]> git.donarmstrong.com Git - biopieces.git/commit
changed layout of ruby source
authormartinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Fri, 13 May 2011 19:46:09 +0000 (19:46 +0000)
committermartinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Fri, 13 May 2011 19:46:09 +0000 (19:46 +0000)
commit494dc53ebd515b1e3e9b91bbebf43059899ca4ce
tree4fe37e42d89cda66b5db5645c927d927e3d2c4cc
parent34ab63ac19cd0277c6b70697b25539fc145dcc22
changed layout of ruby source

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1405 74ccb610-7750-0410-82ae-013aeee3265d
237 files changed:
bp_bin/analyze_assembly
bp_bin/analyze_seq
bp_bin/assemble_seq_idba
bp_bin/assemble_seq_velvet
bp_bin/bin_vals
bp_bin/calc_N50
bp_bin/clip_adaptor
bp_bin/clip_seq
bp_bin/digest_seq
bp_bin/find_adaptor
bp_bin/find_genes
bp_bin/find_homopolymers
bp_bin/find_mids
bp_bin/join_seq
bp_bin/kmer_freq
bp_bin/length_seq
bp_bin/mask_seq
bp_bin/pcr_seq
bp_bin/plot_scores
bp_bin/progress_meter
bp_bin/read_fasta
bp_bin/read_fastq
bp_bin/read_genbank
bp_bin/read_sff
bp_bin/remove_mids
bp_bin/scores_to_dec
bp_bin/shred_seq
bp_bin/shuffle_records
bp_bin/swapcase_seq
bp_bin/uclust_seq
bp_conf/bashrc
code_ruby/Maasha/Rakefile [deleted file]
code_ruby/Maasha/lib/base36.rb [deleted file]
code_ruby/Maasha/lib/biopieces.rb [deleted file]
code_ruby/Maasha/lib/bitarray.rb [deleted file]
code_ruby/Maasha/lib/bits.rb [deleted file]
code_ruby/Maasha/lib/digest.rb [deleted file]
code_ruby/Maasha/lib/doc/Base36.html [deleted file]
code_ruby/Maasha/lib/doc/Base36Error.html [deleted file]
code_ruby/Maasha/lib/doc/Biopieces.html [deleted file]
code_ruby/Maasha/lib/doc/BitArray.html [deleted file]
code_ruby/Maasha/lib/doc/BitArrayError.html [deleted file]
code_ruby/Maasha/lib/doc/Boulder.html [deleted file]
code_ruby/Maasha/lib/doc/BoulderError.html [deleted file]
code_ruby/Maasha/lib/doc/CastError.html [deleted file]
code_ruby/Maasha/lib/doc/Casts.html [deleted file]
code_ruby/Maasha/lib/doc/Digest.html [deleted file]
code_ruby/Maasha/lib/doc/DigestError.html [deleted file]
code_ruby/Maasha/lib/doc/Fasta.html [deleted file]
code_ruby/Maasha/lib/doc/FastaError.html [deleted file]
code_ruby/Maasha/lib/doc/Fastq.html [deleted file]
code_ruby/Maasha/lib/doc/FastqError.html [deleted file]
code_ruby/Maasha/lib/doc/Filesys.html [deleted file]
code_ruby/Maasha/lib/doc/FilesysError.html [deleted file]
code_ruby/Maasha/lib/doc/Genbank.html [deleted file]
code_ruby/Maasha/lib/doc/GenbankError.html [deleted file]
code_ruby/Maasha/lib/doc/GenbankFeatures.html [deleted file]
code_ruby/Maasha/lib/doc/Locator.html [deleted file]
code_ruby/Maasha/lib/doc/LocatorError.html [deleted file]
code_ruby/Maasha/lib/doc/OptionHandler.html [deleted file]
code_ruby/Maasha/lib/doc/Read.html [deleted file]
code_ruby/Maasha/lib/doc/SFF.html [deleted file]
code_ruby/Maasha/lib/doc/SFFError.html [deleted file]
code_ruby/Maasha/lib/doc/Seq.html [deleted file]
code_ruby/Maasha/lib/doc/SeqError.html [deleted file]
code_ruby/Maasha/lib/doc/Status.html [deleted file]
code_ruby/Maasha/lib/doc/Stream.html [deleted file]
code_ruby/Maasha/lib/doc/String.html [deleted file]
code_ruby/Maasha/lib/doc/StringError.html [deleted file]
code_ruby/Maasha/lib/doc/base36_rb.html [deleted file]
code_ruby/Maasha/lib/doc/biopieces_rb.html [deleted file]
code_ruby/Maasha/lib/doc/bitarray_rb.html [deleted file]
code_ruby/Maasha/lib/doc/bits_rb.html [deleted file]
code_ruby/Maasha/lib/doc/boulder_rb.html [deleted file]
code_ruby/Maasha/lib/doc/classes/Biopieces.html [deleted file]
code_ruby/Maasha/lib/doc/classes/Biopieces.src/M000001.html [deleted file]
code_ruby/Maasha/lib/doc/classes/Biopieces.src/M000002.html [deleted file]
code_ruby/Maasha/lib/doc/classes/Biopieces.src/M000003.html [deleted file]
code_ruby/Maasha/lib/doc/classes/Biopieces.src/M000005.html [deleted file]
code_ruby/Maasha/lib/doc/classes/Biopieces.src/M000006.html [deleted file]
code_ruby/Maasha/lib/doc/classes/CastError.html [deleted file]
code_ruby/Maasha/lib/doc/classes/Casts.html [deleted file]
code_ruby/Maasha/lib/doc/classes/Casts.src/M000007.html [deleted file]
code_ruby/Maasha/lib/doc/classes/Fasta.html [deleted file]
code_ruby/Maasha/lib/doc/classes/Fasta.src/M000031.html [deleted file]
code_ruby/Maasha/lib/doc/classes/Fasta.src/M000032.html [deleted file]
code_ruby/Maasha/lib/doc/classes/Fasta.src/M000033.html [deleted file]
code_ruby/Maasha/lib/doc/classes/Fasta.src/M000034.html [deleted file]
code_ruby/Maasha/lib/doc/classes/FastaError.html [deleted file]
code_ruby/Maasha/lib/doc/classes/OptionHandler.html [deleted file]
code_ruby/Maasha/lib/doc/classes/OptionHandler.src/M000008.html [deleted file]
code_ruby/Maasha/lib/doc/classes/OptionHandler.src/M000009.html [deleted file]
code_ruby/Maasha/lib/doc/classes/OptionHandler.src/M000010.html [deleted file]
code_ruby/Maasha/lib/doc/classes/OptionHandler.src/M000011.html [deleted file]
code_ruby/Maasha/lib/doc/classes/OptionHandler.src/M000012.html [deleted file]
code_ruby/Maasha/lib/doc/classes/OptionHandler.src/M000013.html [deleted file]
code_ruby/Maasha/lib/doc/classes/OptionHandler.src/M000014.html [deleted file]
code_ruby/Maasha/lib/doc/classes/OptionHandler.src/M000015.html [deleted file]
code_ruby/Maasha/lib/doc/classes/OptionHandler.src/M000016.html [deleted file]
code_ruby/Maasha/lib/doc/classes/OptionHandler.src/M000017.html [deleted file]
code_ruby/Maasha/lib/doc/classes/OptionHandler.src/M000018.html [deleted file]
code_ruby/Maasha/lib/doc/classes/OptionHandler.src/M000019.html [deleted file]
code_ruby/Maasha/lib/doc/classes/OptionHandler.src/M000020.html [deleted file]
code_ruby/Maasha/lib/doc/classes/OptionHandler.src/M000021.html [deleted file]
code_ruby/Maasha/lib/doc/classes/OptionHandler.src/M000022.html [deleted file]
code_ruby/Maasha/lib/doc/classes/OptionHandler.src/M000023.html [deleted file]
code_ruby/Maasha/lib/doc/classes/OptionHandler.src/M000024.html [deleted file]
code_ruby/Maasha/lib/doc/classes/Seq.html [deleted file]
code_ruby/Maasha/lib/doc/classes/Seq.src/M000001.html [deleted file]
code_ruby/Maasha/lib/doc/classes/Seq.src/M000003.html [deleted file]
code_ruby/Maasha/lib/doc/classes/Seq.src/M000004.html [deleted file]
code_ruby/Maasha/lib/doc/classes/Seq.src/M000005.html [deleted file]
code_ruby/Maasha/lib/doc/classes/Seq.src/M000006.html [deleted file]
code_ruby/Maasha/lib/doc/classes/Seq.src/M000007.html [deleted file]
code_ruby/Maasha/lib/doc/classes/Seq.src/M000008.html [deleted file]
code_ruby/Maasha/lib/doc/classes/Seq.src/M000009.html [deleted file]
code_ruby/Maasha/lib/doc/classes/Seq.src/M000031.html [deleted file]
code_ruby/Maasha/lib/doc/classes/Seq.src/M000032.html [deleted file]
code_ruby/Maasha/lib/doc/classes/Seq.src/M000033.html [deleted file]
code_ruby/Maasha/lib/doc/classes/Seq.src/M000034.html [deleted file]
code_ruby/Maasha/lib/doc/classes/Seq.src/M000035.html [deleted file]
code_ruby/Maasha/lib/doc/classes/Seq.src/M000037.html [deleted file]
code_ruby/Maasha/lib/doc/classes/Seq.src/M000038.html [deleted file]
code_ruby/Maasha/lib/doc/classes/Seq.src/M000039.html [deleted file]
code_ruby/Maasha/lib/doc/classes/Seq.src/M000040.html [deleted file]
code_ruby/Maasha/lib/doc/classes/Seq.src/M000041.html [deleted file]
code_ruby/Maasha/lib/doc/classes/Seq.src/M000042.html [deleted file]
code_ruby/Maasha/lib/doc/classes/Seq.src/M000043.html [deleted file]
code_ruby/Maasha/lib/doc/classes/Seq.src/M000044.html [deleted file]
code_ruby/Maasha/lib/doc/classes/Seq/AA.html [deleted file]
code_ruby/Maasha/lib/doc/classes/Seq/AA.src/M000036.html [deleted file]
code_ruby/Maasha/lib/doc/classes/Seq/AA.src/M000037.html [deleted file]
code_ruby/Maasha/lib/doc/classes/Seq/NA.html [deleted file]
code_ruby/Maasha/lib/doc/classes/Seq/NA/DNA.html [deleted file]
code_ruby/Maasha/lib/doc/classes/Seq/NA/DNA.src/M000038.html [deleted file]
code_ruby/Maasha/lib/doc/classes/Seq/NA/DNA.src/M000039.html [deleted file]
code_ruby/Maasha/lib/doc/classes/Seq/NA/DNA.src/M000040.html [deleted file]
code_ruby/Maasha/lib/doc/classes/Seq/NA/RNA.html [deleted file]
code_ruby/Maasha/lib/doc/classes/Seq/NA/RNA.src/M000041.html [deleted file]
code_ruby/Maasha/lib/doc/classes/Seq/NA/RNA.src/M000042.html [deleted file]
code_ruby/Maasha/lib/doc/classes/Seq/NA/RNA.src/M000043.html [deleted file]
code_ruby/Maasha/lib/doc/classes/SeqError.html [deleted file]
code_ruby/Maasha/lib/doc/classes/Status.html [deleted file]
code_ruby/Maasha/lib/doc/classes/Status.src/M000025.html [deleted file]
code_ruby/Maasha/lib/doc/classes/Status.src/M000026.html [deleted file]
code_ruby/Maasha/lib/doc/classes/Status.src/M000027.html [deleted file]
code_ruby/Maasha/lib/doc/classes/Status.src/M000028.html [deleted file]
code_ruby/Maasha/lib/doc/classes/Status.src/M000029.html [deleted file]
code_ruby/Maasha/lib/doc/classes/Stream.html [deleted file]
code_ruby/Maasha/lib/doc/classes/Stream.src/M000030.html [deleted file]
code_ruby/Maasha/lib/doc/created.rid [deleted file]
code_ruby/Maasha/lib/doc/digest_rb.html [deleted file]
code_ruby/Maasha/lib/doc/fasta_rb.html [deleted file]
code_ruby/Maasha/lib/doc/fastq_rb.html [deleted file]
code_ruby/Maasha/lib/doc/files/biopieces_rb.html [deleted file]
code_ruby/Maasha/lib/doc/files/fasta_rb.html [deleted file]
code_ruby/Maasha/lib/doc/files/seq_rb.html [deleted file]
code_ruby/Maasha/lib/doc/filesys_rb.html [deleted file]
code_ruby/Maasha/lib/doc/fr_class_index.html [deleted file]
code_ruby/Maasha/lib/doc/fr_file_index.html [deleted file]
code_ruby/Maasha/lib/doc/fr_method_index.html [deleted file]
code_ruby/Maasha/lib/doc/genbank_rb.html [deleted file]
code_ruby/Maasha/lib/doc/images/brick.png [deleted file]
code_ruby/Maasha/lib/doc/images/brick_link.png [deleted file]
code_ruby/Maasha/lib/doc/images/bug.png [deleted file]
code_ruby/Maasha/lib/doc/images/bullet_black.png [deleted file]
code_ruby/Maasha/lib/doc/images/bullet_toggle_minus.png [deleted file]
code_ruby/Maasha/lib/doc/images/bullet_toggle_plus.png [deleted file]
code_ruby/Maasha/lib/doc/images/date.png [deleted file]
code_ruby/Maasha/lib/doc/images/find.png [deleted file]
code_ruby/Maasha/lib/doc/images/loadingAnimation.gif [deleted file]
code_ruby/Maasha/lib/doc/images/macFFBgHack.png [deleted file]
code_ruby/Maasha/lib/doc/images/package.png [deleted file]
code_ruby/Maasha/lib/doc/images/page_green.png [deleted file]
code_ruby/Maasha/lib/doc/images/page_white_text.png [deleted file]
code_ruby/Maasha/lib/doc/images/page_white_width.png [deleted file]
code_ruby/Maasha/lib/doc/images/plugin.png [deleted file]
code_ruby/Maasha/lib/doc/images/ruby.png [deleted file]
code_ruby/Maasha/lib/doc/images/tag_green.png [deleted file]
code_ruby/Maasha/lib/doc/images/wrench.png [deleted file]
code_ruby/Maasha/lib/doc/images/wrench_orange.png [deleted file]
code_ruby/Maasha/lib/doc/images/zoom.png [deleted file]
code_ruby/Maasha/lib/doc/index.html [deleted file]
code_ruby/Maasha/lib/doc/js/darkfish.js [deleted file]
code_ruby/Maasha/lib/doc/js/jquery.js [deleted file]
code_ruby/Maasha/lib/doc/js/quicksearch.js [deleted file]
code_ruby/Maasha/lib/doc/js/thickbox-compressed.js [deleted file]
code_ruby/Maasha/lib/doc/rdoc-style.css [deleted file]
code_ruby/Maasha/lib/doc/rdoc.css [deleted file]
code_ruby/Maasha/lib/doc/seq_rb.html [deleted file]
code_ruby/Maasha/lib/doc/sff_rb.html [deleted file]
code_ruby/Maasha/lib/fasta.rb [deleted file]
code_ruby/Maasha/lib/fastq.rb [deleted file]
code_ruby/Maasha/lib/filesys.rb [deleted file]
code_ruby/Maasha/lib/genbank.rb [deleted file]
code_ruby/Maasha/lib/patscan.rb [deleted file]
code_ruby/Maasha/lib/patternmatcher.rb [deleted file]
code_ruby/Maasha/lib/prodigal.rb [deleted file]
code_ruby/Maasha/lib/seq.rb [deleted file]
code_ruby/Maasha/lib/sff.rb [deleted file]
code_ruby/Maasha/test/test_base36.rb [deleted file]
code_ruby/Maasha/test/test_biopieces.rb [deleted file]
code_ruby/Maasha/test/test_bitarray.rb [deleted file]
code_ruby/Maasha/test/test_bits.rb [deleted file]
code_ruby/Maasha/test/test_digest.rb [deleted file]
code_ruby/Maasha/test/test_fasta.rb [deleted file]
code_ruby/Maasha/test/test_fastq.rb [deleted file]
code_ruby/Maasha/test/test_genbank.rb [deleted file]
code_ruby/Maasha/test/test_patternmatcher.rb [deleted file]
code_ruby/Maasha/test/test_seq.rb [deleted file]
code_ruby/Sfern/test_module.rb [deleted file]
code_ruby/lib/maasha/base36.rb [new file with mode: 0644]
code_ruby/lib/maasha/biopieces.rb [new file with mode: 0644]
code_ruby/lib/maasha/bitarray.rb [new file with mode: 0644]
code_ruby/lib/maasha/bits.rb [new file with mode: 0644]
code_ruby/lib/maasha/boulder.rb [new file with mode: 0644]
code_ruby/lib/maasha/digest.rb [new file with mode: 0644]
code_ruby/lib/maasha/fasta.rb [new file with mode: 0644]
code_ruby/lib/maasha/fastq.rb [new file with mode: 0644]
code_ruby/lib/maasha/filesys.rb [new file with mode: 0644]
code_ruby/lib/maasha/genbank.rb [new file with mode: 0644]
code_ruby/lib/maasha/patscan.rb [new file with mode: 0644]
code_ruby/lib/maasha/patternmatcher.rb [new file with mode: 0644]
code_ruby/lib/maasha/prodigal.rb [new file with mode: 0644]
code_ruby/lib/maasha/seq.rb [new file with mode: 0644]
code_ruby/lib/maasha/sff.rb [new file with mode: 0644]
code_ruby/test/maasha/test_base36.rb [new file with mode: 0755]
code_ruby/test/maasha/test_biopieces.rb [new file with mode: 0755]
code_ruby/test/maasha/test_bitarray.rb [new file with mode: 0755]
code_ruby/test/maasha/test_bits.rb [new file with mode: 0755]
code_ruby/test/maasha/test_boulder.rb [new file with mode: 0755]
code_ruby/test/maasha/test_digest.rb [new file with mode: 0755]
code_ruby/test/maasha/test_fasta.rb [new file with mode: 0755]
code_ruby/test/maasha/test_fastq.rb [new file with mode: 0755]
code_ruby/test/maasha/test_genbank.rb [new file with mode: 0755]
code_ruby/test/maasha/test_patternmatcher.rb [new file with mode: 0755]
code_ruby/test/maasha/test_seq.rb [new file with mode: 0755]