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biopieces.git
2012-09-04
martinahansen
added test_math_aux.rb
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2012-09-04
martinahansen
fixed bug in clip_adaptor where LEFT_POS > RIGHT_POS
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2012-09-04
martinahansen
fixed bug in clip_adaptor where LEFT_POS > RIGHT_POS
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2012-09-03
martinahansen
revamped find_adaptor and clip_adaptor
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2012-09-03
martinahansen
updated testing files for find_adaptor and clip_adaptor
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2012-08-30
martinahansen
deleted old QA_454_report script
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2012-08-30
martinahansen
added nucleotide plot to QA_454_report
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2012-08-30
martinahansen
added plot_nucleotide_distribution biopiece
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2012-08-30
martinahansen
finally figured how to change plot color
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2012-08-16
martinahansen
did something to findsim.rb
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2012-08-15
martinahansen
made find_orfs run on DNA or RNA
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2012-08-14
martinahansen
fixed mean_scores to deal with 0 length seqs
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2012-08-14
martinahansen
reverted trim_seq
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2012-08-14
martinahansen
changed trim_seq to omit outputting sequences with...
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2012-08-09
martinahansen
upgraded QA script to use new plot scores count feature
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2012-08-07
martinahansen
last fix on prodigal upgrade
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2012-08-07
martinahansen
upgraded prodigal
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2012-08-07
martinahansen
fixed typo
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2012-08-07
martinahansen
added assemble_seq_idba_ud
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2012-08-07
martinahansen
added relative count to plot_scores + rewrite for speed
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2012-08-06
martinahansen
removed outdated installer
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2012-08-06
martinahansen
updated biopieces installer
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2012-07-13
martinahansen
fixed another bug in find orfs
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2012-07-13
martinahansen
fixed bug in orf finder
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2012-07-13
martinahansen
fixed grave bug in find_orfs
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2012-07-13
martinahansen
made orf finder case insensitive
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2012-07-13
martinahansen
added find_orfs
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2012-07-13
martinahansen
added orf finder to seq.rb
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2012-07-10
martinahansen
ported align_pair_seq to ruby
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2012-07-10
martinahansen
added align/pair.rb to ruby trunk
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2012-07-10
martinahansen
fixed align.rb up a bit
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2012-07-10
martinahansen
minor fix to find_adaptor 2
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2012-07-10
martinahansen
minor fix to find_adaptor
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2012-07-10
martinahansen
added -m hardcoded option to prodigal.rb
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2012-07-10
martinahansen
fixed bug for missing sequence in genbank parser
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2012-07-02
martinahansen
added mum.rb
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2012-07-02
martinahansen
updated order_pairs
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2012-07-02
martinahansen
updated order_pairs
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2012-06-29
martinahansen
clean-up of ruby code to remove rake warnings
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2012-06-29
martinahansen
rewrote mean_scores to fix bug
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2012-06-29
martinahansen
added scores_mean method to seq.rb
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2012-06-28
martinahansen
cleanup of pair stuff in align.rb
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2012-06-27
martinahansen
fixed inline code warning
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2012-06-25
martinahansen
fixed bug in findsim.rb
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2012-06-25
martinahansen
added max_diversity swith to findsim.rb
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2012-06-25
martinahansen
added max_diversity swith to findsim.rb
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2012-06-25
martinahansen
added max_diversity swith to findsim.rb
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2012-06-20
martinahansen
classify_taxonomy work
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2012-06-20
martinahansen
classify_taxonomy work
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2012-06-13
martinahansen
added classify_taxonomy (unfinished biopiece)
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2012-06-08
martinahansen
fixed raw intput bug in read_fasta and read_fastq
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2012-06-08
martinahansen
refactoring biopieces.rb
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2012-06-08
martinahansen
fixed unit tests for test_trim.rb
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2012-06-01
martinahansen
added illumina 1.8 name scheme support to order pairs
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2012-05-31
martinahansen
fixed bad error msg
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2012-05-30
martinahansen
fixed bug in sff.rb clip and mask methods
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2012-05-30
martinahansen
fixed bug in sff.rb to_seq method
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2012-05-30
martinahansen
added to_seq method to sff.rb
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2012-05-25
martinahansen
fixed trim_seq tests
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2012-05-24
martinahansen
fixed ugly bug in trim.rb
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2012-05-24
martinahansen
moved patscan.rb
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2012-05-24
martinahansen
moved backtrack.rb
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2012-05-24
martinahansen
moved patternmatcher.rb
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2012-05-24
martinahansen
moving digest.rb
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2012-05-24
martinahansen
upgraded trim_seq
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2012-05-23
martinahansen
refactored SeqError/TrimError
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2012-05-23
martinahansen
rewrite of seq.rb and addition of seq/trim.rb
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2012-05-23
martinahansen
refactored argument precise to realign
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2012-05-08
martinahansen
reverted findsim_seq and renamed precise switch to...
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2012-05-02
martinahansen
finishing hmmer_seq
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2012-05-02
martinahansen
added hmmer_seq biopiece
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2012-04-30
martinahansen
upgraded write_fixedstep
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2012-04-24
martinahansen
added split of quality scores to split_seq
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2012-04-23
martinahansen
added precise switch to findsim
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2012-04-23
martinahansen
workied on pair wise aligner
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2012-04-19
martinahansen
added precise alignment option to findsim.rb
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2012-04-19
martinahansen
fixed double insertion of indels in alignments (missing...
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2012-04-18
martinahansen
added identity method to align.rb
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2012-04-18
martinahansen
changed report_scores to max_hits in findsim.rb
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2012-04-18
martinahansen
changed record_scores to max_hits refactoring
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2012-04-18
martinahansen
added findsim_seq biopieces
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2012-04-18
martinahansen
added to_bp method to findsim.rb
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2012-04-18
martinahansen
fixed issue 32
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2012-04-18
martinahansen
fixed x bug in compute
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2012-04-18
martinahansen
added q_id and s_id options to findsim.rb
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2012-04-17
martinahansen
added findsim.rb
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2012-04-11
martinahansen
ported write_fastq to ruby and allowed different encodi...
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2012-04-11
martinahansen
cleanup in read_fastq
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2012-04-10
martinahansen
fixed comment
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2012-04-10
martinahansen
upgraded read_fastq to handle illumina1.8 better
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2012-04-10
martinahansen
upgraded tests for read_fastq
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2012-04-10
martinahansen
removing stale test in files
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2012-04-10
martinahansen
making changes to accomodate Illumina18 qual scores
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2012-04-06
martinahansen
upgraded bitmap.rb to a 64bit version
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2012-04-03
martinahansen
upgraded bitmap.rb
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2012-03-26
martinahansen
fixed ugly 1-off bug in locator
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2012-03-26
martinahansen
fixed ugly 1-off bug in locator.rb
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2012-03-26
martinahansen
fixed ugly 1-off bug in locator.rb
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2012-03-22
martinahansen
added bitmap.rb
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2012-03-20
martinahansen
fixed issues in bwa_seq
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