chr20 33593260 33593348 CCDS13257.1_cds_0_0_chr20_33593261_f 0 + +chr21 32707032 32707192 CCDS13614.1_cds_0_0_chr21_32707033_f 0 + +chr21 33744994 33745040 CCDS13625.1_cds_0_0_chr21_33744995_r 0 - +chr22 30665273 30665360 CCDS13901.1_cds_0_0_chr22_30665274_f 0 + +chr22 30939054 30939266 CCDS13903.1_cds_0_0_chr22_30939055_r 0 - +chr5 131847541 131847666 CCDS4155.1_cds_0_0_chr5_131847542_r 0 - +chr9 128882427 128882523 CCDS6917.1_cds_0_0_chr9_128882428_f 0 + +chr9 128937229 128937445 CCDS6919.1_cds_0_0_chr9_128937230_r 0 - diff -r 4e44d29377e3 -r 0da612f8a78e tools/new_operations/complement.xml --- a/tools/new_operations/complement.xml Thu Oct 30 14:46:57 2008 -0400 +++ b/tools/new_operations/complement.xml Thu Oct 30 16:03:11 2008 -0400 @@ -17,6 +17,11 @@ <param name="input1" value="1.bed" /> <param name="allchroms" value="true" /> <output name="output" file="gops_complement_out.bed" /> + </test> + <test> + <param name="input1" value="2_mod.bed" ftype="interval"/> + <param name="allchroms" value="true" /> + <output name="output" file="gops_complement_out_diffCols.dat" /> </test> <test> <param name="input1" value="gops_bigint.interval" /> diff -r 4e44d29377e3 -r 0da612f8a78e tools/new_operations/coverage.xml --- a/tools/new_operations/coverage.xml Thu Oct 30 14:46:57 2008 -0400 +++ b/tools/new_operations/coverage.xml Thu Oct 30 16:03:11 2008 -0400 @@ -18,6 +18,11 @@ <param name="input1" value="1.bed" /> <param name="input2" value="2.bed" /> <output name="output" file="gops_coverage_out.interval" /> + </test> + <test> + <param name="input1" value="1.bed" /> + <param name="input2" value="2_mod.bed" ftype="interval"/> + <output name="output" file="gops_coverage_out_diffCols.interval" /> </test> <test> <param name="input1" value="gops_bigint.interval" /> diff -r 4e44d29377e3 -r 0da612f8a78e tools/new_operations/intersect.xml --- a/tools/new_operations/intersect.xml Thu Oct 30 14:46:57 2008 -0400 +++ b/tools/new_operations/intersect.xml Thu Oct 30 16:03:11 2008 -0400 @@ -21,13 +21,27 @@ <data format="input" name="output" metadata_source="input1" /> </outputs> <code file="operation_filter.py"/> - <tests> + <tests> + <test> + <param name="input1" value="1.bed" /> + <param name="input2" value="2.bed" /> + <param name="min" value="1" /> + <param name="returntype" value="" /> + <output name="output" file="gops_intersect_out.bed" /> + </test> <test> <param name="input1" value="1.bed" /> - <param name="input2" value="2.bed" /> + <param name="input2" value="2_mod.bed" ftype="interval"/> <param name="min" value="1" /> - <param name="returntype" value="" /> - <output name="output" file="gops_intersect_out.bed" /> + <param name="returntype" value="" /> + <output name="output" file="gops_intersect_diffCols.bed" /> + </test> + <test> + <param name="input1" value="1.bed" /> + <param name="input2" value="2_mod.bed" ftype="interval"/> + <param name="min" value="1" /> + <param name="returntype" value="Overlapping pieces of Intervals" /> + <output name="output" file="gops_intersect_p_diffCols.bed" /> </test> <test> <param name="input1" value="1.bed" /> diff -r 4e44d29377e3 -r 0da612f8a78e tools/new_operations/merge.xml --- a/tools/new_operations/merge.xml Thu Oct 30 14:46:57 2008 -0400 +++ b/tools/new_operations/merge.xml Thu Oct 30 16:03:11 2008 -0400 @@ -19,6 +19,11 @@ <test> <param name="input1" value="1.bed" /> <output name="output" file="gops-merge.dat" /> + <param name="returntype" value="true" /> + </test> + <test> + <param name="input1" value="2_mod.bed" ftype="interval"/> + <output name="output" file="gops_merge_diffCols.dat" /> <param name="returntype" value="true" /> </test> <test> diff -r 4e44d29377e3 -r 0da612f8a78e tools/new_operations/subtract.xml --- a/tools/new_operations/subtract.xml Thu Oct 30 14:46:57 2008 -0400 +++ b/tools/new_operations/subtract.xml Thu Oct 30 16:03:11 2008 -0400 @@ -31,6 +31,13 @@ <param name="min" value="1" /> <param name="returntype" value="" /> <output name="output" file="gops-subtract.dat" /> + </test> + <test> + <param name="input1" value="1.bed" /> + <param name="input2" value="2_mod.bed" ftype="interval"/> + <param name="min" value="1" /> + <param name="returntype" value="" /> + <output name="output" file="gops_subtract_diffCols.dat" /> </test> <test> <param name="input1" value="gops_subtract_bigint.bed" />