Toshiki Takeuchi

bgzipped VCF file over HTTP causes infinite loop

3

A bgzipped VCF file over HTTP causes infinite loop. ```console $ gzip -c test-resources/vcf/test-v4_3.vcf > test-resources/vcf/test-v4_3-gzip.vcf.gz $ bgzip -c test-resources/vcf/test-v4_3.vcf > test-resources/vcf/test-v4_3-bgzip.vcf.gz $ python3 -m http.server 8000 ``` ```clj (require...

Remove CLI functionality

1

I removed CLI functionality from cljam and added a notice message about [Gnife](https://github.com/chrovis/gnife) to `README.md`. This PR aims at separating the CLI functionality from cljam and making cljam a pure...

`dict` command after cljam 0.8.2 fails

4

```console $ cljam version 0.8.4 $ cljam dict test-resources/fasta/test.fa /tmp/test.dict Exception in thread "main" java.lang.ExceptionInInitializerError at org.apache.commons.compress.compressors.xz.XZUtils.(XZUtils.java:59) at org.apache.commons.compress.compressors.CompressorStreamFactory.detect(CompressorStreamFactory.java:271) at org.apache.commons.compress.compressors.CompressorStreamFactory.createCompressorInputStream(CompressorStreamFactory.java:522) at cljam.util$compressor_input_stream.invokeStatic(util.clj:122) at cljam.io.fasta.core$reader.invokeStatic(core.clj:38) at cljam.io.sequence$fasta_reader.invokeStatic(sequence.clj:20) at cljam.algo.dict$create_dict.invokeStatic(dict.clj:9) at...

:fact-filter breaks on creation-time checking

2

```clojure (change-defaults :fact-filter (complement :slow)) ``` in `.midje.clj` works when calling `load-facts` or running tests through lein-midje. The test ignores `:slow` facts as expected. However, creation-time checking when loading a...