wwood/finishm issues and pull requests

#43 - Command finished with exitstatus 42

Issue - State: open - Opened by jlli6t over 4 years ago

#42 - roundup 'velvetg' error

Issue - State: open - Opened by epulo5 over 7 years ago - 3 comments

#41 - check for duplicated output file and/or directory names

Issue - State: open - Opened by wwood almost 8 years ago

#40 - 'roundup' command with paired-end reads

Issue - State: closed - Opened by minsookim1983 about 8 years ago - 3 comments

#39 - I got an error on 'roundup' command

Issue - State: closed - Opened by minsookim1983 about 8 years ago - 7 comments

#38 - Can't test finishm

Issue - State: closed - Opened by cwzkevin over 8 years ago - 7 comments

#37 - Having problem running finishm 0.0.7

Issue - State: open - Opened by fauziharoon over 8 years ago - 2 comments

#36 - printing contigs can fail when the middle stretch of nodes is too short

Issue - State: closed - Opened by wwood about 9 years ago - 4 comments

#35 - piece_together_gapfill fails under finishm roundup

Issue - State: closed - Opened by donovan-h-parks about 9 years ago

#34 - Probes written to temporary file with static name

Issue - State: closed - Opened by donovan-h-parks about 9 years ago - 3 comments

#33 - remove dashes from output fasta file

Issue - State: closed - Opened by StevenJRobbins over 9 years ago - 1 comment

#32 - feature to report orf protein sequence

Pull Request - State: closed - Opened by timbalam over 9 years ago - 2 comments

#31 - Find orfs

Pull Request - State: closed - Opened by wwood over 9 years ago

#30 - fix easy to fix big bug

Pull Request - State: closed - Opened by wwood over 9 years ago

#29 - Missing sequences in output file

Issue - State: open - Opened by donovan-h-parks over 9 years ago

#28 - when there is no arcs, no nodes are visualised?

Issue - State: open - Opened by wwood over 9 years ago

#27 - Scaffolding can contain excessive numbers of ambiguous bases

Issue - State: closed - Opened by donovan-h-parks over 9 years ago - 3 comments

#26 - Cyclic bubbler

Pull Request - State: closed - Opened by timbalam over 9 years ago - 3 comments

#25 - Crash on finishm gapfill when applied to entire sample

Issue - State: closed - Opened by donovan-h-parks over 9 years ago - 4 comments

#24 - assemble should have a --min-coverage-at-fork alongside --max-coverage-at-fork

Issue - State: open - Opened by wwood almost 10 years ago

#23 - gap filling statistics

Issue - State: closed - Opened by ctSkennerton almost 10 years ago - 1 comment
Labels: question

#22 - undefined method error

Issue - State: closed - Opened by ctSkennerton almost 10 years ago - 1 comment

#21 - visualise should report when max-nodes or leash-length is reached

Issue - State: open - Opened by wwood almost 10 years ago

#20 - connection file doesn't indicate reverse complement

Issue - State: open - Opened by donovan-h-parks almost 10 years ago

#19 - empty connections file

Issue - State: open - Opened by donovan-h-parks almost 10 years ago

#18 - number of filled gaps not reported

Issue - State: open - Opened by donovan-h-parks almost 10 years ago

#17 - roundup infinite loop?

Issue - State: closed - Opened by wwood almost 10 years ago - 9 comments

#16 - Error running gapfill

Issue - State: open - Opened by ctSkennerton almost 10 years ago - 1 comment

#15 - error when finishm script is a symlink

Issue - State: open - Opened by ctSkennerton almost 10 years ago

#14 - No rule to make target finishm

Issue - State: closed - Opened by ctSkennerton almost 10 years ago - 3 comments

#13 - Find cyclic paths using SingleCoherentPathsBetweenNodesFinder

Pull Request - State: closed - Opened by timbalam almost 10 years ago - 1 comment

#12 - when using --logger, the timestamp is not shown

Issue - State: open - Opened by wwood almost 10 years ago

#11 - velvet counts N characters as A characters

Issue - State: open - Opened by wwood almost 10 years ago

#10 - gap filling should take into account the size of the given gap

Issue - State: open - Opened by wwood almost 10 years ago

#9 - roundup mode should report the number of contig ends that did not connect to anything else

Issue - State: open - Opened by wwood almost 10 years ago - 1 comment

#8 - finishm visualise can only handle one kind of probe definition at a time

Issue - State: open - Opened by wwood almost 10 years ago

#7 - should use velvet bundled by default

Issue - State: closed - Opened by wwood almost 10 years ago

#6 - finishm assemble problem

Issue - State: closed - Opened by wwood almost 10 years ago - 1 comment

#5 - should output fastg format

Issue - State: open - Opened by wwood almost 10 years ago

#4 - use multiple velvet threads

Issue - State: open - Opened by wwood about 10 years ago - 1 comment

#3 - deal with Ns when they fall within the probe sequence

Issue - State: open - Opened by wwood about 10 years ago

#2 - in -h, don't use PATH, instead use DIRECTORY or FILE

Issue - State: open - Opened by wwood about 10 years ago

#1 - missing contigs flag in visualize subcommand

Issue - State: closed - Opened by donovan-h-parks about 10 years ago - 1 comment

GitHub / wwood/finishm issues and pull requests