aaecc271e8
Misc changes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5324 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-26 15:35:49 +00:00
356eb264ab
Now says FNR, not FDR. We really need to clean up VQSR
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5243 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-15 12:28:09 +00:00
9fc45e1234
Use the yaml as an arguemtn to get out squid numbers
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5186 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-03 18:32:05 +00:00
027c91871f
Commenting out something I meant to leave commented out
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5163 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-01 15:47:52 +00:00
393df46055
updates to handle only reporting on a specific SVN revision. Updated the R script to show the domain name of the runner, now that S3 logging is working
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5157 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-01 12:02:12 +00:00
1753f9d864
"Properly handles multiplexed and non multiplex lane data from the picard database."
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5146 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-31 21:14:32 +00:00
23578b7402
Pipeline tests will only start from scratch after "ant clean", making it faster to debug downstream issues when re-running "ant pipelinetest -Dpipeline.run=run".
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Updated the FCP, the test, and the ADPR to handle an issue with the ADPR locating the yaml generated by the FCPTest.
Does not solve the ADPR error: Error in dimnames(x) <- dn : length of 'dimnames' [1] not equal to array extent
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5126 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-29 19:44:03 +00:00
afeb0f63c3
Further, smarter modifications to R script for correctly accessing database data
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5124 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-29 03:32:20 +00:00
4f2882c546
Fixing the way that lanes are pulled into from the database so that multiplexed lanes are handled and older sequence data ids are properly handled.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5123 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-29 02:40:10 +00:00
1d8412d652
Updating a few graphical parameters and making sure everything fits together
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5111 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-28 18:44:23 +00:00
88ea60b864
Updates formatting and combines plots into the tearsheet.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5109 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-28 17:45:23 +00:00
73e2942c62
Reformated backdrop--removed the date
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5086 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-26 18:25:59 +00:00
b22f82d5dd
Minor formatting udpates to deal with long bait names, multiple sequencer types, and date formatting
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5072 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-25 19:02:40 +00:00
1dcdebbc9e
Updating the file path for proper inclusion of the background in the tearsheet.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5056 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-22 19:15:33 +00:00
a50d7f74fa
Change to support plotting of indel quality as a function of covariates - for now, just call different R calling script.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5053 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-22 14:09:23 +00:00
22582960be
Adding the backdrop to the current version of the tearsheet so it is always available
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5026 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-19 20:56:11 +00:00
dfcd45181a
Some minor tweaks to the tearsheet generator that incorperate the gsalib more universally and create a more accurate output
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5021 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-19 20:27:02 +00:00
6b5474a00a
This updates the script to produce a more tearsheet-like output for sample set statistics. Formatting will be updated for aesthetic improvements. There are also several database options that currently pull out misleading information because of changes in sequencing methodology that will be updated to show correct information. Eventually, plot formatting will be updated as well and additional informative plots will be added.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4988 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-13 15:59:06 +00:00
91824f478e
FASTQ directory is gone
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4986 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-13 15:16:06 +00:00
3362f0c280
Private mutation simulator and analysis routines for EOMI paper
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4960 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-07 21:23:29 +00:00
3b76034d50
Namespace changes to avoid conflicts with other packages.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4950 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-06 15:33:26 +00:00
ab143c82af
Selects only the project requested via the Oracle command, rather than selecting everything and then subsetting.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4949 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-06 15:32:32 +00:00
5583fa179b
Now uses PNGs and a very high downsampling value to more clearly display the information
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4928 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-03 13:57:51 +00:00
dba30c4118
Subsampling of points, for the case where we have enormous numbers of points
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4927 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-03 13:48:11 +00:00
54adbd2581
Added instantaneous rate plotting routine to performance log plotter
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4926 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-03 13:33:35 +00:00
5539c2d9f3
--performanceLog (-PF) X.dat argument now enabled. Writes out a table (R-friendly) of the performance of the GATK over time, exactly as a more detailed version of the INFO progress meter. R script for useful plotting of the performance of the GATK over time. Will be helpful for upcoming scalability testing and debugging of memory leaks and other incremental performance problems
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4921 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-02 23:34:21 +00:00
586d3f05d9
Better cumhist function
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4920 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-02 23:32:20 +00:00
b024b85798
misc.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4899 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-22 20:16:41 +00:00
cc909602c7
Vectorize() pDirectlyPhaseHetPairAtDistanceUsingDepth; deal with minor precision issues
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4890 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-21 17:18:26 +00:00
a829284d84
Return analyzed window sizes as well
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4884 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-20 17:00:17 +00:00
6310a524d9
Do not abort integration (over het-het distances) on errors, but warn about them
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4855 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-16 17:20:25 +00:00
b1f0df0047
Handle case where read lengths are longer than fragment size
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4852 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-16 02:19:55 +00:00
a5e1854b3a
Forgot to pass correct parameters to calcPhasingProbsForWindowDistances()
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4851 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-16 01:58:06 +00:00
2b0dc8625c
Updated RBP theoretical model as per Mark's insights regarding the correct understanding of insert sizes being calculated post-hoc from the distance between read lengths. The correct way to think of it is: 1) There's a fragment of length F. 2) Each of it's two ends are read for L bases. 3) The insert size = i = F - 2 * L, after the fragment's assumed identity is determined by mapping the read mates to a reference sequence. Therefore, the external user-defined distribution is on the FRAGMENT SIZES
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4850 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-16 01:45:20 +00:00
aea481ae01
Trivial bug fix
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4848 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-15 18:29:15 +00:00
46cd227613
Stabilitity improvements to GATK run report system. R code is now robust. XML parser uses the C backend in python, 10x faster. Added shell script that runs the daily reports, and linked the /humgen/ runme.csh to this script. Script now emails the group the daily PDFs to gsamembers
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4845 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-15 14:56:12 +00:00
c167c6f9eb
Calculate the phasing probabilities for particular intra-het distances
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4838 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-14 18:44:59 +00:00
4dbdf7a13d
Added ability to sample from intra-het distance distribution
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4836 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-14 18:09:03 +00:00
4403b9d276
Added probability bound on phasing paths, which slightly speeds up calculations. It seems that a real speed-up can only be achieved by considering fewer paths by doing some form of caching of sub-problems (e.g., dynamic programming or matrix multiplication, as Mark suggested)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4832 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-13 23:53:56 +00:00
a6397ed8c3
Default R script now plots sensitivity/specificity curve
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4825 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-13 16:55:11 +00:00
2bf4fc94f0
Try to use more sampling to get a "correct" estimate of multivariate integral
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4815 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-10 02:58:46 +00:00
c64bf80b57
Added theoretical model of read-backed phasing (RBP)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4814 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-10 01:46:09 +00:00
2ac938fe4e
1)
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Minor fixes to avoid crashes vs CG indel files:
- Add count for complex events, not just insertions and deletions
- Handle correctly cases of large indels falling out of bounds of histogram array: added a count of indels ouf of bounds and avoid exceptions.
2) Cosmetic fix for R script assessing UG calling performance: draw red y=x line on top of Simulated vs Estimated AC to get a better view of under/over-estimation of AC.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4758 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-30 21:08:25 +00:00
9cca14acc5
Changed VCF subsetting procedure.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4742 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-28 00:46:29 +00:00
ecd496cf51
Modifications to reflect changes to gsalib. Smarter about figuring out the names of the filtered parts of the callset.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4739 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-27 23:26:03 +00:00
247f33a553
Prefixed all the functions with gsa. in order to distinguish the methods from other possible methods of the same name in the namespace.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4738 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-27 23:24:42 +00:00
8768e1a240
Useful profiling tool that reads in a single rod and evalutes the time it takes to read the file by byte, by line, into pieces, just the sites of the vcf, and finally the full vcf. Emits a useful table for plotting with the associated R script that can be run like Rscript R/analyzeRodProfile.R table.txt table.pdf titleString
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4728 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-24 14:59:16 +00:00
d2fc30d188
Added a debugging statement to plot.venn
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4718 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-23 01:19:31 +00:00
d492eb94ad
Actually subsets the resulting table now, like it was supposed to all along.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4696 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-17 16:18:23 +00:00
50dbbdb8ab
Retrieves per-sample or per-lane metrics from the SQUID database and populates a dataframe with the results.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4693 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-16 22:46:07 +00:00
depristo
corin
kshakir
delangel
kiran
fromer