changes.txt

0.75_28.3.17

* Fix to handle metrichor file type changes.

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0.74_7.3.17

* Tuning minControl to send less frequent data updates.

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0.74_24.02.17

* Bugfix to deal with time stamp changes in minKNOW 1.4.2
* Fix to handle incorrect reporting of non-existent minIONs.
* Fix to script launching to deal with changes in minKNOW 1.4.2
!! To do: minUPgui launching is temperamental on linux

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0.73_14.02.17

* Bugfix to minUPgui to prevent hardcoding of username.


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0.72_1.02.17

* Bugfix to events in sql tables timing.

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0.71_30.01.17

* Bugfix to deal with global time stamps for API.

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0.70_29.01.17

* Updated mincontrol to version 0.3

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0.70_25.01.17

* modified mincontrol to post data only every 30 seconds.
* Fixed hdfTimes sorting bug on evenets['start'] lookup


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0.70_24.01.17

* Fixes for get_main_timings() start_time/sampling_rate in config_general
*

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0.70_23.01.17

* Implemented "cursor_execute(args,db,cursor,sql)" function in db.py to replace calls to cursor.execute() -- so as to reconnect to mySQL if connection dropped.
* Wired in relevant function arguments ...(args,dc,cursor) throughout all calls to cursor_execute()
* Attempt to use db class was unsucessful -- probably due to connection-pool complexity.
* Adopted ML NYork startMincontrol.py script -- seems to be largely same as existing one.


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0.70_18.01.17

* Added alignerBlockSize options to minUP cmd line and gui
* Added optinal args.downloads and args.uploaded to minUP cmd line
* Added args.downloaded = args.watchdir and args.uploaded = 'uploaded' to minUP.py
* Set changed all instances of 'downloads' and 'uploaded' in MyHandler.py to args.dwwnloads and args.uploaded
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0.70_05.01.17

* Fixed gui for "pin" option

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0.70_21.12.16

* Wholesale re-structuring of mT_align.py
* Rename mT_align.py to mT_coverage.py
* Created separate module startMincontrol invoked from checkreads line 778
* Moved startMNincontrol invokation to MyHandler line 260


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0.68_16.12.16

* Checking with ver7 and fixes for on_moved etc
* New mincontrol
* Fixes for minUPgui on OSX etc.

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0.68_23.11.16

* Building mincontrolv4 with autobahn
* Fixed py2exe zope build problems by adding empty __init__.py to site-packages/zope/

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0.68_21.11.16

# New mincontrolv3.py

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0.68_16.11.16

* Changes for new mincontrolv3.py

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0.68_18.10.16

* Incermented version to 0.68

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0.67_17.10.16

* Fixes to depricate pre_align tables

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0.67_14.10.16

* Fixed terminate minup codes for minUPgui on nix systems
* Fixed minUPgui for nix ctrl-c to minUP

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0.67_11.10.16

* Fixed minUPgui for nix
* Fixed munUP ver.txt online checking for offline users
* Deprecated
    -procs
    -n
    -prealign
    -qryStartEnd
    -qScale
    -standalone
    -largeRef
    -telem


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0.67_10.10.16

* Incremnented version to 0.67
* Fixes for basename from filenames for intergrated and nanonet basecallingfats5 files.


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0.66_24.09.16

* Fixed metricoore basecalled_templat qual scores bug

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0.66_24.09.16

* Many bug fixes for handling invalid hdf files
* Move file under debug flag control
* Python stylisitc changes etc.

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0.65_26.09.16

* Fixed python script tab-space issues for uploads to gdrive
* Fixed dat and bwa issues for new file types
* Fixed prealign for r7 file types
* Testing on r7 and three types of r9 files.
* Fixed window size of minUPgui

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0.65_19.09.16

* Fixes for local base called nanonet and integrated RNN (minknow 1.0) files

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0.65_18.08.16

* fixes for metrichor r9 basecalled files

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0.65_25.07.16

* Wholesale refactoring of processFast5.py
8 Now handles r9 metrichore, minKnow wil nanonet and mikKnow w intergrated rrnn fat5 file types

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0.65_20.07.16

* Fixes for hdf5 filetype classification in checkreads
* Fixes for minKnow v1.0 file processing

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0.65_19.07.16

* Fixes for minKnow v 1.0
* Fixes for failed r9 metrichore basecalled files

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0.65_18.07.16

* Fixed processFast5.py line 73 to handle fioles with no minotour_meta groups.

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0.65_04.07.16

* Changes to MyHandler to handle custom"minotour_meta" data insertion onto hdf files
* Currently disabled: Codes to upload custam "minotour_meta" hdf data into mysql tables. See: processFast5.py line 71

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0.65_02.06.16

* Post LC2016
* r9 fast5 file handling
* nanonet local basecalling fast5 file handling
* minotour_barcodes files handling
* Lots of other changes

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0.65_18,05.16

* Changes to sql.py "NOT NULL" removed for "shift, scale etc"
* Changes to toGdrive to do d2u CLRF fixes.

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0.64b_13,05.16a

* Uses Matts new bwaClass() (based on blinkstick examples)
* to bundle up reads sets for bwa and avoid thread blocking

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0.64b_13,05.16

* Fixes for move failed hdf files
* Fixes for RR9 fast5 file format (no models)

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0.64b_29.04.16

* Fixes to moving problem files from RU9

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0.64b_30.03.16

* Fixed problems with raw proccessing
* Tested on abgt, ebola and drop_1D readsets


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0.64b_24.03.16

* Added standalone flag and supporting code to folderDict and MyHandler
* Major cleanup of unecessary syntax in folderDict.py

* Added 1minwin etc timings to fields in sql.py
* Added 1minwin etc timings fields insert statements enad supporting codes to processFast5Raw.py

* Fixed move corrupt fast5 filew to bugged folder so as to continue run
* Fixed gui I/O buffering probelms.
* Added progress bars

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0.64b_22.03.16b

* Fixed broken preBC reader for abgt names w periods in them
* Fixed move corruipt files to bugged for winodows and linux
* Added 1minwin,....g_15minwin min to sql and processFist5Raw for preBC files
* Checked on ebola/agbt_day1, agbt_problem reads and dros-1D reads
* Added terminateMinup and terminateSubprocesses for restarts by mincntrol

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0.64b_18.03.16b

* Further fixes to 2d data upload etc.

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0.64b_18.03.16

* Fixes to MHS code for old read problems.

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16.03.16 0.64a

* Heart surgery (MHS) to checkReads and processFast5 to work with 1D reads
* Seems *A LOT* quicker

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14.03.16 0.64b

* Changes to fix 1minwin start, end times and g_1minwin etc for start,end plut exp_start times.

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11.03.16 0.64b

* As v0.64b
* Added s1minwin etc to sql.py and processFast5.py
* Fixed var.txt bug in minUP.py

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09.03.16 0.64b

* As v0.64a
* And including sort reads using hdf_timestamps using read END time
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09.03.16 0.64a

* Build as v0.64
* bwa/last index dir chenged to be refdir
* Added flag indexToRefDir to control above
* And including sort reads using hdf_timestamps using read START time
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09.03.16 0.63

* Build as v0.63 including linux kill(pid)
* bwa/last index dir chenged to be watchdir
* Not including sort reads using hdf_timestamps
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08.03.16

* Added code to filderDict.py to sort initial reads based on hdfs time stams.
* Added self.hdf.close() to MyHandler except condition.
* Improved kill(pid) in exitGracefully.py

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04.03.16

* Changes to MyHandler line 37-50 to trap and move corrupt reads...

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16.02.16

* Trap illegal sql characters in nanes
Added okSQLnames() to checkRead.py line 29

* Ctrl-C Problems
Fixed in gui.py by changing "pid = os.getpid()" to "pid = 0"


* Search using just start end of read
Fixed changeing align_dtw.py line 113 "re <= rs_" to "re >= rs_"


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04.02.16


* Query Scale Factor
Commented out qScale in align_dtw.py line 51

* Exit on Ctrl-C
MyHandler.py
gui.py
minup.v0.62a.py
Fixes to Keyboardinrterrup handling
Changes exitGracefully to terminateSubProcesses

* Threads not exiting
MyHandler.py line 69 Added t.clear

* Search using just start end of read
Renamed squiggle_search2 calls to squiggle_align and added logic to handle squiggle_search3 in align_dtw.py
Added options and logic for squiggle_search3()
align_dtw.py
minup.v0.62a.py

* Offsets
Added offset default 50 to align_dtw.py

* CustomUP
Moved customup logic from line 327 to line 199 in MyHandler.py

* Add debug flag/info to checkReads.py
Fixed via MyHandler line 218-300 try-except statement indenting ??

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04.02.16-Florida

* mincontrol line 188 channel_states etc.
* MyHandler line 341 muxscan edits for demo only ...

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03.02.16

* Multi-user handling
622 mulit_user bug fix in checkReads.py

* CustomUP
Added customup/timeout flag to minup

* Upload pre-called reads
Added -per and -prealign flags to minup, MyHandler etc.

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