comparativegenomicstoolkit/sonlib

Small general-purpose library for C and Python with an emphasis on bioinformatics.

sonlib's Issues

please tag a release

Hello,

would it be possible to tag a release ?

regards

Eric

make test error

Hi all,

I am trying to install sonLib for CAT and having an issue with make test.
Following are the error messages:
`There were 7 failures:

1. testStPhylogeny_getLinkedSpeciesTree: tests/stPhylogenyTest.c:1368: expected <((a,b)e,(c,d)f)g;> but was <((a:inf,b:inf)e:inf,(c:inf,d:inf)f:inf)g:inf;>
2. testStPhylogeny_greedySplitDecomposition: tests/stPhylogenyTest.c:1348: expected <(10:0,((1:1,11:1):1,(2:1,4:1,7:1):1,(8:1,(6:1,(0:1,5:1):1):1,(3:1,9:1):1):1):1);> but was <(10:0,((1:1,11:1):1,(2:1,4:1,7:1):1,(8:1,(6:1,(0:1,5:1):1):1,(3:1,9:1):1):1):1):inf;>
3. testStPhylogeny_rootByReconciliationAtMostBinary_simpleTests: tests/stPhylogenyTest.c:996: expected <((0:1,1:1):0.5,(2:1,3:2):0.5);> but was <((0:1,1:1):0.5,(2:1,3:2):0.5):inf;>
4. testStPhylogeny_reconcileNonBinary: tests/stPhylogenyTest.c:1163: expected <((((opossum-gene1,tasmanian_devil-gene1)Metatheria,kangaroo-gene1)Metatheria,((mouse-gene,human-gene)Euarchontoglires,cow-gene)Boreoeutheria)Theria,((opossum-gene2,kangaroo-gene2)Metatheria,(bandicoot-gene3,kangaroo-gene3)Metatheria)Metatheria)Theria;> but was <((((opossum-gene1:inf,tasmanian_devil-gene1:inf)Metatheria:inf,kangaroo-gene1:inf)Metatheria:inf,((mouse-gene:inf,human-gene:inf)Euarchontoglires:inf,cow-gene:inf)Boreoeutheria:inf)Theria:inf,((opossum-gene2:inf,kangaroo-gene2:inf)Metatheria:inf,(bandicoot-gene3:inf,kangaroo-gene3:inf)Metatheria:inf)Metatheria:inf)Theria:inf;>
5. test_stTree_getSetBranchLength: tests/sonLibTreeTest.c:93: assert failed
6. test_stTree_newickTreeParser: tests/sonLibTreeTest.c:133: expected <(((a,b,(c,))d),e)f;> but was <(((a:inf,b:inf,(c:inf,:inf):inf)d:inf):inf,e:inf)f:inf;>
7. test_stTree_reRoot: tests/sonLibTreeTest.c:210: expected <((((C:1,D:1)B:8,F:3,G:3)E:5,I:3)H:4,(K:4)J:1);> but was <((((C:1,D:1)B:8,F:3,G:3)E:5,I:3)H:4,(K:4)J:1):inf;>

!!!FAILURES!!!
Runs: 175 Passes: 168 Fails: 7
seems like it will add aninf` to every branch without branch length.
I'm not sure if I've missed something, but would appreciate any advice on how I might correct this.

Best,
Langqing

running 'make all' on CentOS fails to compile

I checked out the repository, then after running
make all I get the following errors
:
g++ -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 g++: fatal error: no input files compilation terminated. make: *** [../../sonLib/lib/sonLib.a] Error 1
it seems like some sort of issue with the make files
I am having to make from source because I do not have root access on the server and a compilation is needed for 'hal'

sonlib should build on syslog definitions rather than make up it's own

It will integrate much better with other packages if it does away with:

enum stLogLevel { off, critical, info, debug };

Redis database needs to support MaxRecordSize

Redis keys and values cannot be greater than 512M. The values of Cactus disk records know no such limits. So cactus crashes with a segfault whenever a record >512M is stored.

Kyoto Tycoon also has an effective record size limit. In Sonlib it is assumed to be 10M. Records bigger than this are split up with special "split record" logic.

I suspect that this splitting logic, which is not advertised as being perfectly robust leads to periodic crashes and database corruptions. The bigger the record the (probably) greater the risk.

I think that we can mirror this splitting logic in Redis using its native features to hopefully be more robust. In particular, its ability to store lists of values for a given key.