CCseqBasicM code changes log file
This log was Last updated by Jelena :
Mon Oct 8 16:56:53 BST 2018
commit c87aa33a76842be0713d64b8811ddf743fda9793
Author: telenius
Date: Mon Oct 8 01:25:17 2018 +0100
release CM5 with multiQC reports
commit ae3f9eb55ff41643a8b3e7e6e6ff24b474bad1ae
Author: telenius
Date: Sun Oct 7 22:10:37 2018 +0100
adding multiQC reports in properly
commit 9fa15e8f9e24ce829d9da8b80c1218a7f891992b
Author: telenius
Date: Sun Oct 7 15:31:19 2018 +0100
release to CM5 with the new features
commit afd292db05cbd76c324ecce95b1e76f44342dc1d
Author: telenius
Date: Sun Oct 7 15:10:08 2018 +0100
first working master cis-only hub
commit 3d9229a1e162b51ceeaa0fec3eb8eed0285d316d
Author: telenius
Date: Sun Oct 7 14:48:09 2018 +0100
starting to build the master hub for all chromosomes
commit 4170a3a6c9db1d560ab2d7b9a58516fd2afd12ef
Author: telenius
Date: Thu Oct 4 18:07:40 2018 +0100
boxplot and finalising the javascript
commit a0a4c65a249f995b3562551c1d78e94adef02105
Author: telenius
Date: Thu Oct 4 16:24:28 2018 +0100
finalising javascript pies and bars
commit 178a81345e3c61cb10efa42e87658e423f0f3527
Author: telenius
Date: Thu Oct 4 16:13:21 2018 +0100
javascript pie charts, bar charts
commit 12ae794f5fb68776b85ccad9456c5ba9041302a9
Author: telenius
Date: Wed Oct 3 19:06:49 2018 +0100
starting javascript made figures
commit eadab6b08b4de839a4c9ad685a940b5324df782a
Author: telenius
Date: Wed Oct 3 18:04:21 2018 +0100
separating stats text file to different file
commit f2195346228aa3121f92aaea6168e629737ede1b
Author: telenius
Date: Wed Oct 3 17:44:39 2018 +0100
detaching the description.html
commit 5620e9899759cfc6051a2493bb35d9e05bfc01fa
Author: telenius
Date: Wed Oct 3 16:15:23 2018 +0100
detaching the description page into index.html
commit b6f4d394a7590789d138e3d9c7ee8e098c94b0fd
Author: telenius
Date: Wed Oct 3 15:42:56 2018 +0100
summary counts folderB
commit c1321bf3c008cb247f65e28092d1a4a0e754ae2f
Author: telenius
Date: Wed Oct 3 15:32:54 2018 +0100
RE cut counters Flashing counters
commit dbc733685e4392baa95cdbf9084bca5ed85720c6
Author: telenius
Date: Wed Oct 3 15:11:10 2018 +0100
combined RE cut counters Flashing counters
commit da0acf0cf5f04ccc3a2323a2416bc0f2040bb2f3
Author: telenius
Date: Wed Oct 3 08:43:09 2018 +0100
raw sams hubbing fix
commit 5e57a4850ab67082ed950d8c2051df689f3fddde
Author: telenius
Date: Tue Oct 2 21:46:22 2018 +0100
fixing tracks, hubs
commit 834807cacf1d4f3be3b8ac0f2f40c90d7676819a
Author: telenius
Date: Tue Oct 2 17:42:32 2018 +0100
some UNFINISHED improvements to tracks and hubs and reports
commit ab7ac1ee70f15d6eaca2fa5f21e53eb254c617bd
Author: telenius
Date: Thu Sep 27 17:19:58 2018 +0100
raw sam tracks support fixes
commit c908b39a727f0619b78f85b8d5ff3bea7500ad62
Author: telenius
Date: Thu Sep 27 12:00:25 2018 +0100
raw mapped sam bigwigs tracks generation
commit b32e22996915fb8c94856b294db1839eafc7e7cd
Author: telenius
Date: Wed Sep 26 16:32:02 2018 +0100
linking hub addresses list to description.html
commit b951bed6e589e88da3be1fa327825313b338b462
Author: telenius
Date: Wed Sep 26 16:23:36 2018 +0100
oligo-wise counters, description.html improvements
commit 9591a293676a757d173afd41b239deeb5d8b4f77
Author: telenius
Date: Wed Sep 26 15:18:13 2018 +0100
hubbing for normalised tracks
commit 078909767c3a3a981b346b0055bde463e838a0f6
Author: telenius
Date: Wed Sep 26 15:05:32 2018 +0100
generating bigwigs for normalised tracks
commit ac14347dbfeb1e19bb7b534ec17683de87c8419f
Author: telenius
Date: Tue Sep 25 18:55:48 2018 +0100
reverting previous
commit 0c68430d3eb71466351491fcca2fee695fcbdae0
Author: telenius
Date: Tue Sep 25 18:42:17 2018 +0100
hubbing typo correction
commit 2f1efc3217db58bcfe81b7412cbe56afcdf778f5
Author: telenius
Date: Tue Sep 25 18:27:26 2018 +0100
threaded runs support
commit ecc8eaf0c4911773b283118e1b31d1f02e8196ca
Author: telenius
Date: Tue Sep 25 18:00:07 2018 +0100
threaded run support
commit bea415781062dccfe43191b330f62871381d43c3
Author: telenius
Date: Tue Sep 25 15:47:50 2018 +0100
exit 1 fixes and threaded support
commit 7613a592465517cd079ccbb4739956e0423d5f55
Author: telenius
Date: Tue Sep 25 14:57:57 2018 +0100
threaded runs support
commit 8e08a3348cf4147b137a006b6de987ecad715ddf
Author: telenius
Date: Sat Sep 22 17:38:28 2018 +0100
typo correction in description.html
commit 03c500aa08eed4b7968ef1240946d5eac45accd1
Author: telenius
Date: Tue Sep 18 21:39:46 2018 +0100
bug fix for filter.sh (FLASHED_FILTERED files went missing)
commit 2f12241ce7dcb1c35dbb4c8eec1345529da574f6
Author: telenius
Date: Tue Sep 18 11:05:38 2018 +0100
finalising hubbing
commit f9decfb8c7a9f8a6dee41c5b4124c2a979ce66a2
Author: telenius
Date: Tue Sep 18 09:25:10 2018 +0100
first working rainbow hubbing
commit 8de92e5ec1853ebf7762e62f655034de7f2143d9
Author: telenius
Date: Tue Sep 18 06:54:40 2018 +0100
hub colors bug fixes
commit d61834bc97fd393ce63d290e2f88f6aea1e59389
Author: telenius
Date: Mon Sep 17 17:49:22 2018 +0100
hub generation bug fixes
commit 95a4483065c7ae449e07a03fb81b8ffad8bca627
Author: telenius
Date: Mon Sep 17 12:58:29 2018 +0100
bug fixes hubbing subroutines
commit e9ddef41e78bf4f3aa396dbfb93544467c543ec9
Author: telenius
Date: Mon Sep 17 08:45:40 2018 +0100
bug fixes for the hubbing protocol
commit 0ea66c10e84c3b91b5a31cac63be773949a0bd29
Author: telenius
Date: Sun Sep 16 22:54:46 2018 +0100
bug fixes for the data hub generation subroutines
commit 4687b62ff8df3aecd8a967ba92930cc53a900ac0
Author: telenius
Date: Sun Sep 16 08:30:17 2018 +0100
--onlyHub and E_cleanupScript_toUse_afterSuccesfull_Run.sh
Adding the final missing subroutines, making the code complete. This is the first alpha testing version.
commit 4d2739123b3957a84484b6253af7d185adf15443
Author: telenius
Date: Sat Sep 8 08:13:17 2018 +0100
typo corrections in if clauses
commit ffe514f5326a554109d3d2ce4d84e3a6422a761a
Author: telenius
Date: Fri Sep 7 23:52:10 2018 +0100
typo correction in if clause
commit 0afcc8f6dd96fac848d6edddc99e06bbb38a56b8
Author: telenius
Date: Fri Sep 7 00:00:04 2018 +0100
fixing LOOP2 crash due to whole chr file being empty
commit 413f0c2e318bca465670cd132cbfe0ab9c7f6bfb
Author: telenius
Date: Tue Sep 4 21:21:27 2018 +0100
summary count log typo fixes
commit 60df2a6adf546bdf77b56660f17b25e7bbae909b
Author: telenius
Date: Mon Sep 3 10:28:36 2018 +0100
bug fixes to log file counters in LOOPs
commit b6bcd4dca3581a4d2d44ce4582a5e1bd49e59bfe
Author: telenius
Date: Mon Sep 3 10:03:43 2018 +0100
adding more run crash testers to parallel loop ends
commit d7eb5e4f7ae3f6310462eac826ff0c5d196d91bf
Author: telenius
Date: Sat Sep 1 21:57:00 2018 +0100
usage reports auto-parser for wholenode runs
commit 2d67a98d42c3f06b80931498be4c6a16cb903daa
Author: telenius
Date: Sat Sep 1 09:35:50 2018 +0100
adding tester for bug-related parallel run crashes
commit cd5040c9b1c78b71ec45c461b48c8c437d2e60b4
Author: telenius
Date: Sat Sep 1 00:18:00 2018 +0100
parse bug fix - capteure site names containing each others caused crashes
commit 1e79223205320cac070bbb4454ec4c815654b9f5
Author: telenius
Date: Thu Aug 30 12:30:01 2018 +0100
taking out the rest of the rate limiting du commands
commit d8aeebc94b79d48b28deb970d9a2b9b0ae74b8df
Author: telenius
Date: Wed Aug 29 11:33:48 2018 +0100
adding folder B and D summary txt files
commit 41b681222661efa7a5e6c1aee68420b39627f996
Author: telenius
Date: Wed Aug 29 10:46:01 2018 +0100
turning off globin combining, adding some LOOPs total counters
commit 533dcf5ee743eff84030d1f3652700ebc3aa46e1
Author: telenius
Date: Thu Aug 23 15:15:14 2018 +0100
adding summary table of all LOOPs
adding summary table of all LOOPs
and fixing LOOP5 table counters and heading line
commit 0b3411a06cd37402871b8863929dc91837f2a57f
Author: telenius
Date: Thu Aug 23 10:33:20 2018 +0100
fixing a LOOP5 counter
commit 17c498cd652e2913605ba42779d90550d96fd311
Author: telenius
Date: Wed Aug 22 14:49:51 2018 +0100
10 min stagger all the way through for folderB
commit 6c789382b93e9d543295cc22257795606df8bb20
Author: telenius
Date: Fri Aug 17 18:52:00 2018 +0100
blat support to missing sam files (if no captures after F3)
commit 3e10ba0c85b9f9035533383bba3bf7eed49b08d4
Author: telenius
Date: Thu Aug 16 17:32:05 2018 +0100
support to oligos which get empty Blat and Ploidy filter
support to oligos which have no reads in RE fragments marked to be blat or ploidy filtered
commit 5edda8dac54e3ea0c1d15c7b82c8f90ab3aa94b6
Author: telenius
Date: Wed Aug 8 17:32:04 2018 +0100
RAM tester addition
commit d642ad249f50a2e1b55895db8c5b15d7ed2a923c
Author: telenius
Date: Wed Aug 8 16:54:46 2018 +0100
faster and more rarely reporting in loopers
commit 81fb717be21c62ba82a5eb5dc9e2986dfaae6f3e
Author: telenius
Date: Tue Aug 7 15:59:35 2018 +0100
the missing top logs fix, and more processors for fast stuff
commit 2712162f229f43d147b9bb95b4720a6a5e2f133e
Author: telenius
Date: Tue Aug 7 15:31:12 2018 +0100
fixing F4 folder blat filter part, disabling globin combining for time being
commit aab792dfde0bf696e2e08a35b0614e92c64d2f3a
Author: telenius
Date: Tue Aug 7 13:12:06 2018 +0100
seeking the missing allRunsJUSTNOW log file
commit 6a0dcd52b2aa03d82042b2a75992cc340a8f1a72
Author: telenius
Date: Mon Aug 6 14:08:11 2018 +0100
adding top counters for bamcombining
commit 1e56f579f93a11379863c7dc54f6d25239bfaed4
Author: telenius
Date: Mon Aug 6 13:01:30 2018 +0100
bam looper sleepseconds to 1
commit 20d6e77f01ff149919844c260769fecbb30623cb
Author: telenius
Date: Fri Aug 3 16:49:46 2018 +0100
adding usage counters from top command
commit 82290843a14d2884d4ee7da6c49fd5c5a75b69d3
Author: telenius
Date: Wed Aug 1 18:33:17 2018 +0100
wrong column in df command
commit 447a3b919cb0cc6f98f2e08330338c0b573d3624
Author: telenius
Date: Wed Aug 1 17:45:26 2018 +0100
more du to df TMPDIR changes
commit 6c9c81d002fccf4cb027d4c38b88794be2127626
Author: telenius
Date: Tue Jul 31 17:12:40 2018 +0100
using df instead of du in TMPDIR memory count
commit 86baea7026ef299d657a86123179efe1936b012c
Author: telenius
Date: Mon Jul 30 14:49:27 2018 +0100
staggering first runs to 10x sleepseconds
staggering first runs to 10x sleepseconds
to avoid mem peak in REdig script
commit 797c71643d269163a2f2ecd7e1c237dd264adb95
Author: telenius
Date: Tue Jul 10 13:16:10 2018 +0100
final changes before Full Scale Test
commit 5c24fcf64064a82095b53e7250c90b16800862ad
Author: telenius
Date: Mon Jul 9 11:07:37 2018 +0100
chromosome parse fix in LOOPs 1-5
commit ba8f1a001ad76e477d7c51872f848bd9356d5a8a
Author: telenius
Date: Fri Jul 6 17:13:42 2018 +0100
looper fix in LOOP3
and safety features add into serial scripts (so that they crash any time something goes wrong - not foolproof still, but better now)
commit 126cd96de2e153d20c40f4c819ac99b0a328daae
Author: telenius
Date: Fri Jul 6 15:17:33 2018 +0100
fix to earlier fix
commit 92d510d72ab9053335307ce5b97ed8ef865afcbf
Author: telenius
Date: Fri Jul 6 12:17:54 2018 +0100
intra-WIMM users public support
commit 4df23926f3be40473d38512624983f0c31c5d77a
Author: telenius
Date: Fri Jul 6 11:48:58 2018 +0100
fix to the trimming glitch
finally a fix to the leaking trimming quality control - if trimgalore crashes, run will crash too (not continue with untrimmed files as before)
commit 108b1c82d531dd04829da644cddf2abf2fc188b7
Author: telenius
Date: Fri Jul 6 10:44:01 2018 +0100
folder B - cleaning up after run
improving log file names, sorting output files to folders, removing temporary files and after-TMPdir-broken-symlinks
commit 21cb888b19276dfc3cc110908a5f843cd2475e24
Author: telenius
Date: Thu Jul 5 16:22:58 2018 +0100
some serial folder scripts fixes to support folder D
commit d205038065941f5ce3e40c6f3f605505def49f4d
Author: telenius
Date: Thu Jul 5 10:38:53 2018 +0100
folderC minor log fixes
1) du errors due to files changing during du -> to dev/null
2) inconsistent counters to consistent in multitaskers.sh
3) stepsABCDtopdir define to top of script (to not to be "" when it's needed)
commit 9c6d56f2d163e24df2b5a4e321dfe3aa814009ae
Author: telenius
Date: Wed Jul 4 10:51:06 2018 +0100
improving folderC logs and counters
commit 1cdbaf436a5bd15051a988d081024f30eb9a446b
Author: telenius
Date: Tue Jul 3 18:08:56 2018 +0100
folder C counters fix
commit 26f817b71556878aa751f0c00c806780e2282725
Author: telenius
Date: Tue Jul 3 17:16:10 2018 +0100
fixes to folderC
some alpha testing fixes to folderC loops and reporting counters
commit 7bc8975821ac64bfb2a04bc2bc5263656643e02f
Author: telenius
Date: Fri Jun 29 12:38:13 2018 +0100
flashed OR nonflashed bams required
not crashing if cannot find BOTH flashed and nonflashed - demanding that one OR the other is found for each oligo, but not demanding both.
commit 3241617be3cf8251481d8828bc23d909084554eb
Author: telenius
Date: Tue Jun 26 21:19:53 2018 +0100
80G buffer to wholenode TMPDIR
commit 919797fa22d1dce70ae07027456fe541c2b87271
Author: telenius
Date: Tue Jun 26 14:05:28 2018 +0100
LOOP1 with trans reads fix
main LOOP1 awk loop fix : wasn't saving the current fragment to the arrays when previous read got printed (thus losing the first fragment of each read)
commit 740690bfb20919f2562ba56983912daff4fb4ca2
Author: telenius
Date: Tue Jun 26 13:20:14 2018 +0100
fixing forever-loop from wholenode loopers
commit 5f8ed4d2f419b90e940b3136d6f4f2836323de3f
Author: Jelena Telenius
Date: Fri Jun 22 19:07:43 2018 +0100
Starting point of testing - basic functionalities work already
commit ea80c667378f88b766159c1e8af464eb626b4f40
Author: Jelena Telenius
Date: Fri Jun 22 19:04:26 2018 +0100
Initial commit