rjpbonnal bioruby-samtools issues

rjpbonnal / bioruby-samtools

Porting of samtools-ruby to BioRuby. Binder of samtools for ruby, on the top of FFI -from original project-

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More minor updates to work on ruby 1.9

#24 homonecloco closed 11 years ago
0
The proper commit of the gitignore file and bumped the version to reflect the minor change in the pileup.

#23 homonecloco closed 11 years ago
0
Removed the gemfile.lock and added to the .gitignore file.

#22 homonecloco closed 11 years ago
0
Query fasta regions/Fasta database

#21 homonecloco closed 9 years ago
3
Quote mpileup cmdline

#20 wwood closed 11 years ago
1
regex change (for issue #18)

#19 bpow closed 11 years ago
0
jruby changed RUBY_DESCRIPTION-- need to update regex to determine library extension

#18 bpow closed 11 years ago
2
Bio::DB::Pileup#to_s

#17 danmaclean closed 11 years ago
0
extra functionality!!

#16 danmaclean closed 11 years ago
0
Bio::DB::Sam#mpileup doesn't escape cmdline args

#15 wwood closed 11 years ago
5
Use travis-ci to test the bio-samtools package

#14 pjotrp closed 12 years ago
2
Dependency issues

#13 wwood closed 12 years ago
5
require bio/db/pileup and ire 'bio/db/vcf' by default.

#12 wwood closed 12 years ago
7
SAM parsing error fixed

#11 gusevfe closed 12 years ago
1
Writing alignments to file

#10 gusevfe opened 12 years ago
3
Bit of a clean up

#9 danmaclean closed 12 years ago
0
fixed fail on large pileup region requests, simple vcf format support

#8 danmaclean closed 12 years ago
8
libbam.so.1 won't compile in bio-samtools on AMD64, same version does from manual make

#7 danmaclean closed 12 years ago
0
doc update. new method for idx stats

#6 danmaclean closed 12 years ago
6
pileup name lost

#5 danmaclean closed 13 years ago
0
Corrected

#4 danmaclean closed 13 years ago
0
Added pileup functionality

#3 danmaclean closed 13 years ago
0
Calling Sam#to_s when Fasta file not specified raises an Exception

#2 timpalpant closed 9 years ago
2
uninitialized constant Bio::DB::SAM::Tools::FFI

#1 antunderwood closed 12 years ago
4