Peter Hickey authored on 23/04/2019 01:03:45
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@@ -2,11 +2,6 @@ |
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#define BSSEQ_H |
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#include "Rcpp.h" |
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-#include "beachmat/integer_matrix.h" |
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-#include "beachmat/numeric_matrix.h" |
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- |
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-// TODO: Remove if not using std::runtime_error() |
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-#include <stdexcept> |
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// Functions to be called from R. |
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extern "C" {
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@@ -16,6 +11,4 @@ extern "C" {
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SEXP check_M_and_Cov(SEXP, SEXP); |
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} |
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-#include "utils.h" |
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- |
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#endif |
- BSseq objects can once again use ordinary matrix objects as assays.
- Reimplement `BSmooth()` more-or-less from scratch:
- Switch from 'parallel' to 'BiocParallel' for parallelization. This brings some notable improvements:
- Smoothed results can now be written directly to an on-disk realization backend by the worker. This dramatically reduces memory usage compared to previous versions of 'bsseq' that required all results be retained in-memory.
- Parallelization is now supported on Windows through the use of a 'SnowParam' object as the value of `BPPARAM`.
- Improved error handling makes it possible to gracefully resume `BSmooth()` jobs that encountered errors by re-doing only the necessary tasks.
- Detailed and extensive job logging facilities.
- Fix bug in `BSmooth()` with the `maxGap` parameter.
- Re-factor BSseq() constructor and add fast, internal .BSseq() constructor.
- Re-factor collapseBSseq() and combine(). Should be much more performant.
- Use beachmat to implement fast validity checking of 'M' and 'Cov' matrices.
- Resave BS.chr22 (supplied data) using integer for storage mode of assays to reduce size.
- Switch from RUnit to testthat. testthat has better integration with code coverage tools that help when refactoring.
Peter Hickey authored on 28/05/2018 23:42:18
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new file mode 100644 |
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+#ifndef BSSEQ_H |
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+#define BSSEQ_H |
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+ |
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+#include "Rcpp.h" |
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+#include "beachmat/integer_matrix.h" |
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+#include "beachmat/numeric_matrix.h" |
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+ |
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+// TODO: Remove if not using std::runtime_error() |
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+#include <stdexcept> |
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+ |
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+// Functions to be called from R. |
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+extern "C" {
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+ |
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+ // Validity checking. |
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+ |
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+ SEXP check_M_and_Cov(SEXP, SEXP); |
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+} |
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+ |
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+#include "utils.h" |
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+ |
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+#endif |