Ecosyste.ms: Issues

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GitHub / hepcat72/codonhomologizer issues and pull requests

#24 - Dividers resulting from indirect overlap interrupt source dividers sometimes

Issue - State: closed - Opened by hepcat72 almost 7 years ago
Labels: TYPE:BUG, code:3 DONE, effort:3 MAJOR, priority:3 HIGH

#23 - Add a check for codon-alignment to stretchMixer.pl

Issue - State: closed - Opened by hepcat72 almost 7 years ago
Labels: TYPE:FEATURE, component:ALIGNMENT, code:3 DONE, code:1 DESIGNED, effort:2 MODERATE, priority:2 MEDIUM

#22 - Mix the identity segments into a single set of sequences

Issue - State: closed - Opened by hepcat72 about 7 years ago
Labels: TYPE:FEATURE, code:2 INPROGRESS, code:3 DONE, effort:3 MAJOR, priority:3 HIGH

#21 - Usage reporting max option changes stretch reporting mins variable

Issue - State: closed - Opened by hepcat72 over 7 years ago - 1 comment
Labels: TYPE:BUG, effort:1 MINOR, code:3 DONE, component:METRICS, priority:2 MEDIUM

#20 - Allow usage scores to be absent from the usage file

Issue - State: closed - Opened by hepcat72 over 7 years ago - 1 comment
Labels: TYPE:FEATURE, effort:1 MINOR, code:1 DESIGNED, priority:1 LOW, component:CODONS

#19 - Add clustalw as an alternative alignment method

Issue - State: closed - Opened by hepcat72 over 7 years ago
Labels: TYPE:FEATURE, component:ALIGNMENT, code:2 INPROGRESS, priority:1 LOW, effort:2 MODERATE, WONTFIX

#18 - Warning about parsing the version number from the script in Makefile.PL

Issue - State: closed - Opened by hepcat72 over 7 years ago - 1 comment
Labels: TYPE:BUG, effort:1 MINOR, code:3 DONE, priority:1 LOW

#17 - Weird warning on Linux

Issue - State: closed - Opened by hepcat72 over 7 years ago - 2 comments
Labels: TYPE:BUG, priority:1 LOW, effort:2 MODERATE

#16 - Make metrics identity-aware

Issue - State: closed - Opened by hepcat72 over 7 years ago - 1 comment
Labels: TYPE:FEATURE, effort:1 MINOR, component:METRICS, priority:1 LOW, WONTFIX

#15 - Add metrics for domain alignment

Issue - State: closed - Opened by hepcat72 over 7 years ago
Labels: TYPE:FEATURE, code:3 DONE, component:METRICS, effort:2 MODERATE, priority:2 MEDIUM

#14 - Allow end gaps in domain alignments to align with neighboring sequences

Issue - State: closed - Opened by hepcat72 over 7 years ago - 3 comments
Labels: TYPE:FEATURE, component:ALIGNMENT, code:1 DESIGNED, effort:3 MAJOR, priority:2 MEDIUM, WONTFIX

#13 - Use NNN for unrecognized AA characters

Issue - State: closed - Opened by hepcat72 over 7 years ago
Labels: TYPE:FEATURE, code:3 DONE, effort:2 MODERATE, priority:2 MEDIUM, component:CODONS

#12 - Incorporate CommandLineInterface module

Issue - State: closed - Opened by hepcat72 over 7 years ago
Labels: TYPE:FEATURE, effort:1 MINOR, code:1 DESIGNED, priority:3 HIGH

#11 - Report the percent of non-gap aligned characters

Issue - State: closed - Opened by hepcat72 over 7 years ago
Labels: TYPE:FEATURE, effort:1 MINOR, code:3 DONE, component:METRICS, priority:3 HIGH

#10 - Report number of frame shifted codons in (supplied) NT alignments

Issue - State: closed - Opened by hepcat72 over 7 years ago
Labels: TYPE:FEATURE, code:3 DONE, component:METRICS, effort:2 MODERATE, priority:2 MEDIUM

#9 - Report the least used codon that was included

Issue - State: closed - Opened by hepcat72 over 7 years ago
Labels: TYPE:FEATURE, effort:1 MINOR, code:3 DONE, component:METRICS, priority:3 HIGH

#8 - Generate Usage table

Issue - State: closed - Opened by hepcat72 over 7 years ago
Labels: TYPE:FEATURE, effort:1 MINOR, code:1 DESIGNED, component:METRICS, priority:1 LOW, WONTFIX

#7 - Report number of occurrences of inclusion of codons with rare usage

Issue - State: closed - Opened by hepcat72 over 7 years ago
Labels: TYPE:FEATURE, effort:1 MINOR, code:3 DONE, component:METRICS, priority:3 HIGH

#6 - Report number of bases involved in contiguous stretches

Issue - State: closed - Opened by hepcat72 over 7 years ago
Labels: TYPE:FEATURE, effort:1 MINOR, code:3 DONE, component:METRICS, priority:3 HIGH

#5 - Report Percent identity

Issue - State: closed - Opened by hepcat72 over 7 years ago
Labels: TYPE:FEATURE, effort:1 MINOR, code:3 DONE, component:METRICS, priority:3 HIGH

#4 - Impose a usage cutoff

Issue - State: closed - Opened by hepcat72 over 7 years ago - 2 comments
Labels: duplicate, TYPE:FEATURE, priority:1 LOW, effort:2 MODERATE, component:CODONS

#3 - Force segments of sequences to align

Issue - State: closed - Opened by hepcat72 over 7 years ago
Labels: TYPE:FEATURE, component:ALIGNMENT, code:3 DONE, effort:3 MAJOR, priority:2 MEDIUM

#2 - Tweak default gap parameters

Issue - State: closed - Opened by hepcat72 over 7 years ago - 1 comment
Labels: TYPE:FEATURE, component:ALIGNMENT, effort:1 MINOR, code:1 DESIGNED, priority:1 LOW

#1 - Warning from MUSCLE

Issue - State: closed - Opened by hepcat72 over 7 years ago - 1 comment
Labels: TYPE:BUG, component:ALIGNMENT, effort:3 MAJOR, priority:1 LOW