bioruby-samtools
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rjpbonnal
Porting of samtools-ruby to BioRuby. Binder of samtools for ruby, on the top of FFI -from original project-
The gem downloads samtools when installing. That can be a serious problem if you need to install it somewhere without internet access -- packaging the gem does not help. Is...
First, thanks for implementing this, it has been very handy for me. I was wondering if there were methods available to iterate through an alignment object for each residue position...
Error building with ruby 2.1.10 due to open-uri. The mkrf_conf.rb and Rakefile both contain http sourceforge urls. These fail to download properly thanks to open-uri. I am surprised this wasn't...
To avoid the Open-URI redirection issue described in #67, I tried installing the 2.3.0 gem for ruby version 2.4.2. In this case, the redirection is successful, but the rake still...
Any additional information I can provide? ```bash >which ruby ruby 2.1.10p492 (2016-04-01 revision 54464) [x86_64-linux] > bundle install ... make[1]: Leaving directory '/home/matt/.rvm/gems/ruby-2.1.10@gemset/gems/bio-samtools-2.5.1/ext/samtools-1.3.1/htslib-1.3.1' gcc -pthread -rdynamic -o samtools bam_index.o bam_plcmd.o...
I've indexed a bam file with samtools and receive `true` on the indexed command and index_stats returns an empty hash.
Samtools 1.x has different options to sort. Right now, the unit test pass, but we need to check all the possible options.
SAMtools v1.2 now contains the following methods, missing from bioruby-samtools 'split' splits a file by read group 'bam2fq' converts a BAM to a FASTQ (although extract_reads() does a very similar...
bioruby-samtools currently only has the -r option implemented. please add options: -p Disable FR proper pair check -c Add template cigar ct tag -O FORMAT Write output as FORMAT ('sam'/'bam'/'cram')
As documented here: http://sourceforge.net/p/samtools/mailman/message/32904732/ providing the SAMtools index method with an outfile name (e.g. 'samtools index aln.bam alignment.bai') causes an error. Removing the code in test_sam.rb test_index() after #as above,...