mdperry/biopieces

Issues

• error downloading by svn

  #50 opened 9 years ago
  0

• custom_require.rb:36:in `require'

  #49 opened 9 years ago
  0

• read_fastq: "Error. You have specified 'C' as an Inline programming language."

  #48 opened 9 years ago
  6

• write_fasta_files keeps too many file handles open

  #47 opened 9 years ago
  2

• max_vals.out.1 typo error

  #46 opened 9 years ago
  1

• pcr_seq example failed

  #45 opened 9 years ago
  2

• missing tests for read_454 and write_454

  #44 opened 9 years ago
  0

• Remove bzip2-ruby gem from requirements

  #43 opened 9 years ago
  0

• read_fasta error

  #42 opened 9 years ago
  8

• Translate does not accept Ns

  #41 opened 9 years ago
  1

• Problem configuring biopieces

  #40 opened 9 years ago
  1

• assemble_pairs error when pandaseq not installed

  #39 opened 9 years ago
  1

• Biopieces: cant read the input fasta or fastq file

  #38 opened 9 years ago
  1

• pcr_seq uses 3'-end to 5'-end reverse primer

  #37 opened 9 years ago
  0

• blast_seq don't raise on missing index file

  #36 opened 9 years ago
  0

• find_genes dont report gene sequences.

  #35 opened 9 years ago
  0

• bwa_seq: sampe not supported

  #34 opened 9 years ago
  2

• ruby version failing on automated installer

  #33 opened 9 years ago
  1

• Compute concatenates?

  #32 opened 9 years ago
  2

• pcr_seq, patscan_seq truncate SEQ_NAME fields at spaces

  #31 opened 9 years ago
  1

• SAM reader behaviour

  #30 opened 9 years ago
  1

• head_records err if Ruby Biopieces in the pipe

  #29 opened 9 years ago
  1

• Make bowtie_seq check for the existence of the index before running.

  #28 opened 9 years ago
  0

• Bad time stamps in Biopieces logfile

  #27 opened 9 years ago
  1

• Error message after installing biopieces

  #26 opened 9 years ago
  6

• test_plot_distribution fails with older versions of gnuplot

  #25 opened 9 years ago
  0

• Patch for /trunk/code_perl/Maasha/Blast.pm

  #24 opened 9 years ago
  2

• undefined method `to_time'

  #23 opened 9 years ago
  2

• Verbose writing to screen all the time

  #22 opened 9 years ago
  1

• format_genome calls undefined subroutine

  #21 opened 9 years ago
  9

• PSL->KISS conversion error

  #20 opened 9 years ago
  1

• plot_karyogram gives a ton of warnings

  #19 opened 9 years ago
  2

• assemble_tag_contigs discarding some usable tags

  #18 opened 9 years ago
  3

• read_solexa does not work correctly with decimal entries.

  #17 opened 9 years ago
  1

• assemble_tag_contigs doesn't work

  #16 opened 9 years ago
  2

• [deleted issue]

  #15 opened 9 years ago
  0

• upload_to_ucsc create redundant my_tracks.ra entries

  #14 opened 9 years ago
  2

• get_genome_align from bed files does not work correctly

  #13 opened 9 years ago
  1

• upload_to_ucsc with rnaSecStr have stopped working

  #12 opened 9 years ago
  1

• upload_to_ucsc writes ucsc.ra config in wrong format

  #11 opened 9 years ago
  1

• Add switch to keep order of keys for write_tab

  #10 opened 9 years ago
  1

• fixedStep score is off by 1 (+) when using upload_to_ucsc -w

  #9 opened 9 years ago
  1

• vmatch_index only work with one sequnce.

  #8 opened 9 years ago
  2

• Add comment line to write_blast

  #7 opened 9 years ago
  1

• write_solid does not handle lower case sequences from the stream

  #6 opened 9 years ago
  1

• remove the REC_TYPE key from split_seq

  #5 opened 9 years ago
  1

• translate_seq does not recompute SEQ_LEN

  #4 opened 9 years ago
  1

• analyze_vals should default analyze all keys - and have both --keys and --no_keys switches

  #3 opened 9 years ago
  2

• analyze_vals should not print a table of its own, should rather put the result to stream and let write_tab do the printing.

  #2 opened 9 years ago
  2

• analize_vals does not calculate the SUM correctly

  #1 opened 9 years ago
  1