diff --git a/README.md b/README.md index f42bbb39..d124f60c 100644 --- a/README.md +++ b/README.md @@ -56,8 +56,6 @@ If your CUDA library is not in the default location /usr/local/cuda/lib64, point ``` make cuda=1 CUDA_LIB=/path/to/cuda/library/ ``` -For instance, it can be something like `/usr/local/cuda-8.0/lib64`. If your system is 32 bit it should be `lib` instead of `lib64`. - Visit [here](https://hasindu2008.github.io/f5c/docs/cuda-troubleshoot) for troubleshooting CUDA related problems. ## Usage @@ -71,7 +69,7 @@ Visit the [man page](https://hasindu2008.github.io/f5c/docs/commands) for all th ### Example -Follow the same steps as in [Nanopolish tutorial](https://nanopolish.readthedocs.io/en/latest/quickstart_call_methylation.html) while replacing `nanopolish` with `f5c`. If you only want to perform a quick test of f5c without aligning reads : +Follow the same steps as in [Nanopolish tutorial](https://nanopolish.readthedocs.io/en/latest/quickstart_call_methylation.html) while replacing `nanopolish` with `f5c`. If you only want to perform a quick test of f5c : ```sh #download and extract the dataset including sorted alignments wget -O f5c_na12878_test.tgz "http://genome.cse.unsw.edu.au/tmp/f5c_na12878_test.tgz" @@ -83,6 +81,6 @@ f5c call-methylation -b chr22_meth_example/reads.sorted.bam -g chr22_meth_exampl ``` ## Acknowledgement -This extensively reuses code and methods from [Nanopolish](https://github.com/jts/nanopolish). +This reuses code and methods from [Nanopolish](https://github.com/jts/nanopolish). The event detection code is from Oxford Nanopore's [Scrappie basecaller](https://github.com/nanoporetech/scrappie). Some code snippets have been taken from [Minimap2](https://github.com/lh3/minimap2) and [Samtools](http://samtools.sourceforge.net/). diff --git a/todo.md b/todo.md deleted file mode 100644 index 6eb1c6db..00000000 --- a/todo.md +++ /dev/null @@ -1,11 +0,0 @@ -Port all the C++ headers to C (and change to std=c11 afterwards) -Fix up autotools stuff (and write Makefile.am) -Fix macros and clean up the header file nest -Merge install-{hts,hdf}.sh scripts into one -Fix up README.md and install instructions -Move source files into src directory -Vectorise the alignment function -Set up autotesting system -Fix all the memory leaks -Add stricter options to Makefile (e.g. -Wextra) -Add link time optimisation flags