-
Notifications
You must be signed in to change notification settings - Fork 6
/
Copy pathHISTORY
1676 lines (1120 loc) · 47.9 KB
/
HISTORY
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
commit 1d4aece20c31d40038c89a2a88e36e29d0dff2ec (HEAD, origin/master, origin/HEAD, master)
Author: Gao Wang <gaow@uchicago.edu>
Date: Sat Apr 9 11:10:14 2016 -0500
Properly handle mlink warnings. Version number boosted to 1.0.0
commit 019ab638fd456d1ce3c8b75f748ca5faf13154bc
Author: Gao Wang <gaow@uchicago.edu>
Date: Fri Apr 8 21:25:51 2016 -0500
Update installation script and author affiliation
commit cd8707b466216e6e97e1bdec5afb752ef1b77779
Author: Hang Dai <hang.dai@bcm.edu>
Date: Tue Aug 18 18:30:41 2015 -0500
add gray figures
commit 8d2f0610854b48855ca3555e895cf575da124a66
Author: Gao Wang <gaow@uchicago.edu>
Date: Wed Jun 10 15:08:18 2015 -0500
fix: ramdisk command
commit 40b29529bd378cdb2de7db66004d6a1b78c12c2c
Merge: 02498ed c8536e9
Author: Gao Wang Office <gaow@bcm.edu>
Date: Wed May 13 20:39:35 2015 -0500
Merge branch 'master' of tigerwang.org:SEQLinkage
commit 02498eddfd2d8d20471a2c76ea67ee4e27a76fab
Author: Gao Wang Office <gaow@bcm.edu>
Date: Wed May 13 20:39:26 2015 -0500
major: add manuscript proof
commit c403d364441829ed7e749f017056bccf26547d2e
Author: Gao Wang Office <gaow@bcm.edu>
Date: Wed Feb 11 15:29:22 2015 -0600
Changes in script to adapt for git behavior
commit c8536e918dc2683f62c37766a252755514a4f8c0
Author: Linhai Zhao <percylinhai@gmail.com>
Date: Sat Feb 7 23:01:37 2015 -0600
revision on makefile
commit a3bec5d2d4d896d67c32e7fbff1d02917c3d84be
Author: Linhai Zhao <percylinhai@gmail.com>
Date: Sat Feb 7 22:44:29 2015 -0600
commands using simulated vcf data w/o missing calls
commit 124d3574547ea410fce5e30a8b3eebdc2e046181
Author: Gao Wang Office <gaow@bcm.edu>
Date: Fri Feb 6 12:25:13 2015 -0600
Add test script for Missing data case; data file pending
commit 9750882a1b03bbf0d561d628caf6e5741a29c5a7
Author: Gao Wang Office <gaow@bcm.edu>
Date: Tue Feb 3 17:31:17 2015 -0600
Format manuscript as requested by the editor
commit fa769b962453b62224a8fd756962b5f26eee66a7
Author: Gao Wang Office <gaow@bcm.edu>
Date: Mon Feb 2 16:58:13 2015 -0600
Upload manuscript for revision 2
commit 175bfed7c4ea58ac3d417a311bee788594e35ae6
Author: Min Qiao <min@lupinus>
Date: Tue Jan 27 22:03:09 2015 -0600
Finalize revision 2 on my end
commit 6ce5d134980163df3e03b17254810aeb5d0d52d9
Author: Gao Wang Office <gaow@bcm.edu>
Date: Tue Jan 27 11:12:07 2015 -0600
Upload updated Figure S1A using 2 million replicates
commit 12447c4ada1ff0d96345389ad68cc066a2004967
Author: Di Zhang <zhangdi.devel@gmail.com>
Date: Tue Jan 27 10:26:03 2015 -0600
add 2 million reps for type I error estimation
commit 3014f369ea57cb17d87340220a84bdafa4158b7a
Author: Di Zhang <zhangdi.devel@gmail.com>
Date: Mon Jan 26 13:35:04 2015 -0600
fix: cleanup files of each rep and the seqlink output dir
commit cf9ba9b0c6b31a6030c66a6e10d6598e46bec140
Author: Di Zhang <zhangdi.devel@gmail.com>
Date: Mon Jan 26 13:03:53 2015 -0600
add NoCache class so seqlink can run without archiving everything into ./cache/
commit 876938eb6e390c4d619c20a46e46c2cb03adfbc4
Author: Di Zhang <zhangdi.devel@gmail.com>
Date: Mon Jan 26 12:09:13 2015 -0600
add env.outdir, distinguished from env.output
commit 758bd8c29d684af95a6d5b73c032e5a6a1be8f17
Author: Di Zhang <zhangdi.devel@gmail.com>
Date: Mon Jan 26 11:59:26 2015 -0600
fix Args.isalnum(), only checking the basename of the --output string
commit 61a554839ff7f1b2172528a7de6c65f987875869
Author: Gao Wang Office <gaow@bcm.edu>
Date: Mon Jan 26 11:06:10 2015 -0600
Ensure each element in an input path is alphanumeric, not the entire path
commit e203ddbf84d79c4f7f0581ec4f6080ab748b6bf4
Author: Di Zhang <zhangdi.devel@gmail.com>
Date: Fri Jan 23 12:07:32 2015 -0600
new lods files
commit 8c84084e5219f6ba350131a2dc787f5b56c654e2
Author: Di Zhang <zhangdi.devel@gmail.com>
Date: Fri Jan 23 12:06:43 2015 -0600
n1a8 final figure-s1
commit 7239cfd1da6ed18954befd1c6d795f6419eb8e6b
Merge: 7c4ba06 4ba868e
Author: Di Zhang <zhangdi.devel@gmail.com>
Date: Fri Jan 23 11:04:16 2015 -0600
Merge branch 'master' of tigerwang.org:SEQLinkage
commit 7c4ba06d526a55d441469fd6ec0fd0c4224550d4
Author: Di Zhang <zhangdi.devel@gmail.com>
Date: Fri Jan 23 11:04:11 2015 -0600
edit length
commit 4ba868eb5b630226eea1eb0f65aefefedff72b2a
Author: Gao Wang Office <gaow@bcm.edu>
Date: Thu Jan 22 11:33:35 2015 -0600
Edit manuscript
commit 8862088b37de717be084e73db67bf54f06b36700
Author: Di Zhang <zhangdi.devel@gmail.com>
Date: Wed Jan 21 21:09:51 2015 -0600
merlin phased ld parentmissing random seed
commit d1599a78d07a27fd2e35149f6593eb86b93a9ba7
Author: Gao Wang Office <gaow@bcm.edu>
Date: Wed Jan 21 16:26:04 2015 -0600
polish qq plot script
commit 7073ef1bb45c3d125e833785fc3271a7ddd5a7bb
Author: Di Zhang <zhangdi.devel@gmail.com>
Date: Wed Jan 21 15:39:31 2015 -0600
makefile edit
commit 138d81eab9982051c45232ff4d5f136c6248e811
Author: Di Zhang <zhangdi.devel@gmail.com>
Date: Wed Jan 21 15:35:37 2015 -0600
prephased random seed ld parent missing bin 0.0 and 0.8
commit 133e8614f9adfd973ca511021466228e2dc829a8
Merge: 26a9d57 891a097
Author: Gao Wang Office <gaow@bcm.edu>
Date: Wed Jan 21 14:28:02 2015 -0600
Merge branch 'master' of tigerwang.org:SEQLinkage
commit 26a9d57ad099d5ebceb8197058ee34c752214d62
Author: Gao Wang Office <gaow@bcm.edu>
Date: Wed Jan 21 14:27:53 2015 -0600
hide help message for --prephased option
commit 891a09792a85377743834a085f359638f841cf08
Author: Di Zhang <zhangdi.devel@gmail.com>
Date: Wed Jan 21 13:32:52 2015 -0600
rm compiled files
commit 23597795425df2d54387b93ad536f49aa973acc6
Author: Di Zhang <zhangdi.devel@gmail.com>
Date: Wed Jan 21 13:31:43 2015 -0600
bug fix for scipy-0.14
commit 8bd7e783c00bc17fe0adb0dfb8329692bd45dac3
Author: Gao Wang Office <gaow@bcm.edu>
Date: Wed Jan 21 11:45:27 2015 -0600
implement makefile for type I error plots
commit 77c811a55b25bb36a67574e5d0f28ce61afb7391
Author: Di Zhang <zhangdi.devel@gmail.com>
Date: Wed Jan 21 10:51:31 2015 -0600
dominant
commit 6595e53ee1a43d69ccba8fa36092c4fced88a8a7
Author: Gao Wang Office <gaow@bcm.edu>
Date: Wed Jan 21 10:26:12 2015 -0600
implelemt prephased option
commit fa265592f55bd9f5f77c729acdba4b5f2a1edfa5
Author: Di Zhang <zhangdi.devel@gmail.com>
Date: Tue Jan 20 10:53:40 2015 -0600
bin 0
commit 484e7975a72fd1b53ec619ad9c82875ae6c9160c
Author: Di Zhang <zhangdi.devel@gmail.com>
Date: Mon Jan 19 23:13:09 2015 -0600
bin 0.8/1.0
commit ab4d2ddc650809c7c94438e5ea71a9af24821e9c
Author: Min Qiao <min@lupinus>
Date: Sun Jan 18 16:50:21 2015 -0600
test interface change
commit 3c35129b368ac2298abb75a8b15712dacffa267b
Author: Di Zhang <zhangdi.devel@gmail.com>
Date: Sun Jan 18 09:23:22 2015 -0600
type I update
commit 7bcc6e8291b13726e924055f96b13c2d3c50cc7e
Merge: fd2cd2c 9667d30
Author: Di Zhang <zhangdi.devel@gmail.com>
Date: Fri Jan 16 11:27:41 2015 -0600
Merge branch 'master' of tigerwang.org:SEQLinkage
commit fd2cd2c99c52407fac6ab066ff032fb70d974f8b
Author: Di Zhang <zhangdi.devel@gmail.com>
Date: Fri Jan 16 11:27:10 2015 -0600
null vs. rec
commit 9667d30c50d208812c59040a7b29123818c6812d
Author: Min Qiao <min@lupinus>
Date: Fri Jan 16 08:37:04 2015 -0600
add QQplots
commit 9160d6cd0ffb9f2e7ed0b8a39d8d71ae17386f19
Author: Di Zhang <zhangdi.devel@gmail.com>
Date: Thu Jan 15 21:40:09 2015 -0600
lods updated
commit 1eb977ff48d44b071897fd6701d1d357ffee0d30
Author: Di Zhang <zhangdi.devel@gmail.com>
Date: Thu Jan 15 21:30:46 2015 -0600
sort tsv
commit 33a45095262018a102f6d189d645d7375ac9588b
Author: Di Zhang <zhangdi.devel@gmail.com>
Date: Thu Jan 15 14:58:23 2015 -0600
sort tsv
commit c24dcc87ec36760c3187261d25f92235da189bee
Merge: 92d5050 2992002
Author: Gao Wang Office <gaow@bcm.edu>
Date: Wed Jan 14 15:54:12 2015 -0600
Merge branch 'master' of tigerwang.org:SEQLinkage
commit 92d50508b6e28d15457f053f574002b2cef29f1c
Author: Gao Wang Office <gaow@bcm.edu>
Date: Wed Jan 14 15:53:57 2015 -0600
Add revision 2 draft
commit 29920024aec4f3cf992dfe74e442295e11619051
Author: Biao Li <libiaospe@gmail.com>
Date: Wed Jan 14 14:32:27 2015 -0600
modify recombination rate calculation from centimorgan
commit 25748c23de25bcb2eab9bfc19aa3fbdb9946a81f
Author: Gao Wang Office <gaow@bcm.edu>
Date: Wed Jan 14 12:35:13 2015 -0600
add updated simulation data with map distances
commit 69ff2450d71f604a04d5c5a791f92848b5015658
Author: Biao Li <libiaospe@gmail.com>
Date: Wed Jan 14 12:32:01 2015 -0600
modify recombination scheme in LinkagePowerCalc.py script
commit 5a56d27c953c21ee08a51dbbbeaec4e4d4431ae7
Author: gw <gw@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Sun Nov 16 18:48:06 2014 +0000
add references papers
commit 8aa6698de193ac71d9353f1d22ea8e08cd8113d9
Author: gw <gw@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Fri Nov 7 16:27:59 2014 +0000
upload final ms
commit 152dde7d21eebda351ef3eb73b964008d8cd2e11
Author: gw <gw@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Wed Nov 5 00:32:52 2014 +0000
revision 1 update, submitted to Suzanne
commit fec6bb0af12a2046879ac6fcd8d1390b91ceb4b8
Author: zhangdi <zhangdi@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Tue Nov 4 19:54:26 2014 +0000
remove DDDDD
commit 19557af30969dbd84abc6e5da9a49bf8e4dbb2df
Author: biao <biao@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Tue Nov 4 19:52:21 2014 +0000
update
commit 28a9eb49d72936d41d29e11c3315836fd1f48bc5
Author: biao <biao@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Tue Nov 4 19:51:25 2014 +0000
update
commit 0bb654ad3d9681017495ad0c8964e29816ca8a5b
Author: zhangdi <zhangdi@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Tue Nov 4 19:19:22 2014 +0000
bug fixed for lod collector
commit 2b265d5b82b10bc79160e3c6dd9d45d1307c2b73
Author: zhangdi <zhangdi@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Tue Nov 4 04:41:51 2014 +0000
RunGeneHunter.py ready
commit f42fe98babd3d81a3cac5e9c2cb0c3a03f056181
Author: zhangdi <zhangdi@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Mon Nov 3 22:07:59 2014 +0000
add RunGeneHunter.py, but with bugs
commit 54d2f9f31d6c019fae588868e7ccfd0ddd80262b
Author: gw <gw@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Thu Oct 30 20:27:57 2014 +0000
revision update
commit 34284c605ac7b44cbd57d1e2c5b0e9a4b6b3a5db
Author: biao <biao@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Thu Oct 30 16:59:11 2014 +0000
update
commit bc7b8ecdeaea9a89a0ca33f3d915833536c6cf0c
Author: gw <gw@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Wed Oct 29 22:33:10 2014 +0000
update revision and respond for ejhg
commit 5fa2137aff3a7f5f61d051e1d57a1119a45ef4e3
Author: biao <biao@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Wed Oct 29 20:24:37 2014 +0000
update
commit 67840df4f45d2a53786af442859d15bdea83762c
Author: gw <gw@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Tue Oct 28 22:17:21 2014 +0000
updates to CHP frequency calculation
commit 5708dc2439672b9c44e1121fbed4e53a0677a289
Author: gw <gw@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Tue Oct 28 19:26:40 2014 +0000
fix getColumn bug
commit ad94b8c3257c721cfc40b24a4be557605296b037
Author: biao <biao@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Tue Oct 28 18:08:02 2014 +0000
add fakeLD feature to simulation program
commit c39757a8fa8a387cc14e866dad2b936a8c0ede3a
Author: biao <biao@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Fri Oct 24 17:39:45 2014 +0000
update
commit 66aa2cddfe43b1acf50ad876916e88d00df4a4ae
Author: gw <gw@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Thu Oct 23 23:22:03 2014 +0000
update R1 respond
commit c0793167b83cbefe82e4734cf67179d9478bba47
Author: biao <biao@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Thu Oct 23 22:24:33 2014 +0000
update LinkagePowerCal.py
commit 10766385a35cc2e08f1e274e7f3713aed77f6c5d
Author: gw <gw@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Mon Oct 13 20:03:43 2014 +0000
finalize poster
commit 2278339bc78d0d4e5ff8181faa8954053d8037ea
Author: gw <gw@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Fri Oct 10 17:04:29 2014 +0000
Add SEQLinkage poster
commit 6ca6d0a1d97f393d9b489ee7ba219c5100fe8841
Author: gw <gw@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Fri Oct 3 21:07:17 2014 +0000
change mkpath implementation
commit dbb28453bb12d67529550582cfe068f54d9754ce
Author: gw <gw@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Fri Oct 3 19:41:20 2014 +0000
safely delete empty dirs
commit 45ba576251bc3224e787c64f598d509749d3912e
Author: gw <gw@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Wed Oct 1 19:07:09 2014 +0000
add material for seqlinkage presentation
commit acc4f71f71d32567b96c1af81fda9f1fcefdcb91
Author: gw <gw@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Wed Aug 20 22:09:31 2014 +0000
update ms
commit d0ec50fdf30bcf5a859ba82b0b346a448608c328
Author: gw <gw@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Mon Aug 11 22:28:52 2014 +0000
format EJHG short report
commit 5e65e7da702aaf45945363379730294afdca3d1b
Author: gw <gw@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Tue Jul 8 22:53:46 2014 +0000
update wiki
commit f7e2d3098fa88209d6a0e79e5eb47c2b122b089f
Author: gw <gw@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Sun May 18 23:35:21 2014 +0000
update supplemental
commit ec9bb68395e049d0e7e84dc2e9c2570f68a8faf4
Author: min <min@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Thu May 8 23:15:09 2014 +0000
update docs
commit cccf5aae4cb6154b36dbcb1a1819164669003bca
Author: zhangdi <zhangdi@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Thu May 8 22:46:54 2014 +0000
linkage programs added
commit 2e2bdbfea0e9a5597158ea05b46eaa15e203306f
Author: gw <gw@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Thu May 8 22:25:31 2014 +0000
lower case for file names
commit 1911af9a3cba72245e975ebf351643cb3ab90ff4
Author: gw <gw@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Thu May 8 21:41:17 2014 +0000
disallow imp, use __import__ to check instead
commit f8aa7947c1f0573663da94b9fa44716dc75bb7fe
Author: zhangdi <zhangdi@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Thu May 8 20:20:54 2014 +0000
format counter bug fixed
commit 30cd0894eb3c6458c5cc7dd597bf56441a9eae94
Author: gw <gw@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Thu May 8 14:43:11 2014 +0000
update wiki
commit 8535c32038d02da50275d14613d3b9ba241cc6b8
Author: gw <gw@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Wed May 7 22:51:18 2014 +0000
minor bug fixes
commit 6b004d5aeb18762bd8c90b2ba6b6a3c81af218b6
Author: zhangdi <zhangdi@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Wed May 7 22:09:32 2014 +0000
add mega2 and merlin examples
commit c4fa96d399c39987a58bac46da56fd15fff8cbb4
Author: gw <gw@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Wed May 7 21:35:10 2014 +0000
fix release script
commit d280e76e401a355983475d98ff77d38b4a7260e5
Author: zhangdi <zhangdi@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Wed May 7 20:37:58 2014 +0000
finish Runner alpha
commit c32cef6a43d691acae429f66759705b8c4df3030
Author: gw <gw@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Wed May 7 20:26:17 2014 +0000
finish up rutgers map documentation
commit e9e2dc67a92d3bc47cc29daae8235cff6e88b6b6
Author: kb <kb@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Wed May 7 20:03:49 2014 +0000
add the script making blueprint
commit fd430dc5bd4046b34ee7d91646be6bf8998bac65
Author: kb <kb@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Wed May 7 19:58:32 2014 +0000
add blueprint
commit fc2ceee56e1074a581effdf0c1192ea92116c0b8
Author: zhangdi <zhangdi@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Wed May 7 19:32:19 2014 +0000
merlin format added
commit 29fa74bd652314c99d4218844e3536a8b67a10f6
Author: zhangdi <zhangdi@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Wed May 7 18:51:30 2014 +0000
bug fixed
commit f743bd3713213b0b506f187feed8ece0fc9e2c33
Author: zhangdi <zhangdi@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Wed May 7 18:50:02 2014 +0000
bug fixed
commit b9a6921a1b896363be4cecbb70845268168a6ef0
Author: zhangdi <zhangdi@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Wed May 7 18:33:09 2014 +0000
mega2 added
commit 8d22bc0fb7eefa2000fed1713e67f06ca0b15052
Author: gw <gw@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Wed May 7 16:20:28 2014 +0000
update manuscript
commit 9051091ba94fc79ae76ffa91513b24ee41101a7d
Author: gw <gw@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Mon May 5 22:38:44 2014 +0000
add power db
commit 75983541308481989dabd6af2a2d9f88ac0fc6f7
Author: gw <gw@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Mon May 5 22:37:39 2014 +0000
upload power figs
commit c43be95e69bc9657eb4a2b078ad83ac5e077cf30
Author: gw <gw@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Fri May 2 02:38:29 2014 +0000
upload data
commit 582af6b6375e4db820464bd780078b44c9a67eed
Author: zhangdi <zhangdi@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Thu May 1 19:04:53 2014 +0000
add demo data
commit 44b1816d092e864d8cc3f9476ecd7d49dfc7fa79
Author: gw <gw@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Thu May 1 14:05:55 2014 +0000
add plot update
commit ad5e4bbe628cab4f7d94d13ed54473a8e7f46033
Author: min <min@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Thu May 1 14:01:42 2014 +0000
upload power notes
commit 95ed5354491283f29e6dc81c035232fa422d5ba2
Author: gw <gw@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Mon Apr 28 23:09:01 2014 +0000
update website
commit 8dd70576b6ba15484fd7a4b56bebf0e859441e22
Author: min <min@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Sat Apr 26 03:24:19 2014 +0000
simulation script is now indep of seqlink
commit 13898f70e490c6d7084ddaa7d2ff5a824285690d
Author: gw <gw@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Tue Apr 22 04:47:07 2014 +0000
update ms
commit a8125c22e511f0f0a44fbaf29d7c77c4d644111e
Author: zhangdi <zhangdi@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Mon Apr 21 19:22:25 2014 +0000
SubmitJobs.pbs updated
commit d68e0e12d5ff1dfd2d87c8548d9cb9a503fdfd4d
Author: gw <gw@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Mon Apr 21 18:18:16 2014 +0000
update simulation results
commit abad4655fb10bf091510b831ed496a994480daf2
Author: gw <gw@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Fri Apr 18 19:36:27 2014 +0000
bug fix to hlod score collection in simulatio nscript ... have to thus rerun the simulation
commit 9cb2ebc552a377d8b7736d3fb647d1fdf9c3bf80
Author: gw <gw@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Wed Apr 16 20:57:16 2014 +0000
update docs
commit 25d4669638eb1d1c4ca1e2296aadbaaa880bfcbb
Author: gw <gw@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Wed Apr 16 03:40:54 2014 +0000
update wiki
commit 8d8aa9ab3f2acddaacfd525d708e88a339eaf7a7
Author: gw <gw@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Tue Apr 15 22:51:20 2014 +0000
update wiki
commit d52e6c45d55f935c4cbb2dbab6b0a1f18a500ff6
Author: gw <gw@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Tue Apr 15 22:34:49 2014 +0000
minor fixes
commit 5b87f7f006a32f46b0849366820682aa5bdac4d2
Author: gw <gw@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Tue Apr 15 18:02:36 2014 +0000
polish html output style
commit 4b403a93399665ead1a2088598c0b2a23f3e8132
Author: gw <gw@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Tue Apr 15 15:58:42 2014 +0000
more clean up of code
commit 8a9d882e5074b3880c5e9efdae13ba22ea4f7e56
Author: gw <gw@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Tue Apr 15 04:34:50 2014 +0000
clean up codes
commit 4432a653e6031bac4067ba3ef3c2d8f7e85cd695
Author: zhangdi <zhangdi@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Fri Apr 11 21:56:08 2014 +0000
progress percent added for linkage pipeline
commit 060d1563a0f702cb78fd299395c489bfb9ef9649
Author: zhangdi <zhangdi@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Fri Apr 11 15:11:46 2014 +0000
handle freq
commit 6bb4f702978d6f04f5ed088ec3861d2ab3b8146a
Author: gw <gw@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Fri Apr 11 15:00:43 2014 +0000
allow non zero return code from fastlink
commit 02da0ae215a02108b1d533f19bc3cac5d9f55dc7
Author: gw <gw@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Thu Apr 10 22:56:50 2014 +0000
add script to build binary release
commit d33d18e6ac11346396b85450abfd3f4345b388c4
Author: gw <gw@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Thu Apr 10 21:27:56 2014 +0000
update doc
commit a996a53d4a38dd94ceed0da20cfe84d9f142eccb
Author: gw <gw@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Thu Apr 10 18:56:49 2014 +0000
update doc
commit 8716cf14ac9576235b06a2141db22d66cc76f481
Author: zhangdi <zhangdi@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Thu Apr 10 16:38:14 2014 +0000
minor fix
commit a37fc8f1fe2eb92655864da41a922d5904dab2ff
Author: gw <gw@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Thu Apr 10 02:54:54 2014 +0000
accept genemap.txt change
commit 3bb5410db90fee16780dc9d14e1550fa6675d9c6
Author: kb <kb@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Thu Apr 10 00:30:00 2014 +0000
add genemap_cleaned.txt
commit 73f9d56c821a71793f0ed1d25af7c0b124941dab
Author: kb <kb@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Thu Apr 10 00:29:02 2014 +0000
cM_genemap_cleaned.txt is new genetic position file for genes
commit 5dbf5f4b12f58bdd2c77c470d499b01ea2b48571
Author: zhangdi <zhangdi@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Wed Apr 9 22:20:48 2014 +0000
freq handling bug fixed
commit 47ee92902a71df5bdeaea2a9c09b35cf7f6c36a1
Author: zhangdi <zhangdi@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Wed Apr 9 22:17:48 2014 +0000
freq handle bug fixed
commit 383e8172af31f1ea8ab71743ea707116492f0ba8
Author: zhangdi <zhangdi@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Wed Apr 9 21:54:36 2014 +0000
freq handle bug fixed
commit 720ea9c1a8a3248a0c6154e03fec5187ee6f3628
Author: zhangdi <zhangdi@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Wed Apr 9 21:35:00 2014 +0000
Runner bugs fixed
commit 048f4456ab7c5ee7ca35466a87bd9c2487423125
Author: zhangdi <zhangdi@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Wed Apr 9 21:31:32 2014 +0000
genemap.txt updated
commit 0e095e9398a3defb4365aa230c3dd333252c6571
Author: gw <gw@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Wed Apr 9 15:56:53 2014 +0000
add --quiet argument
commit 90a392d06cf82c12db9ecc0b24cbb4327aad241d
Author: min <min@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Wed Apr 9 03:48:45 2014 +0000
update documentation
commit 69c9f0c4e401cb2f2b920062f4a1aab2b1ccf950
Author: gw <gw@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Tue Apr 8 23:33:12 2014 +0000
update wiki and interface
commit b27174dfe61f1a053d3d09c11a34607096f71355
Author: zhangdi <zhangdi@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Tue Apr 8 16:33:35 2014 +0000
Simlation in cluster
commit c019d9976f91a4c55c290c84b2f8996c88b0bf60
Author: gw <gw@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Mon Apr 7 20:37:11 2014 +0000
fix critical bug in simulation script
commit f4ffeba62dd0e119a9e6bfe71bbab795dd6e7da8
Author: gw <gw@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Mon Apr 7 18:29:43 2014 +0000
fix stupid bu
commit 59f313740ca7be70580da05f2f9b123b0e0a0f17
Author: gw <gw@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Mon Apr 7 17:04:05 2014 +0000
more fix to simulation script
commit c6f7f2765f316833aefc54d58094b04f2e157b3d
Author: gw <gw@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Fri Apr 4 21:39:43 2014 +0000
update manuscript and documentation
commit b54c573fdb74a8d29afa660278f5c79c2381ba7d
Author: kb <kb@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Fri Apr 4 20:37:10 2014 +0000
add symbolic link script
commit 5a19a3edcffe438ed4f82e96b72c2bebefcc6d4a
Author: kb <kb@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Fri Apr 4 19:29:02 2014 +0000
modified blueprint
commit fe8a31bc8703f93275b2e8008fd396dec17d9f32
Author: gw <gw@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Fri Apr 4 19:12:44 2014 +0000
update simulation data
commit c6bdab426a7ec4e060e7438251cb30cb6966111a
Author: kb <kb@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Fri Apr 4 19:10:23 2014 +0000
sorted data
commit e86f1f90f6a9811b39da3464f44bbe0669d1d75e
Author: kb <kb@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Fri Apr 4 17:24:17 2014 +0000
data daihang
commit f21cc3373809c47e72bd5ea489f909463959734b
Author: gw <gw@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Fri Apr 4 16:47:54 2014 +0000
minor fix to temp dir
commit 4cea8aa700d7e151631c86fac7595eddd21f4e5e
Author: gw <gw@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Fri Apr 4 14:18:51 2014 +0000
minor fix
commit f135019b9895fcdec80a47a79f000d3cf9a326e1
Author: gw <gw@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Fri Apr 4 04:43:02 2014 +0000
fix simulation script: concept was wrong for allelic het and compound recessive\!
commit 07b90c5d89fdcdc04ea208bb58aa7176018a8171
Author: gw <gw@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Thu Apr 3 22:15:08 2014 +0000
add power plot script and results
commit 502b594b80ba298c3750740cf86387ad21976073
Author: gw <gw@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Thu Apr 3 18:37:06 2014 +0000
initial simulation result data
commit 5f62e5f95becc2ee7cc973f8abe4e3cf9d0e89d7
Author: gw <gw@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Thu Apr 3 03:09:59 2014 +0000
update MS and simulation
commit 7852cac9b1117470360937c0ab95766e0d377089
Author: gw <gw@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Thu Apr 3 03:09:02 2014 +0000
disable plot if --output-entry is zero
commit acb67b942ce37287d63974f7ff2d0c18afe9add2
Author: gw <gw@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Wed Apr 2 22:23:30 2014 +0000
update simulation scrhip
commit 6c2eeb4dbe6cdb4e927348afde5a4c0f2e683c96
Author: gw <gw@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Wed Apr 2 22:23:13 2014 +0000
minor bug fix
commit 86a8daa5b8523de41d2a76d62faabbed35d5932b
Author: zhangdi <zhangdi@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Wed Apr 2 20:59:39 2014 +0000
Empty dir bug fixed
commit e22dd2e77cb595ab1bea6ceb1db19c7a8fc38530
Author: gw <gw@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Wed Apr 2 20:25:39 2014 +0000
tempdir option
commit b7676ee4b7f2c85ca461cbba65b88dcb2a26eca6
Author: gw <gw@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Wed Apr 2 19:43:36 2014 +0000
fix env.error exit behavior
commit aa88b9fcc0e662e5bac02c22914b20d6d37da656
Author: zhangdi <zhangdi@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Wed Apr 2 19:30:34 2014 +0000
rm linkmap lodscore
commit 33e455afa76e466a4493756900007eaa29a473ee
Author: gw <gw@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Wed Apr 2 19:28:19 2014 +0000
bug fixes
commit 404cd38dfb806a0684d3a95d7f871da1a2409515
Author: zhangdi <zhangdi@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Wed Apr 2 18:21:21 2014 +0000
indentation bug
commit 324c56294da5c5f22c1ef0aac3040b86108d941f
Author: min <min@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Wed Apr 2 04:13:40 2014 +0000
reimplement tmp dir mechanism ot allow for multiple instances of the program
commit e6d5301f73bdecb02b106a430473b81bf8227533
Author: gw <gw@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Tue Apr 1 23:23:54 2014 +0000
add additional parameter single_markers
commit f89016ffc5b05f4ea8f925c6ee38a65ff6f8ed5e
Author: gw <gw@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Tue Apr 1 23:15:05 2014 +0000
implemented cache
commit 208bf4ff5c37b74509cfd7eeb19b1d47d911435b
Author: zhangdi <zhangdi@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Tue Apr 1 21:30:10 2014 +0000
tmp_cache
commit da70e41ba722b03c0e1ea391ccbe99c5c2f9cff3
Author: zhangdi <zhangdi@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Tue Apr 1 21:16:27 2014 +0000
env output
commit 5be0027a1bd289753be29fc222f60d419f870d0b
Author: zhangdi <zhangdi@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Tue Apr 1 19:42:49 2014 +0000
handle bp
commit 3e2ecdd5d1202102e3bcc68ce1e2f9b1e4a3bb03
Author: gw <gw@493babdc-ab97-468b-a2ee-949ea25b5092>
Date: Tue Apr 1 19:22:40 2014 +0000
minor fixes, still not working