Code Log


Commit Date  
[r83] by acenglishbcm

Fixed some bugs and added functionality to Honey

2014-03-20 22:23:18 Tree
[r82] by acenglishbcm

just some work to make summarizeAssembly do more and look better

2014-01-23 02:02:17 Tree
[r81] by acenglishbcm

removed lib and ToyExample.txt because they're useless
Changed bampie so that it can read from/write to a .sam
This change takes the detailed workflow for Honey Processing from 7 to 6 steps and removes an intermediate file.
updated the HoneyReadme.txt and workflow.sh to represent this change.

2014-01-16 04:53:22 Tree
[r80] by acenglishbcm

Did some pimp documentation for Honey before I create my first release. I also did some lingering work that fixed the
output formats to what I wanted... there are a couple of changes to jelly that are in the release but not in the code
base(out of order)

2014-01-15 23:58:26 Tree
[r79] by acenglishbcm

made some more minor bux fixes to Jelly. Beginning separation of Honey

2014-01-13 22:01:30 Tree
[r78] by acenglishbcm

hoho

2013-12-14 03:41:20 Tree
[r77] by acenglishbcm

kay

2013-12-14 03:12:05 Tree
[r76] by acenglishbcm
2013-10-24 19:54:17 Tree
[r75] by acenglishbcm
2013-10-14 19:54:05 Tree
[r74] by acenglishbcm
2013-09-11 23:33:20 Tree
[r73] by acenglishbcm
2013-09-11 23:31:46 Tree
[r72] by acenglishbcm
2013-09-11 22:35:24 Tree
[r71] by acenglishbcm
2013-08-23 20:39:51 Tree
[r70] by acenglishbcm

Updated Jelly readme

2013-08-16 18:36:16 Tree
[r69] by acenglishbcm

Finished beta of J2

2013-08-15 21:31:48 Tree
[r68] by acenglishbcm

Finishing touches on Jelly. Major progress on Honey

2013-08-12 19:44:16 Tree
[r67] by acenglishbcm

Worked on tgraf

2013-07-25 00:08:27 Tree
[r66] by acenglishbcm

made recall spots so that I can go back and process data
edited sam2bam so that it's more user-friendly
created epipro.py so that we can identify, map, and reunite tails really awesomely in .bam files
remove the h5view and turned it to h5dump like it really is -- still need samtools coordinate support
created bamToFastq that will help extract the sequences from .bams really equickly/easily
created mergeFaQU so that fasta/quals can be merged easily
made spotViz so that we can visualie the metrics around a spot easily
fixed the blasrToBed code for M5Entry objects
made longCCSCombine work properly(?)
modified honey so that... it's a different program alltogether, now
created tgraf.py -- the beginnings of the program that will help resolve breakpoints.

2013-07-24 00:35:43 Tree
[r65] by acenglishbcm

Created simplier Assembly that doesn't use Allora

2013-07-17 00:32:00 Tree
[r64] by acenglishbcm

Finished svm integration, but then found it to be impractical - so now I have sweet convolution that is working. I'm checking in to save the changes I've made, but I'll be removing everything SVM from Honey.py and placing it into SVMachine for storage

2013-07-16 15:26:25 Tree
[r63] by acenglishbcm

Completed 80% of the new assembly technique for pbj and lots of pbh

2013-07-11 06:28:46 Tree
[r62] by acenglishbcm

added libsvmNotes, this contains the work I've done so far in evaluating and implementing svm. Note that it is super incomplete and really just a bunch of playing around. muscch sttructure must be added to this code. see Notes.txt for more information
I added the three programs i've created for denovo assembly. the comparative group is still using it.
HoneyReadme.txt now has program versions for everything Honey uses
I changed CommandRunner with hopes that it would make life easer for submitting a bunch of jobs to the cluster. Unfortunately it is still difficult and I've created a crappy, hard to use Valence... This refactoring almost certanily broke Jelly.py. Testing is needed

2013-07-03 00:27:51 Tree
[r61] by acenglishbcm

working

2013-06-27 21:40:57 Tree
[r60] by acenglishbcm

Honey now does better insertion calling
realign actually calls stuff
spotsH5View doesn't work yet

2013-06-26 15:25:59 Tree
[r59] by acenglishbcm

Worked on Honey, fixed some bugs from refactoring rearrangement and stuff in everything else

2013-06-20 05:51:04 Tree
Older >