| e952027 | Luca Venturini | 29 June 2015, 16:21:40 UTC | Other BF same issue | 29 June 2015, 16:21:40 UTC |
| 61f7596 | Luca Venturini | 29 June 2015, 16:19:13 UTC | Other BF same issue | 29 June 2015, 16:19:13 UTC |
| e6ef2b4 | Luca Venturini | 29 June 2015, 16:16:00 UTC | Tentative BF for monoexonic transcripts | 29 June 2015, 16:16:00 UTC |
| 0a7877f | Luca Venturini | 29 June 2015, 15:54:37 UTC | The compare branch should be finalised by now. Merging back into development. | 29 June 2015, 15:54:37 UTC |
| ce91a08 | Luca Venturini | 29 June 2015, 15:54:00 UTC | The compare branch should be finalised - statistics are correct | 29 June 2015, 15:54:00 UTC |
| b3d1d9b | Luca Venturini | 29 June 2015, 08:22:41 UTC | Weekend work | 29 June 2015, 08:22:41 UTC |
| a0c87be | Luca Venturini | 26 June 2015, 12:49:19 UTC | Still going on the Shanghai compare ... | 26 June 2015, 12:49:19 UTC |
| 009d52d | Luca Venturini | 25 June 2015, 17:07:56 UTC | Revert "BF for assigner" This reverts commit e9b237c98dc15402e86c28d060350bb7f2ff4185. | 25 June 2015, 17:07:56 UTC |
| 2905fe7 | Luca Venturini | 25 June 2015, 16:17:55 UTC | Started to rework the logic to have flexible statistics like in RGASP. Still not functional. | 25 June 2015, 16:17:55 UTC |
| e9b237c | Luca Venturini | 25 June 2015, 13:25:43 UTC | BF for assigner | 25 June 2015, 13:25:43 UTC |
| 183c75b | Luca Venturini | 25 June 2015, 13:21:23 UTC | Some BFs for assigner | 25 June 2015, 13:21:23 UTC |
| 4ab23d1 | Luca Venturini | 25 June 2015, 12:46:17 UTC | BF for logging done transcripts | 25 June 2015, 12:46:17 UTC |
| da8b507 | Luca Venturini | 25 June 2015, 12:45:29 UTC | BF for run-ons | 25 June 2015, 12:45:29 UTC |
| b7bbdcb | Luca Venturini | 25 June 2015, 12:36:03 UTC | Moved all things related to compare.py into the shanghai_lib.compare library. Added intron chain stats. | 25 June 2015, 12:36:03 UTC |
| 5176ecc | Luca Venturini | 25 June 2015, 08:01:28 UTC | Switched from threading to simple classes in compare.py - this should reduce a lot of the overhead | 25 June 2015, 08:01:28 UTC |
| 4ca000c | Luca Venturini | 24 June 2015, 19:58:23 UTC | BF - I had introduced an infinite loop by mistake | 24 June 2015, 19:58:23 UTC |
| 25450ce | Luca Venturini | 24 June 2015, 19:43:44 UTC | BF in the binary search | 24 June 2015, 19:43:44 UTC |
| 1f577bf | Luca Venturini | 24 June 2015, 19:11:50 UTC | Added CL to stats output | 24 June 2015, 19:11:50 UTC |
| bd6c3c6 | Luca Venturini | 24 June 2015, 19:07:05 UTC | Downgraded the warning messages to debug messages when I find a non-coding transcript in PC mode | 24 June 2015, 19:07:05 UTC |
| dc22669 | Luca Venturini | 24 June 2015, 18:53:40 UTC | Trying to get only coding genes from the reference | 24 June 2015, 18:53:40 UTC |
| a318b47 | Luca Venturini | 24 June 2015, 18:37:18 UTC | BF - I was ignoring transcripts in unannotated scaffolds for the statistics! | 24 June 2015, 18:37:18 UTC |
| 1869cd8 | Luca Venturini | 24 June 2015, 18:20:10 UTC | Now also skipped transcripts are added to the counter | 24 June 2015, 18:20:10 UTC |
| 67a303b | Luca Venturini | 24 June 2015, 18:13:17 UTC | Tentative to speed up the PC version of compare.py | 24 June 2015, 18:13:17 UTC |
| da37cfb | Luca Venturini | 24 June 2015, 16:43:53 UTC | Added support for having all outputs into a folder | 24 June 2015, 16:43:53 UTC |
| 487db75 | Luca Venturini | 24 June 2015, 16:11:05 UTC | Switched to put_nowait ... hopefully it will not break the program | 24 June 2015, 16:11:05 UTC |
| a122724 | Luca Venturini | 24 June 2015, 15:43:30 UTC | No static storing of bases for the statistics; they are generated dynamically and discarded once finished with a chrom. | 24 June 2015, 15:43:30 UTC |
| 0714172 | Luca Venturini | 24 June 2015, 14:53:17 UTC | Switched to itertools.chain to generate nucls; downgraded to "debug" some logging messages | 24 June 2015, 14:53:17 UTC |
| 8c1b000 | Luca Venturini | 24 June 2015, 13:45:37 UTC | Added "task_done" calls to hopefully speed up the queue | 24 June 2015, 13:45:37 UTC |
| a2a5097 | Luca Venturini | 24 June 2015, 13:14:38 UTC | Moved the result_storer class to a file of its own, otherwise cProfile fails miserably. | 24 June 2015, 13:14:38 UTC |
| 0871996 | Luca Venturini | 24 June 2015, 11:56:24 UTC | BF for compare - wrong variable name | 24 June 2015, 11:56:24 UTC |
| 5b980e9 | Luca Venturini | 24 June 2015, 11:48:55 UTC | BF for compare - tr.parent is a list, not a string | 24 June 2015, 11:48:55 UTC |
| e05f0d9 | Luca Venturini | 24 June 2015, 11:46:33 UTC | BF for compare - (u,) instead of bare u when checking if a hit is non-placed | 24 June 2015, 11:46:33 UTC |
| c3aaec4 | Luca Venturini | 24 June 2015, 11:44:24 UTC | BF for compare - distance is not necessarily an int | 24 June 2015, 11:44:24 UTC |
| fe68678 | Luca Venturini | 24 June 2015, 11:37:07 UTC | Modified the gitignore. Compare now has proper intron/exon/base level support. | 24 June 2015, 11:37:07 UTC |
| 4ec1609 | Luca Venturini | 24 June 2015, 07:53:23 UTC | Now the RefMap has also the best gene match, not only the best transcript match | 24 June 2015, 07:53:23 UTC |
| 5a969ad | Luca Venturini | 23 June 2015, 16:09:25 UTC | Added global statistics to compare.py. It is not perfect .. the numbers of missed/novel exons are too high compared to CCompare, I am too stringent with the match definition. | 23 June 2015, 16:09:25 UTC |
| 9f59f4c | Luca Venturini | 23 June 2015, 10:49:25 UTC | Switched from namedtuple to a __slots__-powered class for the results. Makes sorting, passing through queues, etc. much easier. | 23 June 2015, 10:49:25 UTC |
| 292b646 | Luca Venturini | 22 June 2015, 17:59:10 UTC | Gff_stats should be OK now. | 22 June 2015, 17:59:10 UTC |
| 22e106a | Luca Venturini | 22 June 2015, 17:20:45 UTC | BF for get_best | 22 June 2015, 17:20:45 UTC |
| 10c492d | Luca Venturini | 22 June 2015, 17:12:56 UTC | BF for get_best | 22 June 2015, 17:12:56 UTC |
| 7f53222 | Luca Venturini | 22 June 2015, 16:58:58 UTC | BF for get_best | 22 June 2015, 16:58:58 UTC |
| 6084afa | Luca Venturini | 22 June 2015, 16:56:26 UTC | BF for get_best | 22 June 2015, 16:56:26 UTC |
| d5d46f3 | Luca Venturini | 22 June 2015, 16:54:34 UTC | BF for get_best | 22 June 2015, 16:54:34 UTC |
| 23563e9 | Luca Venturini | 22 June 2015, 16:50:44 UTC | Fixed ordering for non-fused transcripts | 22 June 2015, 16:50:44 UTC |
| a24431f | Luca Venturini | 22 June 2015, 15:57:34 UTC | Third BF for the distance | 22 June 2015, 15:57:34 UTC |
| ce1db9c | Luca Venturini | 22 June 2015, 15:55:44 UTC | Second BF for the distance | 22 June 2015, 15:55:44 UTC |
| 69256fa | Luca Venturini | 22 June 2015, 15:50:31 UTC | BF for the distance and the fusion genes in refmap | 22 June 2015, 15:50:31 UTC |
| 9804e80 | Luca Venturini | 22 June 2015, 14:00:44 UTC | Solved the logging issue | 22 June 2015, 14:00:44 UTC |
| f1fe248 | Luca Venturini | 22 June 2015, 13:01:14 UTC | BF for reporting output | 22 June 2015, 13:01:14 UTC |
| 0db6de8 | Luca Venturini | 22 June 2015, 12:53:09 UTC | Log BF | 22 June 2015, 12:53:09 UTC |
| 02c30c4 | Luca Venturini | 22 June 2015, 12:51:58 UTC | Switched from typecheck to boolean flag - should be faster | 22 June 2015, 12:51:58 UTC |
| 6e06c7f | Luca Venturini | 22 June 2015, 12:48:51 UTC | Fixed GFF3/GTF support | 22 June 2015, 12:48:51 UTC |
| 735e6e9 | Luca Venturini | 22 June 2015, 11:33:57 UTC | Finished with the implementation of refmap. Added the "distance" field to double-check the polymerase run-ons | 22 June 2015, 11:33:57 UTC |
| 88a54dd | Luca Venturini | 22 June 2015, 10:54:57 UTC | Added GFF support for compare.py | 22 June 2015, 10:54:57 UTC |
| ec13d7d | Luca Venturini | 22 June 2015, 09:34:41 UTC | Added GFF support for compare | 22 June 2015, 09:34:41 UTC |
| f01727a | Luca Venturini | 22 June 2015, 07:32:17 UTC | Minor weekend modifications | 22 June 2015, 07:32:17 UTC |
| 4c05f39 | Luca Venturini | 19 June 2015, 16:31:54 UTC | Removed unused imports/variables | 19 June 2015, 16:31:54 UTC |
| 2198f10 | Luca Venturini | 19 June 2015, 12:13:01 UTC | Hopefully fix for the strand filtering | 19 June 2015, 12:13:01 UTC |
| 7d1adb5 | Luca Venturini | 19 June 2015, 12:08:09 UTC | BFs and debugging | 19 June 2015, 12:08:09 UTC |
| 4de6a59 | Luca Venturini | 19 June 2015, 11:54:40 UTC | Fix for the fusions .. again ... | 19 June 2015, 11:54:40 UTC |
| ed824ba | Luca Venturini | 19 June 2015, 11:34:05 UTC | Now fusions are detected only if genes are on the same strand, not opposite strands. | 19 June 2015, 11:34:05 UTC |
| 623864d | Luca Venturini | 19 June 2015, 08:31:07 UTC | BF for compare | 19 June 2015, 08:31:07 UTC |
| b122603 | Luca Venturini | 19 June 2015, 08:19:57 UTC | Added a "protein-coding" option to compare.py | 19 June 2015, 08:19:57 UTC |
| b8c97ac | Luca Venturini | 19 June 2015, 07:50:11 UTC | Disabled MP completely. Added CL to log. | 19 June 2015, 07:50:11 UTC |
| dba42c6 | Luca Venturini | 19 June 2015, 07:38:49 UTC | Disabled multiprocessing ... let's have a look .. | 19 June 2015, 07:38:49 UTC |
| 62d6529 | Luca Venturini | 19 June 2015, 07:29:34 UTC | Switch from context to module level for pool | 19 June 2015, 07:29:34 UTC |
| c6f20f7 | Luca Venturini | 19 June 2015, 07:09:24 UTC | Switched to multiprocessing.Pool. Tired of this. | 19 June 2015, 07:09:24 UTC |
| c208722 | Luca Venturini | 19 June 2015, 06:53:21 UTC | Switched to concurrent.futures for compare. This time it seems to function. | 19 June 2015, 06:53:21 UTC |
| 0a018f2 | Luca Venturini | 18 June 2015, 22:04:42 UTC | BF for checking chromosomes with no transcripts | 18 June 2015, 22:04:42 UTC |
| 384492c | Luca Venturini | 18 June 2015, 21:54:50 UTC | Added a sleep for checking the jobs in the while loop | 18 June 2015, 21:54:50 UTC |
| 60fdb3f | Luca Venturini | 18 June 2015, 21:43:22 UTC | Switched to multiprocessing. I am going to kill whoever invented the pickling mechanism.... | 18 June 2015, 21:43:22 UTC |
| 67fbf00 | Luca Venturini | 18 June 2015, 20:33:29 UTC | Minor output fixing | 18 June 2015, 20:33:29 UTC |
| ab3bdba | Luca Venturini | 18 June 2015, 20:27:13 UTC | Removed verbose flags put there for debugging | 18 June 2015, 20:27:13 UTC |
| cb9ba6f | Luca Venturini | 18 June 2015, 20:16:37 UTC | Hopefully fixed the hanging issue in compare.py | 18 June 2015, 20:16:37 UTC |
| 7822296 | Luca Venturini | 18 June 2015, 18:11:16 UTC | Changed definition of polymerase run-on to consider the strand | 18 June 2015, 18:11:16 UTC |
| 2b29c7d | Luca Venturini | 18 June 2015, 17:26:02 UTC | Add gene name - BF6 | 18 June 2015, 17:26:02 UTC |
| b2498b1 | Luca Venturini | 18 June 2015, 17:24:41 UTC | Add gene name - BF5 | 18 June 2015, 17:24:41 UTC |
| 33c90af | Luca Venturini | 18 June 2015, 17:23:56 UTC | Add gene name - BF4 | 18 June 2015, 17:23:56 UTC |
| 5081e8e | Luca Venturini | 18 June 2015, 17:22:05 UTC | Add gene name - BF3 | 18 June 2015, 17:22:05 UTC |
| 17e3f30 | Luca Venturini | 18 June 2015, 17:20:40 UTC | Add gene name - BF2 | 18 June 2015, 17:20:40 UTC |
| 58ed707 | Luca Venturini | 18 June 2015, 17:19:51 UTC | Add gene name - BF | 18 June 2015, 17:19:51 UTC |
| b35b59e | Luca Venturini | 18 June 2015, 17:17:02 UTC | Add gene name | 18 June 2015, 17:17:02 UTC |
| d49f8c3 | Luca Venturini | 18 June 2015, 17:05:02 UTC | BF for library loading | 18 June 2015, 17:05:02 UTC |
| 3552534 | Luca Venturini | 18 June 2015, 17:03:36 UTC | BF for invalid transcripts | 18 June 2015, 17:03:36 UTC |
| f3b717e | Luca Venturini | 18 June 2015, 16:59:53 UTC | First BF | 18 June 2015, 16:59:53 UTC |
| 3c8eeac | Luca Venturini | 18 June 2015, 16:55:27 UTC | debugging compare .. | 18 June 2015, 16:55:27 UTC |
| 146cb12 | Luca Venturini | 18 June 2015, 16:46:32 UTC | BF for compare, bad tuple assignment | 18 June 2015, 16:46:32 UTC |
| 68591b1 | Luca Venturini | 18 June 2015, 16:35:56 UTC | BF for compare | 18 June 2015, 16:35:56 UTC |
| d5880f3 | Luca Venturini | 18 June 2015, 16:32:39 UTC | BF for GTF class | 18 June 2015, 16:32:39 UTC |
| 8404762 | Luca Venturini | 18 June 2015, 16:20:47 UTC | Added multithreading to the compare utility | 18 June 2015, 16:20:47 UTC |
| 8bfc32f | Luca Venturini | 18 June 2015, 15:53:25 UTC | Removed the dependencies from multiprocessing, transitioned to queue, threading and concurrent.futures. No more pickling problems! | 18 June 2015, 15:53:25 UTC |
| 346818c | Luca Venturini | 18 June 2015, 15:40:08 UTC | The compare utility seems to have reached a good maturity. Time to test it on the whole input. | 18 June 2015, 15:40:08 UTC |
| 77894bc | Luca Venturini | 17 June 2015, 16:58:20 UTC | Still a long way to go for compare | 17 June 2015, 16:58:20 UTC |
| 72cdcad | Luca Venturini | 17 June 2015, 10:21:52 UTC | Reverted to the threading approach. As feared, the coroutine approach was a bad idea(TM) because the printer gets started only AFTER the processing has finished ... cue massive and useless memory usage .. | 17 June 2015, 10:21:52 UTC |
| bd784c7 | Luca Venturini | 17 June 2015, 10:15:18 UTC | Modified setup.py | 17 June 2015, 10:15:18 UTC |
| 2afc0b1 | Luca Venturini | 17 June 2015, 09:55:35 UTC | Minor BF for creator | 17 June 2015, 09:55:35 UTC |
| 9876ca2 | Luca Venturini | 17 June 2015, 07:40:24 UTC | Removed a stray asyncio.sleep | 17 June 2015, 07:40:24 UTC |
| a7a45fc | Luca Venturini | 17 June 2015, 07:39:26 UTC | Switched to a coroutine for the printing process. | 17 June 2015, 07:39:26 UTC |
| e9f7cf3 | Luca Venturini | 17 June 2015, 00:45:32 UTC | Using 3 instead of 10 max sequences improves runtime. It might be the only solution for the DB lookup, short of moving to MySQL | 17 June 2015, 00:45:32 UTC |
| 8a43713 | Luca Venturini | 17 June 2015, 00:28:29 UTC | Switched to concurrent.futures for the execution pool. AsyncIO proved to be much more efficient than threading. | 17 June 2015, 00:28:29 UTC |
