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19 Open 45 Closed
19 Open 45 Closed
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Issues list

Reimplement fasta parsers with Bioperl
#64 opened Oct 22, 2019 by suryasaha
@suryasaha
script to parse SL3.0 chrs using SL2.93 TPF files and extract contigs
#63 opened Feb 12, 2017 by suryasaha
@MFlores2021
Refactor ACE file code out of place_bacs.pl into separate pre-processing script feature
#55 opened Aug 8, 2015 by suryasaha
Solo BAC end alignments are not handled correctly in get_tpf_sp_tp_with_bacs_inserted_in_sequences_and_gaps bug
#54 opened Jul 16, 2015 by suryasaha SL3.0
1
Singleton BACs should be inserted in the order of occurence in the filtered group_coords file bug
#53 opened Jul 10, 2015 by suryasaha SL3.0
1
Generate trim files for TPF in NCBI GRC format feature
#45 opened May 11, 2015 by suryasaha SL3.0
Add test routine that processes a test ACE file from phrap (process_bac_assembly.pl) testing
#44 opened May 7, 2015 by suryasaha
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
#43 opened May 7, 2015 by suryasaha
Fix contig_mismatch() to work with ACE files from phrap. (process_bac_assembly.pl) bug
#42 opened May 7, 2015 by suryasaha
Write a LOG file with Contig name and accessions of member BACs (process_bac_assembly.pl) feature
#41 opened May 7, 2015 by suryasaha
Upgrade Bio::GenomeUpdate::TPF to TPF v1.8 feature
#29 opened Apr 14, 2015 by suryasaha
1
Need script to identify BACs with source chromosomes that align to other chrs feature
#25 opened Mar 27, 2015 by suryasaha
Add mixed orientation and out of order cases to test data (align_BACends_group_coords.pl) testing
#22 opened Mar 19, 2015 by suryasaha
Output Fasta of valid, mixed, outoforder and both_errors from align_BACends_group_coords.pl feature
#21 opened Mar 18, 2015 by suryasaha
Check for BAC ends that are align too close on ref chr (align_BACends_group_coords.pl) bug
#20 opened Mar 18, 2015 by suryasaha
Remove mixed and outoforder output files and stats (align_BACends_group_coords.pl)
#18 opened Mar 8, 2015 by suryasaha
1
Output fasta from group_coords.pl feature
#7 opened Feb 16, 2015 by suryasaha
Make GFF3 module mx-runnable feature
#4 opened May 19, 2014 by suryasaha
@suryasaha
summarize.pl - globbing and tabular reports
#3 opened May 13, 2014 by suryasaha
ProTip! no:milestone will show everything without a milestone.