Mercurial > repos > greg > cwpair2
changeset 11:6383cae47688 draft
Uploaded
| author | greg |
|---|---|
| date | Wed, 16 Dec 2015 14:18:28 -0500 |
| parents | b52d6705aed0 |
| children | 79a10fe09b66 |
| files | cwpair2.xml static/images/._cwpair2.png static/images/cwpair2.png test-data/closest_f_output2.pdf test-data/closest_mp_output1.gff test-data/closest_mp_output2.gff test-data/closest_s_output1.gff test-data/closest_s_output2.gff test-data/largest_f_output2.pdf test-data/largest_mp_output1.gff test-data/largest_mp_output2.gff test-data/largest_s_output1.gff test-data/largest_s_output2.gff test-data/mode_c_output2.pdf test-data/mode_f_output2.pdf test-data/mode_mp_output1.gff test-data/mode_mp_output2.gff test-data/mode_p_output2.pdf test-data/mode_s_output1.gff test-data/mode_s_output2.gff test-data/statistics1.tabular test-data/statistics2.tabular tool_dependencies.xml |
| diffstat | 23 files changed, 413 insertions(+), 388 deletions(-) [+] |
line wrap: on
line diff
--- a/cwpair2.xml Wed Dec 02 16:14:07 2015 -0500 +++ b/cwpair2.xml Wed Dec 16 14:18:28 2015 -0500 @@ -27,8 +27,8 @@ </command> <inputs> <param name="input" type="data" format="gff" multiple="True" label="Find matched pairs on" /> - <param name="up_distance" type="integer" value="50" min="0" label="Distance upstream from a peak to allow a pair" /> - <param name="down_distance" type="integer" value="100" min="0" label="Distance downstream from a peak to allow a pair" /> + <param name="up_distance" type="integer" value="50" min="0" label="Distance upstream from a peak to allow a pair" help="The maximum distance upstream or 5’ to the primary peak"/> + <param name="down_distance" type="integer" value="100" min="0" label="Distance downstream from a peak to allow a pair" help="The maximum distance downstream or 3’ to the primary peak"/> <param name="method" type="select" label="Method of finding a match"> <option value="mode" selected="True">Mode</option> <option value="closest">Closest</option> @@ -127,33 +127,58 @@ <help> **What it does** -Takes a list of called peaks on both strands and produces lists of matched pairs and unmatched peaks using a -specified method for finding matched pairs. Methods for finding matched pairs are mode, closest, largest or -all (where the analysis is run for each method). A statistics dataset is generated and a collection of datasets -is produced for each method as follows. +CWPair accepts one or more gff files as input and takes the peak location to be the midpoint between the +exclusion zone start and end coordinate (columns D and E). CWPair starts with the highest peak (primary peak) +in the dataset, and then looks on the opposite strand for another peak located within the distance defined by +a combination of the tool's **Distance upstream from a peak to allow a pair** (the distance upstream or 5’ to +the primary peak) and **Distance downstream from a peak to allow a pair** (the distance downstream or 3’ to the +primary peak) parameters. So "upstream" value 30 "downstream" value 20 makes the tool look 30 bp upstream and +20 bp downstream (inclusive). Consequently, the search space would be 51 bp, since it includes the primary peak +coordinate. The use of a negative number changes the direction of the search limits. So, "upstream" -30 and +"downstream" 20 produces an 11 bp downstream search window (20-30 bp downstream, inclusive). -**Data Files** +.. image:: $PATH_TO_IMAGES/cwpair2.png + +When encountering multiple candidate peaks within the search window, CWPair uses the resolution method defined by +the tool's **Method of finding a match** parameter as follows: + + + * **mode** - This is an iterative process in which all peak-pair distances within the search window are determined, and the mode calculated. The pair whose distance apart is closest to the mode is then selected. + * **closest** - Pairs the peak that has the closest absolute distance from the primary peak. + * **largest** - Pairs the peak that has the highest tag count. + * **all** - Runs all three methods, producing separate outputs for each. -* **closest/largest/mode MP** - the Matched Pairs in gff format -* **closest/largest/mode O** - the Orphans in tabular format -* **closest/largest/mode D** - the Details in tabular format +When considering the candidate peaks for pairing to a primary peak, a tag-count threshold may also be set using +the tool's **Filter using relative/absolute threshold** parameter. A relative threshold determines the tag counts +at the 95th percentile of peak occupancy (i.e. top 5% in terms of tag counts), then uses a tag count threshold at +the specified percentage of this 95th percentile. So if the peak at the 95th percentile has 200 tags, and "relative +threshold" 50 is used, then it will not consider any peak having less than 100 tags. + +----- + +**Output Data Files** -**Statistics Files** + * **closest/largest/mode MP** - gff file containing the Matched Pairs and includes the peak-pair midpoint coordinate (column D) and the coordinate +1 (column E). The tag count sum is reported in column F, along with the C-W distance in bp in column I. + * **closest/largest/mode O** - tabular file containing the Orphans (all peaks that are not in pairs). + * **closest/largest/mode D** - tabular file containing the Details, which lists + and – strand information separately. The start and end represent the lower and higher coordinates of the exclusion zone from GeneTrack, and “Value” is the tag count sum within the exclusion zone. The peak pair midpoint is calculated along with the distance between the two paired peaks (midpoint-to-midpoint or C-W distance). -* **closest/largest/mode C** - the stastics graph in pdf format -* **closest/largest/mode P** - the preview plots graph in pdf format -* **closest/largest/mode F** - the final plots graph in pdf format +**Output Statistics Files** + + * **closest/largest/mode C** - pdf file that provides the frequency distribution of peak pair distances. + * **closest/largest/mode P** - pdf file that provides the preview plots graph (the initial iteration of the process for finding the mode). + * **closest/largest/mode F** - pdf file that provides the final plots graph. + * **Statistics Table** - provides the number of peaks in pairs (dividing this by 2 provides the number of peak-pairs). ----- **Options** -* **Method of finding match** - Method of finding matched pair, mode, closest, largest, or all (run with each method). -* **Distance upstream from a peak to allow a pair** - Distance upstream from a Watson peak to allow a Crick pair. -* **Distance downstream from a peak to allow a pair** - Distance downstream from a Watson peak to allow a Crick pair. -* **Percentage of the 95 percentile value to filter below** - Percentage of the 95 percentile value below which to filter when using a relative threshold. -* **Absolute value to filter below** - Absolute value below which to filter when using an absolute threshold. -* **Output files** - Restrict output dataset collections to matched pairs only or one of several combinations of collection types. + * **Method of finding match** - Method of finding matched pair, mode, closest, largest, or all (run with each method). + * **Distance upstream from a peak to allow a pair** - The maximum distance (inclusive) upstream on the opposite strand from the primary peak to locate another peak, resulting in a pair. + * **Distance downstream from a peak to allow a pair** - The maximum distance (inclusive) downstream on the opposite strand from the primary peak to locate another peak, resulting in a pair. + * **Percentage of the 95 percentile value to filter below** - Percentage of the 95 percentile value below which to filter when using a relative threshold. + * **Absolute value to filter below** - Absolute value below which to filter when using an absolute threshold. + * **Output files** - Restrict output dataset collections to matched pairs only or one of several combinations of collection types. </help> <expand macro="citations" />
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/closest_mp_output1.gff Wed Dec 16 14:18:28 2015 -0500 @@ -0,0 +1,56 @@ +chr1 cwpair . 87162 87163 5531.0 . . cw_distance=11 +chr1 cwpair . 229759 229760 4531.0 . . cw_distance=16 +chr1 cwpair . 123 124 4204.0 . . cw_distance=52 +chr1 cwpair . 268 269 4088.0 . . cw_distance=6 +chr1 cwpair . 218 219 4022.0 . . cw_distance=14 +chr1 cwpair . 87194 87195 3643.0 . . cw_distance=27 +chr1 cwpair . 59 60 2881.0 . . cw_distance=2 +chr1 cwpair . 265 266 2474.0 . . cw_distance=48 +chr1 cwpair . 92645 92646 2397.0 . . cw_distance=8 +chr1 cwpair . 87109 87110 2259.0 . . cw_distance=3 +chr1 cwpair . 156 157 2177.0 . . cw_distance=59 +chr1 cwpair . 70792 70793 2146.0 . . cw_distance=12 +chr1 cwpair . 6218 6219 2125.0 . . cw_distance=91 +chr1 cwpair . 86982 86983 2013.0 . . cw_distance=37 +chr1 cwpair . 155079 155080 1573.0 . . cw_distance=83 +chr1 cwpair . 92421 92422 1388.0 . . cw_distance=0 +chr1 cwpair . 185109 185110 1371.0 . . cw_distance=46 +chr1 cwpair . 6454 6455 1249.0 . . cw_distance=63 +chr1 cwpair . 87044 87045 1191.0 . . cw_distance=30 +chr1 cwpair . 25305 25306 1183.0 . . cw_distance=99 +chr1 cwpair . 139230 139231 1179.0 . . cw_distance=15 +chr1 cwpair . 325 326 1171.0 . . cw_distance=16 +chr1 cwpair . 55548 55549 956.0 . . cw_distance=86 +chr1 cwpair . 370 371 899.0 . . cw_distance=25 +chr1 cwpair . 72805 72806 869.0 . . cw_distance=29 +chr1 cwpair . 22580 22581 863.0 . . cw_distance=-2 +chr1 cwpair . 92567 92568 789.0 . . cw_distance=28 +chr1 cwpair . 19213 19214 778.0 . . cw_distance=-25 +chr1 cwpair . 113782 113783 716.0 . . cw_distance=-20 +chr1 cwpair . 138876 138877 711.0 . . cw_distance=-4 +chr1 cwpair . 72731 72732 710.0 . . cw_distance=100 +chr1 cwpair . 229762 229763 699.0 . . cw_distance=63 +chr1 cwpair . 95955 95956 689.0 . . cw_distance=51 +chr1 cwpair . 134230 134231 659.0 . . cw_distance=100 +chr1 cwpair . 170134 170135 657.0 . . cw_distance=10 +chr1 cwpair . 228672 228673 626.0 . . cw_distance=58 +chr1 cwpair . 65160 65161 618.0 . . cw_distance=-4 +chr1 cwpair . 106047 106048 572.0 . . cw_distance=7 +chr1 cwpair . 477 478 566.0 . . cw_distance=1 +chr1 cwpair . 59228 59229 565.0 . . cw_distance=56 +chr1 cwpair . 173276 173277 546.0 . . cw_distance=8 +chr1 cwpair . 452 453 504.0 . . cw_distance=8 +chr1 cwpair . 31670 31671 490.0 . . cw_distance=66 +chr1 cwpair . 32483 32484 478.0 . . cw_distance=48 +chr1 cwpair . 6714 6715 433.0 . . cw_distance=-4 +chr1 cwpair . 136369 136370 365.0 . . cw_distance=-14 +chr1 cwpair . 39237 39238 362.0 . . cw_distance=61 +chr1 cwpair . 388 389 359.0 . . cw_distance=20 +chr1 cwpair . 627 628 247.0 . . cw_distance=33 +chr1 cwpair . 98551 98552 122.0 . . cw_distance=27 +chr1 cwpair . 180331 180332 97.0 . . cw_distance=82 +chr1 cwpair . 230178 230179 56.0 . . cw_distance=10 +chr1 cwpair . 230125 230126 44.0 . . cw_distance=10 +chr1 cwpair . 230157 230158 15.0 . . cw_distance=5 +chr1 cwpair . 96919 96920 12.0 . . cw_distance=3 +chr1 cwpair . 197535 197536 5.0 . . cw_distance=73
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/closest_mp_output2.gff Wed Dec 16 14:18:28 2015 -0500 @@ -0,0 +1,66 @@ +chr1 cwpair . 87162 87163 5531.0 . . cw_distance=11 +chr1 cwpair . 229759 229760 4531.0 . . cw_distance=16 +chr1 cwpair . 123 124 4204.0 . . cw_distance=52 +chr1 cwpair . 268 269 4088.0 . . cw_distance=6 +chr1 cwpair . 218 219 4022.0 . . cw_distance=14 +chr1 cwpair . 87194 87195 3643.0 . . cw_distance=27 +chr1 cwpair . 59 60 2881.0 . . cw_distance=2 +chr1 cwpair . 265 266 2474.0 . . cw_distance=48 +chr1 cwpair . 92645 92646 2397.0 . . cw_distance=8 +chr1 cwpair . 101399 101400 2361.0 . . cw_distance=-44 +chr1 cwpair . 87109 87110 2259.0 . . cw_distance=3 +chr1 cwpair . 156 157 2177.0 . . cw_distance=59 +chr1 cwpair . 70792 70793 2146.0 . . cw_distance=12 +chr1 cwpair . 6218 6219 2125.0 . . cw_distance=91 +chr1 cwpair . 86982 86983 2013.0 . . cw_distance=37 +chr1 cwpair . 169095 169096 1887.0 . . cw_distance=-43 +chr1 cwpair . 155079 155080 1573.0 . . cw_distance=83 +chr1 cwpair . 203863 203864 1476.0 . . cw_distance=-37 +chr1 cwpair . 92421 92422 1388.0 . . cw_distance=0 +chr1 cwpair . 185109 185110 1371.0 . . cw_distance=46 +chr1 cwpair . 39076 39077 1350.0 . . cw_distance=-29 +chr1 cwpair . 6454 6455 1249.0 . . cw_distance=63 +chr1 cwpair . 87044 87045 1191.0 . . cw_distance=30 +chr1 cwpair . 25305 25306 1183.0 . . cw_distance=99 +chr1 cwpair . 139230 139231 1179.0 . . cw_distance=15 +chr1 cwpair . 325 326 1171.0 . . cw_distance=16 +chr1 cwpair . 55548 55549 956.0 . . cw_distance=86 +chr1 cwpair . 370 371 899.0 . . cw_distance=25 +chr1 cwpair . 72805 72806 869.0 . . cw_distance=29 +chr1 cwpair . 22580 22581 863.0 . . cw_distance=-2 +chr1 cwpair . 199413 199414 810.0 . . cw_distance=-30 +chr1 cwpair . 92567 92568 789.0 . . cw_distance=28 +chr1 cwpair . 19213 19214 778.0 . . cw_distance=-25 +chr1 cwpair . 116649 116650 773.0 . . cw_distance=-41 +chr1 cwpair . 124306 124307 761.0 . . cw_distance=-43 +chr1 cwpair . 113782 113783 716.0 . . cw_distance=-20 +chr1 cwpair . 138876 138877 711.0 . . cw_distance=-4 +chr1 cwpair . 72731 72732 710.0 . . cw_distance=100 +chr1 cwpair . 229762 229763 699.0 . . cw_distance=63 +chr1 cwpair . 95955 95956 689.0 . . cw_distance=51 +chr1 cwpair . 134230 134231 659.0 . . cw_distance=100 +chr1 cwpair . 170134 170135 657.0 . . cw_distance=10 +chr1 cwpair . 228672 228673 626.0 . . cw_distance=58 +chr1 cwpair . 65160 65161 618.0 . . cw_distance=-4 +chr1 cwpair . 151365 151366 595.0 . . cw_distance=-28 +chr1 cwpair . 108611 108612 573.0 . . cw_distance=-45 +chr1 cwpair . 106047 106048 572.0 . . cw_distance=7 +chr1 cwpair . 500 501 569.0 . . cw_distance=-44 +chr1 cwpair . 59228 59229 565.0 . . cw_distance=56 +chr1 cwpair . 173276 173277 546.0 . . cw_distance=8 +chr1 cwpair . 452 453 504.0 . . cw_distance=8 +chr1 cwpair . 45670 45671 493.0 . . cw_distance=-35 +chr1 cwpair . 31670 31671 490.0 . . cw_distance=66 +chr1 cwpair . 32483 32484 478.0 . . cw_distance=48 +chr1 cwpair . 6714 6715 433.0 . . cw_distance=-4 +chr1 cwpair . 136369 136370 365.0 . . cw_distance=-14 +chr1 cwpair . 39237 39238 362.0 . . cw_distance=61 +chr1 cwpair . 388 389 359.0 . . cw_distance=20 +chr1 cwpair . 668 669 319.0 . . cw_distance=-48 +chr1 cwpair . 98551 98552 122.0 . . cw_distance=27 +chr1 cwpair . 180331 180332 97.0 . . cw_distance=82 +chr1 cwpair . 230178 230179 56.0 . . cw_distance=10 +chr1 cwpair . 230125 230126 44.0 . . cw_distance=10 +chr1 cwpair . 230157 230158 15.0 . . cw_distance=5 +chr1 cwpair . 96919 96920 12.0 . . cw_distance=3 +chr1 cwpair . 197535 197536 5.0 . . cw_distance=73
--- a/test-data/closest_s_output1.gff Wed Dec 02 16:14:07 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,56 +0,0 @@ -chr1 cwpair . 59 60 2881.0 . . cw_distance=2 -chr1 cwpair . 123 124 4204.0 . . cw_distance=52 -chr1 cwpair . 156 157 2177.0 . . cw_distance=59 -chr1 cwpair . 218 219 4022.0 . . cw_distance=14 -chr1 cwpair . 265 266 2474.0 . . cw_distance=48 -chr1 cwpair . 268 269 4088.0 . . cw_distance=6 -chr1 cwpair . 325 326 1171.0 . . cw_distance=16 -chr1 cwpair . 370 371 899.0 . . cw_distance=25 -chr1 cwpair . 388 389 359.0 . . cw_distance=20 -chr1 cwpair . 452 453 504.0 . . cw_distance=8 -chr1 cwpair . 477 478 566.0 . . cw_distance=1 -chr1 cwpair . 627 628 247.0 . . cw_distance=33 -chr1 cwpair . 6218 6219 2125.0 . . cw_distance=91 -chr1 cwpair . 6454 6455 1249.0 . . cw_distance=63 -chr1 cwpair . 6714 6715 433.0 . . cw_distance=-4 -chr1 cwpair . 19213 19214 778.0 . . cw_distance=-25 -chr1 cwpair . 22580 22581 863.0 . . cw_distance=-2 -chr1 cwpair . 25305 25306 1183.0 . . cw_distance=99 -chr1 cwpair . 31670 31671 490.0 . . cw_distance=66 -chr1 cwpair . 32483 32484 478.0 . . cw_distance=48 -chr1 cwpair . 39237 39238 362.0 . . cw_distance=61 -chr1 cwpair . 55548 55549 956.0 . . cw_distance=86 -chr1 cwpair . 59228 59229 565.0 . . cw_distance=56 -chr1 cwpair . 65160 65161 618.0 . . cw_distance=-4 -chr1 cwpair . 70792 70793 2146.0 . . cw_distance=12 -chr1 cwpair . 72731 72732 710.0 . . cw_distance=100 -chr1 cwpair . 72805 72806 869.0 . . cw_distance=29 -chr1 cwpair . 86982 86983 2013.0 . . cw_distance=37 -chr1 cwpair . 87044 87045 1191.0 . . cw_distance=30 -chr1 cwpair . 87109 87110 2259.0 . . cw_distance=3 -chr1 cwpair . 87162 87163 5531.0 . . cw_distance=11 -chr1 cwpair . 87194 87195 3643.0 . . cw_distance=27 -chr1 cwpair . 92421 92422 1388.0 . . cw_distance=0 -chr1 cwpair . 92567 92568 789.0 . . cw_distance=28 -chr1 cwpair . 92645 92646 2397.0 . . cw_distance=8 -chr1 cwpair . 95955 95956 689.0 . . cw_distance=51 -chr1 cwpair . 96919 96920 12.0 . . cw_distance=3 -chr1 cwpair . 98551 98552 122.0 . . cw_distance=27 -chr1 cwpair . 106047 106048 572.0 . . cw_distance=7 -chr1 cwpair . 113782 113783 716.0 . . cw_distance=-20 -chr1 cwpair . 134230 134231 659.0 . . cw_distance=100 -chr1 cwpair . 136369 136370 365.0 . . cw_distance=-14 -chr1 cwpair . 138876 138877 711.0 . . cw_distance=-4 -chr1 cwpair . 139230 139231 1179.0 . . cw_distance=15 -chr1 cwpair . 155079 155080 1573.0 . . cw_distance=83 -chr1 cwpair . 170134 170135 657.0 . . cw_distance=10 -chr1 cwpair . 173276 173277 546.0 . . cw_distance=8 -chr1 cwpair . 180331 180332 97.0 . . cw_distance=82 -chr1 cwpair . 185109 185110 1371.0 . . cw_distance=46 -chr1 cwpair . 197535 197536 5.0 . . cw_distance=73 -chr1 cwpair . 228672 228673 626.0 . . cw_distance=58 -chr1 cwpair . 229759 229760 4531.0 . . cw_distance=16 -chr1 cwpair . 229762 229763 699.0 . . cw_distance=63 -chr1 cwpair . 230125 230126 44.0 . . cw_distance=10 -chr1 cwpair . 230157 230158 15.0 . . cw_distance=5 -chr1 cwpair . 230178 230179 56.0 . . cw_distance=10
--- a/test-data/closest_s_output2.gff Wed Dec 02 16:14:07 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,66 +0,0 @@ -chr1 cwpair . 59 60 2881.0 . . cw_distance=2 -chr1 cwpair . 123 124 4204.0 . . cw_distance=52 -chr1 cwpair . 156 157 2177.0 . . cw_distance=59 -chr1 cwpair . 218 219 4022.0 . . cw_distance=14 -chr1 cwpair . 265 266 2474.0 . . cw_distance=48 -chr1 cwpair . 268 269 4088.0 . . cw_distance=6 -chr1 cwpair . 325 326 1171.0 . . cw_distance=16 -chr1 cwpair . 370 371 899.0 . . cw_distance=25 -chr1 cwpair . 388 389 359.0 . . cw_distance=20 -chr1 cwpair . 452 453 504.0 . . cw_distance=8 -chr1 cwpair . 500 501 569.0 . . cw_distance=-44 -chr1 cwpair . 668 669 319.0 . . cw_distance=-48 -chr1 cwpair . 6218 6219 2125.0 . . cw_distance=91 -chr1 cwpair . 6454 6455 1249.0 . . cw_distance=63 -chr1 cwpair . 6714 6715 433.0 . . cw_distance=-4 -chr1 cwpair . 19213 19214 778.0 . . cw_distance=-25 -chr1 cwpair . 22580 22581 863.0 . . cw_distance=-2 -chr1 cwpair . 25305 25306 1183.0 . . cw_distance=99 -chr1 cwpair . 31670 31671 490.0 . . cw_distance=66 -chr1 cwpair . 32483 32484 478.0 . . cw_distance=48 -chr1 cwpair . 39076 39077 1350.0 . . cw_distance=-29 -chr1 cwpair . 39237 39238 362.0 . . cw_distance=61 -chr1 cwpair . 45670 45671 493.0 . . cw_distance=-35 -chr1 cwpair . 55548 55549 956.0 . . cw_distance=86 -chr1 cwpair . 59228 59229 565.0 . . cw_distance=56 -chr1 cwpair . 65160 65161 618.0 . . cw_distance=-4 -chr1 cwpair . 70792 70793 2146.0 . . cw_distance=12 -chr1 cwpair . 72731 72732 710.0 . . cw_distance=100 -chr1 cwpair . 72805 72806 869.0 . . cw_distance=29 -chr1 cwpair . 86982 86983 2013.0 . . cw_distance=37 -chr1 cwpair . 87044 87045 1191.0 . . cw_distance=30 -chr1 cwpair . 87109 87110 2259.0 . . cw_distance=3 -chr1 cwpair . 87162 87163 5531.0 . . cw_distance=11 -chr1 cwpair . 87194 87195 3643.0 . . cw_distance=27 -chr1 cwpair . 92421 92422 1388.0 . . cw_distance=0 -chr1 cwpair . 92567 92568 789.0 . . cw_distance=28 -chr1 cwpair . 92645 92646 2397.0 . . cw_distance=8 -chr1 cwpair . 95955 95956 689.0 . . cw_distance=51 -chr1 cwpair . 96919 96920 12.0 . . cw_distance=3 -chr1 cwpair . 98551 98552 122.0 . . cw_distance=27 -chr1 cwpair . 101399 101400 2361.0 . . cw_distance=-44 -chr1 cwpair . 106047 106048 572.0 . . cw_distance=7 -chr1 cwpair . 108611 108612 573.0 . . cw_distance=-45 -chr1 cwpair . 113782 113783 716.0 . . cw_distance=-20 -chr1 cwpair . 116649 116650 773.0 . . cw_distance=-41 -chr1 cwpair . 124306 124307 761.0 . . cw_distance=-43 -chr1 cwpair . 134230 134231 659.0 . . cw_distance=100 -chr1 cwpair . 136369 136370 365.0 . . cw_distance=-14 -chr1 cwpair . 138876 138877 711.0 . . cw_distance=-4 -chr1 cwpair . 139230 139231 1179.0 . . cw_distance=15 -chr1 cwpair . 151365 151366 595.0 . . cw_distance=-28 -chr1 cwpair . 155079 155080 1573.0 . . cw_distance=83 -chr1 cwpair . 169095 169096 1887.0 . . cw_distance=-43 -chr1 cwpair . 170134 170135 657.0 . . cw_distance=10 -chr1 cwpair . 173276 173277 546.0 . . cw_distance=8 -chr1 cwpair . 180331 180332 97.0 . . cw_distance=82 -chr1 cwpair . 185109 185110 1371.0 . . cw_distance=46 -chr1 cwpair . 197535 197536 5.0 . . cw_distance=73 -chr1 cwpair . 199413 199414 810.0 . . cw_distance=-30 -chr1 cwpair . 203863 203864 1476.0 . . cw_distance=-37 -chr1 cwpair . 228672 228673 626.0 . . cw_distance=58 -chr1 cwpair . 229759 229760 4531.0 . . cw_distance=16 -chr1 cwpair . 229762 229763 699.0 . . cw_distance=63 -chr1 cwpair . 230125 230126 44.0 . . cw_distance=10 -chr1 cwpair . 230157 230158 15.0 . . cw_distance=5 -chr1 cwpair . 230178 230179 56.0 . . cw_distance=10
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/largest_mp_output1.gff Wed Dec 16 14:18:28 2015 -0500 @@ -0,0 +1,55 @@ +chr1 cwpair . 87182 87183 5699.0 . . cw_distance=51 +chr1 cwpair . 176 177 4774.0 . . cw_distance=98 +chr1 cwpair . 229759 229760 4531.0 . . cw_distance=16 +chr1 cwpair . 123 124 4204.0 . . cw_distance=52 +chr1 cwpair . 277 278 4138.0 . . cw_distance=24 +chr1 cwpair . 87174 87175 3475.0 . . cw_distance=-13 +chr1 cwpair . 59 60 2881.0 . . cw_distance=2 +chr1 cwpair . 92601 92602 2836.0 . . cw_distance=96 +chr1 cwpair . 241 242 2689.0 . . cw_distance=60 +chr1 cwpair . 87011 87012 2370.0 . . cw_distance=95 +chr1 cwpair . 87109 87110 2259.0 . . cw_distance=3 +chr1 cwpair . 70792 70793 2146.0 . . cw_distance=12 +chr1 cwpair . 6218 6219 2125.0 . . cw_distance=91 +chr1 cwpair . 287 288 1632.0 . . cw_distance=92 +chr1 cwpair . 155079 155080 1573.0 . . cw_distance=83 +chr1 cwpair . 92421 92422 1388.0 . . cw_distance=0 +chr1 cwpair . 185109 185110 1371.0 . . cw_distance=46 +chr1 cwpair . 6454 6455 1249.0 . . cw_distance=63 +chr1 cwpair . 25305 25306 1183.0 . . cw_distance=99 +chr1 cwpair . 139230 139231 1179.0 . . cw_distance=15 +chr1 cwpair . 72786 72787 1063.0 . . cw_distance=-10 +chr1 cwpair . 55548 55549 956.0 . . cw_distance=86 +chr1 cwpair . 370 371 899.0 . . cw_distance=25 +chr1 cwpair . 22580 22581 863.0 . . cw_distance=-2 +chr1 cwpair . 357 358 852.0 . . cw_distance=81 +chr1 cwpair . 463 464 802.0 . . cw_distance=30 +chr1 cwpair . 19213 19214 778.0 . . cw_distance=-25 +chr1 cwpair . 113782 113783 716.0 . . cw_distance=-20 +chr1 cwpair . 138876 138877 711.0 . . cw_distance=-4 +chr1 cwpair . 229762 229763 699.0 . . cw_distance=63 +chr1 cwpair . 95955 95956 689.0 . . cw_distance=51 +chr1 cwpair . 134230 134231 659.0 . . cw_distance=100 +chr1 cwpair . 170134 170135 657.0 . . cw_distance=10 +chr1 cwpair . 228672 228673 626.0 . . cw_distance=58 +chr1 cwpair . 65160 65161 618.0 . . cw_distance=-4 +chr1 cwpair . 87006 87007 615.0 . . cw_distance=-11 +chr1 cwpair . 106047 106048 572.0 . . cw_distance=7 +chr1 cwpair . 59228 59229 565.0 . . cw_distance=56 +chr1 cwpair . 173276 173277 546.0 . . cw_distance=8 +chr1 cwpair . 31670 31671 490.0 . . cw_distance=66 +chr1 cwpair . 32483 32484 478.0 . . cw_distance=48 +chr1 cwpair . 178 179 465.0 . . cw_distance=16 +chr1 cwpair . 92657 92658 447.0 . . cw_distance=33 +chr1 cwpair . 6714 6715 433.0 . . cw_distance=-4 +chr1 cwpair . 136369 136370 365.0 . . cw_distance=-14 +chr1 cwpair . 417 418 362.0 . . cw_distance=78 +chr1 cwpair . 39237 39238 362.0 . . cw_distance=61 +chr1 cwpair . 627 628 247.0 . . cw_distance=33 +chr1 cwpair . 98551 98552 122.0 . . cw_distance=27 +chr1 cwpair . 180331 180332 97.0 . . cw_distance=82 +chr1 cwpair . 230151 230152 75.0 . . cw_distance=63 +chr1 cwpair . 230166 230167 30.0 . . cw_distance=-13 +chr1 cwpair . 96919 96920 12.0 . . cw_distance=3 +chr1 cwpair . 230142 230143 10.0 . . cw_distance=-25 +chr1 cwpair . 197535 197536 5.0 . . cw_distance=73
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/largest_mp_output2.gff Wed Dec 16 14:18:28 2015 -0500 @@ -0,0 +1,64 @@ +chr1 cwpair . 87182 87183 5699.0 . . cw_distance=51 +chr1 cwpair . 245 246 5421.0 . . cw_distance=-40 +chr1 cwpair . 229759 229760 4531.0 . . cw_distance=16 +chr1 cwpair . 123 124 4204.0 . . cw_distance=52 +chr1 cwpair . 87174 87175 3475.0 . . cw_distance=-13 +chr1 cwpair . 59 60 2881.0 . . cw_distance=2 +chr1 cwpair . 92601 92602 2836.0 . . cw_distance=96 +chr1 cwpair . 250 251 2739.0 . . cw_distance=78 +chr1 cwpair . 256 257 2424.0 . . cw_distance=30 +chr1 cwpair . 87011 87012 2370.0 . . cw_distance=95 +chr1 cwpair . 101399 101400 2361.0 . . cw_distance=-44 +chr1 cwpair . 87109 87110 2259.0 . . cw_distance=3 +chr1 cwpair . 156 157 2177.0 . . cw_distance=59 +chr1 cwpair . 70792 70793 2146.0 . . cw_distance=12 +chr1 cwpair . 6218 6219 2125.0 . . cw_distance=91 +chr1 cwpair . 169095 169096 1887.0 . . cw_distance=-43 +chr1 cwpair . 155079 155080 1573.0 . . cw_distance=83 +chr1 cwpair . 203863 203864 1476.0 . . cw_distance=-37 +chr1 cwpair . 92421 92422 1388.0 . . cw_distance=0 +chr1 cwpair . 185109 185110 1371.0 . . cw_distance=46 +chr1 cwpair . 39076 39077 1350.0 . . cw_distance=-29 +chr1 cwpair . 6454 6455 1249.0 . . cw_distance=63 +chr1 cwpair . 345 346 1185.0 . . cw_distance=-25 +chr1 cwpair . 25305 25306 1183.0 . . cw_distance=99 +chr1 cwpair . 139230 139231 1179.0 . . cw_distance=15 +chr1 cwpair . 72786 72787 1063.0 . . cw_distance=-10 +chr1 cwpair . 55548 55549 956.0 . . cw_distance=86 +chr1 cwpair . 350 351 885.0 . . cw_distance=66 +chr1 cwpair . 22580 22581 863.0 . . cw_distance=-2 +chr1 cwpair . 87015 87016 834.0 . . cw_distance=-28 +chr1 cwpair . 199413 199414 810.0 . . cw_distance=-30 +chr1 cwpair . 463 464 802.0 . . cw_distance=30 +chr1 cwpair . 19213 19214 778.0 . . cw_distance=-25 +chr1 cwpair . 116649 116650 773.0 . . cw_distance=-41 +chr1 cwpair . 124306 124307 761.0 . . cw_distance=-43 +chr1 cwpair . 113782 113783 716.0 . . cw_distance=-20 +chr1 cwpair . 138876 138877 711.0 . . cw_distance=-4 +chr1 cwpair . 229762 229763 699.0 . . cw_distance=63 +chr1 cwpair . 95955 95956 689.0 . . cw_distance=51 +chr1 cwpair . 134230 134231 659.0 . . cw_distance=100 +chr1 cwpair . 170134 170135 657.0 . . cw_distance=10 +chr1 cwpair . 228672 228673 626.0 . . cw_distance=58 +chr1 cwpair . 65160 65161 618.0 . . cw_distance=-4 +chr1 cwpair . 151365 151366 595.0 . . cw_distance=-28 +chr1 cwpair . 108611 108612 573.0 . . cw_distance=-45 +chr1 cwpair . 106047 106048 572.0 . . cw_distance=7 +chr1 cwpair . 59228 59229 565.0 . . cw_distance=56 +chr1 cwpair . 173276 173277 546.0 . . cw_distance=8 +chr1 cwpair . 45670 45671 493.0 . . cw_distance=-35 +chr1 cwpair . 31670 31671 490.0 . . cw_distance=66 +chr1 cwpair . 32483 32484 478.0 . . cw_distance=48 +chr1 cwpair . 92657 92658 447.0 . . cw_distance=33 +chr1 cwpair . 6714 6715 433.0 . . cw_distance=-4 +chr1 cwpair . 136369 136370 365.0 . . cw_distance=-14 +chr1 cwpair . 417 418 362.0 . . cw_distance=78 +chr1 cwpair . 39237 39238 362.0 . . cw_distance=61 +chr1 cwpair . 668 669 319.0 . . cw_distance=-48 +chr1 cwpair . 98551 98552 122.0 . . cw_distance=27 +chr1 cwpair . 180331 180332 97.0 . . cw_distance=82 +chr1 cwpair . 230151 230152 75.0 . . cw_distance=63 +chr1 cwpair . 230166 230167 30.0 . . cw_distance=-13 +chr1 cwpair . 96919 96920 12.0 . . cw_distance=3 +chr1 cwpair . 230142 230143 10.0 . . cw_distance=-25 +chr1 cwpair . 197535 197536 5.0 . . cw_distance=73
--- a/test-data/largest_s_output1.gff Wed Dec 02 16:14:07 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,55 +0,0 @@ -chr1 cwpair . 59 60 2881.0 . . cw_distance=2 -chr1 cwpair . 123 124 4204.0 . . cw_distance=52 -chr1 cwpair . 176 177 4774.0 . . cw_distance=98 -chr1 cwpair . 178 179 465.0 . . cw_distance=16 -chr1 cwpair . 241 242 2689.0 . . cw_distance=60 -chr1 cwpair . 277 278 4138.0 . . cw_distance=24 -chr1 cwpair . 287 288 1632.0 . . cw_distance=92 -chr1 cwpair . 357 358 852.0 . . cw_distance=81 -chr1 cwpair . 370 371 899.0 . . cw_distance=25 -chr1 cwpair . 417 418 362.0 . . cw_distance=78 -chr1 cwpair . 463 464 802.0 . . cw_distance=30 -chr1 cwpair . 627 628 247.0 . . cw_distance=33 -chr1 cwpair . 6218 6219 2125.0 . . cw_distance=91 -chr1 cwpair . 6454 6455 1249.0 . . cw_distance=63 -chr1 cwpair . 6714 6715 433.0 . . cw_distance=-4 -chr1 cwpair . 19213 19214 778.0 . . cw_distance=-25 -chr1 cwpair . 22580 22581 863.0 . . cw_distance=-2 -chr1 cwpair . 25305 25306 1183.0 . . cw_distance=99 -chr1 cwpair . 31670 31671 490.0 . . cw_distance=66 -chr1 cwpair . 32483 32484 478.0 . . cw_distance=48 -chr1 cwpair . 39237 39238 362.0 . . cw_distance=61 -chr1 cwpair . 55548 55549 956.0 . . cw_distance=86 -chr1 cwpair . 59228 59229 565.0 . . cw_distance=56 -chr1 cwpair . 65160 65161 618.0 . . cw_distance=-4 -chr1 cwpair . 70792 70793 2146.0 . . cw_distance=12 -chr1 cwpair . 72786 72787 1063.0 . . cw_distance=-10 -chr1 cwpair . 87006 87007 615.0 . . cw_distance=-11 -chr1 cwpair . 87011 87012 2370.0 . . cw_distance=95 -chr1 cwpair . 87109 87110 2259.0 . . cw_distance=3 -chr1 cwpair . 87174 87175 3475.0 . . cw_distance=-13 -chr1 cwpair . 87182 87183 5699.0 . . cw_distance=51 -chr1 cwpair . 92421 92422 1388.0 . . cw_distance=0 -chr1 cwpair . 92601 92602 2836.0 . . cw_distance=96 -chr1 cwpair . 92657 92658 447.0 . . cw_distance=33 -chr1 cwpair . 95955 95956 689.0 . . cw_distance=51 -chr1 cwpair . 96919 96920 12.0 . . cw_distance=3 -chr1 cwpair . 98551 98552 122.0 . . cw_distance=27 -chr1 cwpair . 106047 106048 572.0 . . cw_distance=7 -chr1 cwpair . 113782 113783 716.0 . . cw_distance=-20 -chr1 cwpair . 134230 134231 659.0 . . cw_distance=100 -chr1 cwpair . 136369 136370 365.0 . . cw_distance=-14 -chr1 cwpair . 138876 138877 711.0 . . cw_distance=-4 -chr1 cwpair . 139230 139231 1179.0 . . cw_distance=15 -chr1 cwpair . 155079 155080 1573.0 . . cw_distance=83 -chr1 cwpair . 170134 170135 657.0 . . cw_distance=10 -chr1 cwpair . 173276 173277 546.0 . . cw_distance=8 -chr1 cwpair . 180331 180332 97.0 . . cw_distance=82 -chr1 cwpair . 185109 185110 1371.0 . . cw_distance=46 -chr1 cwpair . 197535 197536 5.0 . . cw_distance=73 -chr1 cwpair . 228672 228673 626.0 . . cw_distance=58 -chr1 cwpair . 229759 229760 4531.0 . . cw_distance=16 -chr1 cwpair . 229762 229763 699.0 . . cw_distance=63 -chr1 cwpair . 230142 230143 10.0 . . cw_distance=-25 -chr1 cwpair . 230151 230152 75.0 . . cw_distance=63 -chr1 cwpair . 230166 230167 30.0 . . cw_distance=-13
--- a/test-data/largest_s_output2.gff Wed Dec 02 16:14:07 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,64 +0,0 @@ -chr1 cwpair . 59 60 2881.0 . . cw_distance=2 -chr1 cwpair . 123 124 4204.0 . . cw_distance=52 -chr1 cwpair . 156 157 2177.0 . . cw_distance=59 -chr1 cwpair . 245 246 5421.0 . . cw_distance=-40 -chr1 cwpair . 250 251 2739.0 . . cw_distance=78 -chr1 cwpair . 256 257 2424.0 . . cw_distance=30 -chr1 cwpair . 345 346 1185.0 . . cw_distance=-25 -chr1 cwpair . 350 351 885.0 . . cw_distance=66 -chr1 cwpair . 417 418 362.0 . . cw_distance=78 -chr1 cwpair . 463 464 802.0 . . cw_distance=30 -chr1 cwpair . 668 669 319.0 . . cw_distance=-48 -chr1 cwpair . 6218 6219 2125.0 . . cw_distance=91 -chr1 cwpair . 6454 6455 1249.0 . . cw_distance=63 -chr1 cwpair . 6714 6715 433.0 . . cw_distance=-4 -chr1 cwpair . 19213 19214 778.0 . . cw_distance=-25 -chr1 cwpair . 22580 22581 863.0 . . cw_distance=-2 -chr1 cwpair . 25305 25306 1183.0 . . cw_distance=99 -chr1 cwpair . 31670 31671 490.0 . . cw_distance=66 -chr1 cwpair . 32483 32484 478.0 . . cw_distance=48 -chr1 cwpair . 39076 39077 1350.0 . . cw_distance=-29 -chr1 cwpair . 39237 39238 362.0 . . cw_distance=61 -chr1 cwpair . 45670 45671 493.0 . . cw_distance=-35 -chr1 cwpair . 55548 55549 956.0 . . cw_distance=86 -chr1 cwpair . 59228 59229 565.0 . . cw_distance=56 -chr1 cwpair . 65160 65161 618.0 . . cw_distance=-4 -chr1 cwpair . 70792 70793 2146.0 . . cw_distance=12 -chr1 cwpair . 72786 72787 1063.0 . . cw_distance=-10 -chr1 cwpair . 87011 87012 2370.0 . . cw_distance=95 -chr1 cwpair . 87015 87016 834.0 . . cw_distance=-28 -chr1 cwpair . 87109 87110 2259.0 . . cw_distance=3 -chr1 cwpair . 87174 87175 3475.0 . . cw_distance=-13 -chr1 cwpair . 87182 87183 5699.0 . . cw_distance=51 -chr1 cwpair . 92421 92422 1388.0 . . cw_distance=0 -chr1 cwpair . 92601 92602 2836.0 . . cw_distance=96 -chr1 cwpair . 92657 92658 447.0 . . cw_distance=33 -chr1 cwpair . 95955 95956 689.0 . . cw_distance=51 -chr1 cwpair . 96919 96920 12.0 . . cw_distance=3 -chr1 cwpair . 98551 98552 122.0 . . cw_distance=27 -chr1 cwpair . 101399 101400 2361.0 . . cw_distance=-44 -chr1 cwpair . 106047 106048 572.0 . . cw_distance=7 -chr1 cwpair . 108611 108612 573.0 . . cw_distance=-45 -chr1 cwpair . 113782 113783 716.0 . . cw_distance=-20 -chr1 cwpair . 116649 116650 773.0 . . cw_distance=-41 -chr1 cwpair . 124306 124307 761.0 . . cw_distance=-43 -chr1 cwpair . 134230 134231 659.0 . . cw_distance=100 -chr1 cwpair . 136369 136370 365.0 . . cw_distance=-14 -chr1 cwpair . 138876 138877 711.0 . . cw_distance=-4 -chr1 cwpair . 139230 139231 1179.0 . . cw_distance=15 -chr1 cwpair . 151365 151366 595.0 . . cw_distance=-28 -chr1 cwpair . 155079 155080 1573.0 . . cw_distance=83 -chr1 cwpair . 169095 169096 1887.0 . . cw_distance=-43 -chr1 cwpair . 170134 170135 657.0 . . cw_distance=10 -chr1 cwpair . 173276 173277 546.0 . . cw_distance=8 -chr1 cwpair . 180331 180332 97.0 . . cw_distance=82 -chr1 cwpair . 185109 185110 1371.0 . . cw_distance=46 -chr1 cwpair . 197535 197536 5.0 . . cw_distance=73 -chr1 cwpair . 199413 199414 810.0 . . cw_distance=-30 -chr1 cwpair . 203863 203864 1476.0 . . cw_distance=-37 -chr1 cwpair . 228672 228673 626.0 . . cw_distance=58 -chr1 cwpair . 229759 229760 4531.0 . . cw_distance=16 -chr1 cwpair . 229762 229763 699.0 . . cw_distance=63 -chr1 cwpair . 230142 230143 10.0 . . cw_distance=-25 -chr1 cwpair . 230151 230152 75.0 . . cw_distance=63 -chr1 cwpair . 230166 230167 30.0 . . cw_distance=-13
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mode_mp_output1.gff Wed Dec 16 14:18:28 2015 -0500 @@ -0,0 +1,57 @@ +chr1 cwpair . 87182 87183 5699.0 . . cw_distance=51 +chr1 cwpair . 123 124 4204.0 . . cw_distance=52 +chr1 cwpair . 299 300 3296.0 . . cw_distance=68 +chr1 cwpair . 229749 229750 3235.0 . . cw_distance=36 +chr1 cwpair . 87138 87139 3164.0 . . cw_distance=60 +chr1 cwpair . 197 198 3062.0 . . cw_distance=55 +chr1 cwpair . 59 60 2881.0 . . cw_distance=2 +chr1 cwpair . 92601 92602 2836.0 . . cw_distance=96 +chr1 cwpair . 241 242 2689.0 . . cw_distance=60 +chr1 cwpair . 265 266 2474.0 . . cw_distance=48 +chr1 cwpair . 156 157 2177.0 . . cw_distance=59 +chr1 cwpair . 70792 70793 2146.0 . . cw_distance=12 +chr1 cwpair . 6218 6219 2125.0 . . cw_distance=91 +chr1 cwpair . 87212 87213 2073.0 . . cw_distance=63 +chr1 cwpair . 86982 86983 2013.0 . . cw_distance=37 +chr1 cwpair . 229772 229773 1995.0 . . cw_distance=43 +chr1 cwpair . 87070 87071 1903.0 . . cw_distance=82 +chr1 cwpair . 155079 155080 1573.0 . . cw_distance=83 +chr1 cwpair . 92421 92422 1388.0 . . cw_distance=0 +chr1 cwpair . 185109 185110 1371.0 . . cw_distance=46 +chr1 cwpair . 6454 6455 1249.0 . . cw_distance=63 +chr1 cwpair . 25305 25306 1183.0 . . cw_distance=99 +chr1 cwpair . 139230 139231 1179.0 . . cw_distance=15 +chr1 cwpair . 87035 87036 972.0 . . cw_distance=47 +chr1 cwpair . 55548 55549 956.0 . . cw_distance=86 +chr1 cwpair . 350 351 885.0 . . cw_distance=66 +chr1 cwpair . 72805 72806 869.0 . . cw_distance=29 +chr1 cwpair . 22580 22581 863.0 . . cw_distance=-2 +chr1 cwpair . 463 464 802.0 . . cw_distance=30 +chr1 cwpair . 19213 19214 778.0 . . cw_distance=-25 +chr1 cwpair . 113782 113783 716.0 . . cw_distance=-20 +chr1 cwpair . 138876 138877 711.0 . . cw_distance=-4 +chr1 cwpair . 72731 72732 710.0 . . cw_distance=100 +chr1 cwpair . 389 390 707.0 . . cw_distance=62 +chr1 cwpair . 95955 95956 689.0 . . cw_distance=51 +chr1 cwpair . 134230 134231 659.0 . . cw_distance=100 +chr1 cwpair . 170134 170135 657.0 . . cw_distance=10 +chr1 cwpair . 228672 228673 626.0 . . cw_distance=58 +chr1 cwpair . 65160 65161 618.0 . . cw_distance=-4 +chr1 cwpair . 106047 106048 572.0 . . cw_distance=7 +chr1 cwpair . 59228 59229 565.0 . . cw_distance=56 +chr1 cwpair . 173276 173277 546.0 . . cw_distance=8 +chr1 cwpair . 31670 31671 490.0 . . cw_distance=66 +chr1 cwpair . 32483 32484 478.0 . . cw_distance=48 +chr1 cwpair . 92657 92658 447.0 . . cw_distance=33 +chr1 cwpair . 6714 6715 433.0 . . cw_distance=-4 +chr1 cwpair . 136369 136370 365.0 . . cw_distance=-14 +chr1 cwpair . 417 418 362.0 . . cw_distance=78 +chr1 cwpair . 39237 39238 362.0 . . cw_distance=61 +chr1 cwpair . 627 628 247.0 . . cw_distance=33 +chr1 cwpair . 98551 98552 122.0 . . cw_distance=27 +chr1 cwpair . 180331 180332 97.0 . . cw_distance=82 +chr1 cwpair . 230151 230152 75.0 . . cw_distance=63 +chr1 cwpair . 230166 230167 30.0 . . cw_distance=-13 +chr1 cwpair . 96919 96920 12.0 . . cw_distance=3 +chr1 cwpair . 230148 230149 10.0 . . cw_distance=-13 +chr1 cwpair . 197535 197536 5.0 . . cw_distance=73
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mode_mp_output2.gff Wed Dec 16 14:18:28 2015 -0500 @@ -0,0 +1,67 @@ +chr1 cwpair . 87182 87183 5699.0 . . cw_distance=51 +chr1 cwpair . 123 124 4204.0 . . cw_distance=52 +chr1 cwpair . 299 300 3296.0 . . cw_distance=68 +chr1 cwpair . 229749 229750 3235.0 . . cw_distance=36 +chr1 cwpair . 87138 87139 3164.0 . . cw_distance=60 +chr1 cwpair . 197 198 3062.0 . . cw_distance=55 +chr1 cwpair . 59 60 2881.0 . . cw_distance=2 +chr1 cwpair . 92601 92602 2836.0 . . cw_distance=96 +chr1 cwpair . 241 242 2689.0 . . cw_distance=60 +chr1 cwpair . 265 266 2474.0 . . cw_distance=48 +chr1 cwpair . 101399 101400 2361.0 . . cw_distance=-44 +chr1 cwpair . 156 157 2177.0 . . cw_distance=59 +chr1 cwpair . 70792 70793 2146.0 . . cw_distance=12 +chr1 cwpair . 6218 6219 2125.0 . . cw_distance=91 +chr1 cwpair . 87212 87213 2073.0 . . cw_distance=63 +chr1 cwpair . 86982 86983 2013.0 . . cw_distance=37 +chr1 cwpair . 229772 229773 1995.0 . . cw_distance=43 +chr1 cwpair . 87070 87071 1903.0 . . cw_distance=82 +chr1 cwpair . 169095 169096 1887.0 . . cw_distance=-43 +chr1 cwpair . 155079 155080 1573.0 . . cw_distance=83 +chr1 cwpair . 203863 203864 1476.0 . . cw_distance=-37 +chr1 cwpair . 92421 92422 1388.0 . . cw_distance=0 +chr1 cwpair . 185109 185110 1371.0 . . cw_distance=46 +chr1 cwpair . 39076 39077 1350.0 . . cw_distance=-29 +chr1 cwpair . 6454 6455 1249.0 . . cw_distance=63 +chr1 cwpair . 25305 25306 1183.0 . . cw_distance=99 +chr1 cwpair . 139230 139231 1179.0 . . cw_distance=15 +chr1 cwpair . 87077 87078 1098.0 . . cw_distance=-36 +chr1 cwpair . 55548 55549 956.0 . . cw_distance=86 +chr1 cwpair . 350 351 885.0 . . cw_distance=66 +chr1 cwpair . 72805 72806 869.0 . . cw_distance=29 +chr1 cwpair . 22580 22581 863.0 . . cw_distance=-2 +chr1 cwpair . 199413 199414 810.0 . . cw_distance=-30 +chr1 cwpair . 463 464 802.0 . . cw_distance=30 +chr1 cwpair . 19213 19214 778.0 . . cw_distance=-25 +chr1 cwpair . 116649 116650 773.0 . . cw_distance=-41 +chr1 cwpair . 124306 124307 761.0 . . cw_distance=-43 +chr1 cwpair . 113782 113783 716.0 . . cw_distance=-20 +chr1 cwpair . 138876 138877 711.0 . . cw_distance=-4 +chr1 cwpair . 72731 72732 710.0 . . cw_distance=100 +chr1 cwpair . 389 390 707.0 . . cw_distance=62 +chr1 cwpair . 95955 95956 689.0 . . cw_distance=51 +chr1 cwpair . 134230 134231 659.0 . . cw_distance=100 +chr1 cwpair . 170134 170135 657.0 . . cw_distance=10 +chr1 cwpair . 228672 228673 626.0 . . cw_distance=58 +chr1 cwpair . 65160 65161 618.0 . . cw_distance=-4 +chr1 cwpair . 151365 151366 595.0 . . cw_distance=-28 +chr1 cwpair . 108611 108612 573.0 . . cw_distance=-45 +chr1 cwpair . 106047 106048 572.0 . . cw_distance=7 +chr1 cwpair . 59228 59229 565.0 . . cw_distance=56 +chr1 cwpair . 173276 173277 546.0 . . cw_distance=8 +chr1 cwpair . 45670 45671 493.0 . . cw_distance=-35 +chr1 cwpair . 31670 31671 490.0 . . cw_distance=66 +chr1 cwpair . 32483 32484 478.0 . . cw_distance=48 +chr1 cwpair . 92657 92658 447.0 . . cw_distance=33 +chr1 cwpair . 6714 6715 433.0 . . cw_distance=-4 +chr1 cwpair . 136369 136370 365.0 . . cw_distance=-14 +chr1 cwpair . 417 418 362.0 . . cw_distance=78 +chr1 cwpair . 39237 39238 362.0 . . cw_distance=61 +chr1 cwpair . 668 669 319.0 . . cw_distance=-48 +chr1 cwpair . 98551 98552 122.0 . . cw_distance=27 +chr1 cwpair . 180331 180332 97.0 . . cw_distance=82 +chr1 cwpair . 230151 230152 75.0 . . cw_distance=63 +chr1 cwpair . 230166 230167 30.0 . . cw_distance=-13 +chr1 cwpair . 96919 96920 12.0 . . cw_distance=3 +chr1 cwpair . 230148 230149 10.0 . . cw_distance=-13 +chr1 cwpair . 197535 197536 5.0 . . cw_distance=73
--- a/test-data/mode_s_output1.gff Wed Dec 02 16:14:07 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,57 +0,0 @@ -chr1 cwpair . 59 60 2881.0 . . cw_distance=2 -chr1 cwpair . 123 124 4204.0 . . cw_distance=52 -chr1 cwpair . 156 157 2177.0 . . cw_distance=59 -chr1 cwpair . 197 198 3062.0 . . cw_distance=55 -chr1 cwpair . 241 242 2689.0 . . cw_distance=60 -chr1 cwpair . 265 266 2474.0 . . cw_distance=48 -chr1 cwpair . 299 300 3296.0 . . cw_distance=68 -chr1 cwpair . 350 351 885.0 . . cw_distance=66 -chr1 cwpair . 389 390 707.0 . . cw_distance=62 -chr1 cwpair . 417 418 362.0 . . cw_distance=78 -chr1 cwpair . 463 464 802.0 . . cw_distance=30 -chr1 cwpair . 627 628 247.0 . . cw_distance=33 -chr1 cwpair . 6218 6219 2125.0 . . cw_distance=91 -chr1 cwpair . 6454 6455 1249.0 . . cw_distance=63 -chr1 cwpair . 6714 6715 433.0 . . cw_distance=-4 -chr1 cwpair . 19213 19214 778.0 . . cw_distance=-25 -chr1 cwpair . 22580 22581 863.0 . . cw_distance=-2 -chr1 cwpair . 25305 25306 1183.0 . . cw_distance=99 -chr1 cwpair . 31670 31671 490.0 . . cw_distance=66 -chr1 cwpair . 32483 32484 478.0 . . cw_distance=48 -chr1 cwpair . 39237 39238 362.0 . . cw_distance=61 -chr1 cwpair . 55548 55549 956.0 . . cw_distance=86 -chr1 cwpair . 59228 59229 565.0 . . cw_distance=56 -chr1 cwpair . 65160 65161 618.0 . . cw_distance=-4 -chr1 cwpair . 70792 70793 2146.0 . . cw_distance=12 -chr1 cwpair . 72731 72732 710.0 . . cw_distance=100 -chr1 cwpair . 72805 72806 869.0 . . cw_distance=29 -chr1 cwpair . 86982 86983 2013.0 . . cw_distance=37 -chr1 cwpair . 87035 87036 972.0 . . cw_distance=47 -chr1 cwpair . 87070 87071 1903.0 . . cw_distance=82 -chr1 cwpair . 87138 87139 3164.0 . . cw_distance=60 -chr1 cwpair . 87182 87183 5699.0 . . cw_distance=51 -chr1 cwpair . 87212 87213 2073.0 . . cw_distance=63 -chr1 cwpair . 92421 92422 1388.0 . . cw_distance=0 -chr1 cwpair . 92601 92602 2836.0 . . cw_distance=96 -chr1 cwpair . 92657 92658 447.0 . . cw_distance=33 -chr1 cwpair . 95955 95956 689.0 . . cw_distance=51 -chr1 cwpair . 96919 96920 12.0 . . cw_distance=3 -chr1 cwpair . 98551 98552 122.0 . . cw_distance=27 -chr1 cwpair . 106047 106048 572.0 . . cw_distance=7 -chr1 cwpair . 113782 113783 716.0 . . cw_distance=-20 -chr1 cwpair . 134230 134231 659.0 . . cw_distance=100 -chr1 cwpair . 136369 136370 365.0 . . cw_distance=-14 -chr1 cwpair . 138876 138877 711.0 . . cw_distance=-4 -chr1 cwpair . 139230 139231 1179.0 . . cw_distance=15 -chr1 cwpair . 155079 155080 1573.0 . . cw_distance=83 -chr1 cwpair . 170134 170135 657.0 . . cw_distance=10 -chr1 cwpair . 173276 173277 546.0 . . cw_distance=8 -chr1 cwpair . 180331 180332 97.0 . . cw_distance=82 -chr1 cwpair . 185109 185110 1371.0 . . cw_distance=46 -chr1 cwpair . 197535 197536 5.0 . . cw_distance=73 -chr1 cwpair . 228672 228673 626.0 . . cw_distance=58 -chr1 cwpair . 229749 229750 3235.0 . . cw_distance=36 -chr1 cwpair . 229772 229773 1995.0 . . cw_distance=43 -chr1 cwpair . 230148 230149 10.0 . . cw_distance=-13 -chr1 cwpair . 230151 230152 75.0 . . cw_distance=63 -chr1 cwpair . 230166 230167 30.0 . . cw_distance=-13
--- a/test-data/mode_s_output2.gff Wed Dec 02 16:14:07 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,67 +0,0 @@ -chr1 cwpair . 59 60 2881.0 . . cw_distance=2 -chr1 cwpair . 123 124 4204.0 . . cw_distance=52 -chr1 cwpair . 156 157 2177.0 . . cw_distance=59 -chr1 cwpair . 197 198 3062.0 . . cw_distance=55 -chr1 cwpair . 241 242 2689.0 . . cw_distance=60 -chr1 cwpair . 265 266 2474.0 . . cw_distance=48 -chr1 cwpair . 299 300 3296.0 . . cw_distance=68 -chr1 cwpair . 350 351 885.0 . . cw_distance=66 -chr1 cwpair . 389 390 707.0 . . cw_distance=62 -chr1 cwpair . 417 418 362.0 . . cw_distance=78 -chr1 cwpair . 463 464 802.0 . . cw_distance=30 -chr1 cwpair . 668 669 319.0 . . cw_distance=-48 -chr1 cwpair . 6218 6219 2125.0 . . cw_distance=91 -chr1 cwpair . 6454 6455 1249.0 . . cw_distance=63 -chr1 cwpair . 6714 6715 433.0 . . cw_distance=-4 -chr1 cwpair . 19213 19214 778.0 . . cw_distance=-25 -chr1 cwpair . 22580 22581 863.0 . . cw_distance=-2 -chr1 cwpair . 25305 25306 1183.0 . . cw_distance=99 -chr1 cwpair . 31670 31671 490.0 . . cw_distance=66 -chr1 cwpair . 32483 32484 478.0 . . cw_distance=48 -chr1 cwpair . 39076 39077 1350.0 . . cw_distance=-29 -chr1 cwpair . 39237 39238 362.0 . . cw_distance=61 -chr1 cwpair . 45670 45671 493.0 . . cw_distance=-35 -chr1 cwpair . 55548 55549 956.0 . . cw_distance=86 -chr1 cwpair . 59228 59229 565.0 . . cw_distance=56 -chr1 cwpair . 65160 65161 618.0 . . cw_distance=-4 -chr1 cwpair . 70792 70793 2146.0 . . cw_distance=12 -chr1 cwpair . 72731 72732 710.0 . . cw_distance=100 -chr1 cwpair . 72805 72806 869.0 . . cw_distance=29 -chr1 cwpair . 86982 86983 2013.0 . . cw_distance=37 -chr1 cwpair . 87070 87071 1903.0 . . cw_distance=82 -chr1 cwpair . 87077 87078 1098.0 . . cw_distance=-36 -chr1 cwpair . 87138 87139 3164.0 . . cw_distance=60 -chr1 cwpair . 87182 87183 5699.0 . . cw_distance=51 -chr1 cwpair . 87212 87213 2073.0 . . cw_distance=63 -chr1 cwpair . 92421 92422 1388.0 . . cw_distance=0 -chr1 cwpair . 92601 92602 2836.0 . . cw_distance=96 -chr1 cwpair . 92657 92658 447.0 . . cw_distance=33 -chr1 cwpair . 95955 95956 689.0 . . cw_distance=51 -chr1 cwpair . 96919 96920 12.0 . . cw_distance=3 -chr1 cwpair . 98551 98552 122.0 . . cw_distance=27 -chr1 cwpair . 101399 101400 2361.0 . . cw_distance=-44 -chr1 cwpair . 106047 106048 572.0 . . cw_distance=7 -chr1 cwpair . 108611 108612 573.0 . . cw_distance=-45 -chr1 cwpair . 113782 113783 716.0 . . cw_distance=-20 -chr1 cwpair . 116649 116650 773.0 . . cw_distance=-41 -chr1 cwpair . 124306 124307 761.0 . . cw_distance=-43 -chr1 cwpair . 134230 134231 659.0 . . cw_distance=100 -chr1 cwpair . 136369 136370 365.0 . . cw_distance=-14 -chr1 cwpair . 138876 138877 711.0 . . cw_distance=-4 -chr1 cwpair . 139230 139231 1179.0 . . cw_distance=15 -chr1 cwpair . 151365 151366 595.0 . . cw_distance=-28 -chr1 cwpair . 155079 155080 1573.0 . . cw_distance=83 -chr1 cwpair . 169095 169096 1887.0 . . cw_distance=-43 -chr1 cwpair . 170134 170135 657.0 . . cw_distance=10 -chr1 cwpair . 173276 173277 546.0 . . cw_distance=8 -chr1 cwpair . 180331 180332 97.0 . . cw_distance=82 -chr1 cwpair . 185109 185110 1371.0 . . cw_distance=46 -chr1 cwpair . 197535 197536 5.0 . . cw_distance=73 -chr1 cwpair . 199413 199414 810.0 . . cw_distance=-30 -chr1 cwpair . 203863 203864 1476.0 . . cw_distance=-37 -chr1 cwpair . 228672 228673 626.0 . . cw_distance=58 -chr1 cwpair . 229749 229750 3235.0 . . cw_distance=36 -chr1 cwpair . 229772 229773 1995.0 . . cw_distance=43 -chr1 cwpair . 230148 230149 10.0 . . cw_distance=-13 -chr1 cwpair . 230151 230152 75.0 . . cw_distance=63 -chr1 cwpair . 230166 230167 30.0 . . cw_distance=-13
--- a/test-data/statistics1.tabular Wed Dec 02 16:14:07 2015 -0500 +++ b/test-data/statistics1.tabular Wed Dec 16 14:18:28 2015 -0500 @@ -1,4 +1,4 @@ fname final_mode preview_mode perc95 paired orphans +mode: data 1 63.5 63.5 1437.0 114 384 closest: data 1 10.5 NA 1437.0 112 386 largest: data 1 -3.5 NA 1437.0 110 388 -mode: data 1 63.5 63.5 1437.0 114 384
--- a/test-data/statistics2.tabular Wed Dec 02 16:14:07 2015 -0500 +++ b/test-data/statistics2.tabular Wed Dec 16 14:18:28 2015 -0500 @@ -1,4 +1,4 @@ fname final_mode preview_mode perc95 paired orphans +mode: data 1 63.5 63.5 1437.0 134 364 closest: data 1 8.5 NA 1437.0 132 366 largest: data 1 -24.5 NA 1437.0 128 370 -mode: data 1 63.5 63.5 1437.0 134 364
--- a/tool_dependencies.xml Wed Dec 02 16:14:07 2015 -0500 +++ b/tool_dependencies.xml Wed Dec 16 14:18:28 2015 -0500 @@ -1,6 +1,6 @@ <?xml version="1.0"?> <tool_dependency> <package name="anaconda" version="2.3.0"> - <repository changeset_revision="1da77309352e" name="package_anaconda_2_3_0" owner="greg" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="d3f29b11da06" name="package_anaconda_2_3_0" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> </tool_dependency>