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Pairedbug #77

Closed
wants to merge 64 commits into from
Closed

Pairedbug #77

wants to merge 64 commits into from

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gaborcsardi
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Seemed to be fixed now.

@gaborcsardi
Update example SAM to match seq names in the GFF
02afafa 
The GFF has chrx, the SAM had just x.
@gaborcsardi
No not print out number of chains from the C code
a5c28f4
@gaborcsardi
Add some simple tests in the new /tests directory
b6d4219
@gaborcsardi
Add test for setting the RNG seed
f0bb66e
@gaborcsardi
Tests check generated reads and MISO results
46f01ad
@gaborcsardi
Create a Python level doMISO function
4b5106c
@gaborcsardi
Use read classes for single-end reads
5aaf3fe
@gaborcsardi
Add logistic prior parameter (does not work yet)
1968ddb
@gaborcsardi
Get rid of most C function check warnings & temp files
be22d95
@gaborcsardi
C: use isfinite() instead of deprecated finite()
4eb90a2
@gaborcsardi
Remove unused data files from config to avoid warnings
02bb038
@gaborcsardi
Fix compiler warnings, mostly long -> int implicit conversion
70c9e4c 
There are still a lot of warnings coming form lapack/blas/f2c.
Not sure what to do with these.
@gaborcsardi
Logistic prior
fc1b7d9
@gaborcsardi
Create 'temp' dir before build/install
9c781af
@gaborcsardi
Add Travis testing
e6afbb6
@gaborcsardi
Fix an invalid read that caused segfaults on OSX
de5c9f0
@gaborcsardi
Fix setup.py: only create temp if it does not exist
f88a3ce
@gaborcsardi
README in MarkDown, add Travis shield
53e8498
@gaborcsardi
README is actually needed, put it back
e92f43d
@gaborcsardi
Add /tags to git ignore file
f1f8308
@gaborcsardi
Replicates: most of the Python boilerplate
2c40ff1 
Replicates can be simply specified by listing multiple
BAM files. So BAM files are now in a list at the Python
level.
@gaborcsardi
Parse multiple BAM files in --compute-genes-from-file
45073d4
@gaborcsardi
Logistic prior for the paired-end sampler
bf13503
@gaborcsardi
Run tests from setup.py, #4
1a2ffd1 
So that we don't need to install the package:
python setup.py nosetests
@gaborcsardi
Make miso, run_miso, etc. callable from within Python
c1fe316 
Also index_gff and sam_to_bam. This is needed for testing.
The command line arguments are just passed in a list, and sys.argv[1:]
is the default.
@gaborcsardi
Pass argv to summarize_miso as well
89a4268
@gaborcsardi
Test running miso.main
d19ffe4
@gaborcsardi
Travis: run test via setup.py
60ea594
@gaborcsardi
CLI arg for prior, check prior and number of files
5ef78ae
@gaborcsardi
Trying to pysam on Travis
c7a18e1
@gaborcsardi
Put # of replicates and chains in the output file
28d16fa
@gaborcsardi
Include prior type in output file
2d499f5
@gaborcsardi
Always use the Dirichlet prior by default
00f4db7 
For compatibility.
@gaborcsardi
Logistic prior parameters per chain
da32ae3 
This is needed for inferring them.
@gaborcsardi
Get population parameters from Python, return pop samples
4e48c33
@gaborcsardi
Draw population mean and variance for replicates
8b71d01
@gaborcsardi
Gabor's email address Harvard -> Gmail
8ebdd2b
@gaborcsardi
Monkey patch distutils to speed up rebuilding, fixes #9
6c79bcc
@gaborcsardi
Ooops, fix compiler monkey patch for #9 if env it not set
1a81de9
@gaborcsardi
Suppress samtols output in sam_to_bam, fixes #5
fbe977a 
Suppresses everything on stderr, unfortunately.
But MISO should check the exit code of the
shell command, anyway, I think.
@gaborcsardi
Test inverse chi squared RNG, closes #8
43ebfab
@gaborcsardi
Smaller GFF for tests, #10
54dcd9c 
It takes ~17 seconds now, much better, but still way
too long.
@gaborcsardi
MISO CLI test: restore WD between tests
6c3b047
@gaborcsardi
Fix RNG seeding in test case, fixes #1
08282b4
@gaborcsardi
Proper test case for logistic prior
655e2ee
@gaborcsardi
Fix a replicate bug, pop_samples was the wrong size
064f3c2
@gaborcsardi
A test case for replicates, does not work (yet)
3adff3d 
[ci skip]
@gaborcsardi
Fix some samples/pop_samples bugs, more to come
3517cd3 
[ci skip]
@gaborcsardi
Fix bugs with storeing samples/pop_samples
f94f972
@gaborcsardi
Fix another pop_samples bug with one replicate only
c9cab92
@gaborcsardi
Git ignore files, cleanups in setup and test
c448324
@gaborcsardi
Another logistic prior test case
6ded5a1
@gaborcsardi
Fix a replicate conditional draw bug
c4b0dda
@gaborcsardi
Test case for non-paired end replicates, #12
85f343f 
Kind of working.
@gaborcsardi
Fix a test case
17604a6
@gaborcsardi
Replicates for paired-end reads
350c361
@gaborcsardi
Fixing a segfault in the paired-end replicate code
c49c95d
@gaborcsardi
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Sorry, not what I wanted!

@gaborcsardi gaborcsardi deleted the pairedbug branch May 27, 2015 15:38
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@gaborcsardi