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 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


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


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 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 -- 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 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 Testing is needed

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


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
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