added .Rinstignore

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Repitools@74000 bc3139a8-67e5-0310-9ffc-ced21a209358
first inclusion of BayMeth

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Repitools@74022 bc3139a8-67e5-0310-9ffc-ced21a209358
BAM2GRanges now appropriately calculates read widths when insertions and deletions are present. It also errors if the user tries to pass a list to it.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Repitools@74218 bc3139a8-67e5-0310-9ffc-ced21a209358
added Rmath.h in hyp2f1.c

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Repitools@74267 bc3139a8-67e5-0310-9ffc-ced21a209358
changed gamma to gammafn (i.e. change from cephes definition to Rmath.h)

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Repitools@74323 bc3139a8-67e5-0310-9ffc-ced21a209358
use a platform-independent way to determine # of cores (parallel::detectCores())

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Repitools@74460 bc3139a8-67e5-0310-9ffc-ced21a209358
inclusion of basic SssI-free BayMeth

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Repitools@74482 bc3139a8-67e5-0310-9ffc-ced21a209358
changed .Rinstignore to exclude tex files

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Repitools@74737 bc3139a8-67e5-0310-9ffc-ced21a209358
small changes in class functions and documentation

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Repitools@74777 bc3139a8-67e5-0310-9ffc-ced21a209358
inclusion of HPD and quantile CI; adding labels

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Repitools@74986 bc3139a8-67e5-0310-9ffc-ced21a209358
small changes on documentation

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Repitools@74992 bc3139a8-67e5-0310-9ffc-ced21a209358
changed email address

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Repitools@75082 bc3139a8-67e5-0310-9ffc-ced21a209358
bump y of x.y.z version number for BioC 2.12 release

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Repitools@75263 bc3139a8-67e5-0310-9ffc-ced21a209358
Bump y in version x.y.z to odd number in devel

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Repitools@75270 bc3139a8-67e5-0310-9ffc-ced21a209358
Use readGAlignments(), new name for readGappedAlignments().

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Repitools@75558 bc3139a8-67e5-0310-9ffc-ced21a209358
addition of non SssI-option, beta mixture and Dirac-beta-Dirac mixture priors

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Repitools@76170 bc3139a8-67e5-0310-9ffc-ced21a209358
small change in offset when using copy number information

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Repitools@76285 bc3139a8-67e5-0310-9ffc-ced21a209358
correct small bug  in offset when using copy number information

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Repitools@76286 bc3139a8-67e5-0310-9ffc-ced21a209358
small fix in empBayes

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Repitools@76425 bc3139a8-67e5-0310-9ffc-ced21a209358
small change in one access function when using copy number information

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Repitools@76542 bc3139a8-67e5-0310-9ffc-ced21a209358