Issues

• Reimplement fasta parsers with Bioperl

  solgenomics/Bio-GenomeUpdate#64 · Filter by author suryasaha opened on Oct 22, 2019
  

• script to parse SL3.0 chrs using SL2.93 TPF files and extract contigs

  solgenomics/Bio-GenomeUpdate#63 · Filter by author suryasaha opened on Feb 12, 2017
  

• Refactor ACE file code out of place_bacs.pl into separate pre-processing script

  feature
  solgenomics/Bio-GenomeUpdate#55 · Filter by author suryasaha opened on Aug 8, 2015

• Solo BAC end alignments are not handled correctly in get_tpf_sp_tp_with_bacs_inserted_in_sequences_and_gaps

  bug
  solgenomics/Bio-GenomeUpdate#54 · Filter by author suryasaha opened on Jul 16, 2015 · SL3.0
  1

• Singleton BACs should be inserted in the order of occurence in the filtered group_coords file

  bug
  solgenomics/Bio-GenomeUpdate#53 · Filter by author suryasaha opened on Jul 10, 2015 · SL3.0
  1

• Generate trim files for TPF in NCBI GRC format

  feature
  solgenomics/Bio-GenomeUpdate#45 · Filter by author suryasaha opened on May 11, 2015 · SL3.0

• Add test routine that processes a test ACE file from phrap (process_bac_assembly.pl)

  testing
  solgenomics/Bio-GenomeUpdate#44 · Filter by author suryasaha opened on May 7, 2015

• Fix add_contig_to_scaffold() to work with test ACE object (wrong aligned coordinates reported) and ACE files from phrap. (process_bac_assembly.pl)

  bug
  solgenomics/Bio-GenomeUpdate#43 · Filter by author suryasaha opened on May 7, 2015

• Fix contig_mismatch() to work with ACE files from phrap. (process_bac_assembly.pl)

  bug
  solgenomics/Bio-GenomeUpdate#42 · Filter by author suryasaha opened on May 7, 2015

• Write a LOG file with Contig name and accessions of member BACs (process_bac_assembly.pl)

  feature
  solgenomics/Bio-GenomeUpdate#41 · Filter by author suryasaha opened on May 7, 2015

• Upgrade Bio::GenomeUpdate::TPF to TPF v1.8

  feature
  solgenomics/Bio-GenomeUpdate#29 · Filter by author suryasaha opened on Apr 14, 2015
  1

• Need script to identify BACs with source chromosomes that align to other chrs

  feature
  solgenomics/Bio-GenomeUpdate#25 · Filter by author suryasaha opened on Mar 27, 2015

• Add mixed orientation and out of order cases to test data (align_BACends_group_coords.pl)

  testing
  solgenomics/Bio-GenomeUpdate#22 · Filter by author suryasaha opened on Mar 19, 2015

• Output Fasta of valid, mixed, outoforder and both_errors from align_BACends_group_coords.pl

  feature
  solgenomics/Bio-GenomeUpdate#21 · Filter by author suryasaha opened on Mar 18, 2015

• Check for BAC ends that are align too close on ref chr (align_BACends_group_coords.pl)

  bug
  solgenomics/Bio-GenomeUpdate#20 · Filter by author suryasaha opened on Mar 18, 2015

• Remove mixed and outoforder output files and stats (align_BACends_group_coords.pl)

  solgenomics/Bio-GenomeUpdate#18 · Filter by author suryasaha opened on Mar 8, 2015
  1

• Output fasta from group_coords.pl

  feature
  solgenomics/Bio-GenomeUpdate#7 · Filter by author suryasaha opened on Feb 16, 2015

• Make GFF3 module mx-runnable

  feature
  solgenomics/Bio-GenomeUpdate#4 · Filter by author suryasaha opened on May 19, 2014
  

• summarize.pl - globbing and tabular reports

  solgenomics/Bio-GenomeUpdate#3 · Filter by author suryasaha opened on May 13, 2014