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Analyzed about 1 year ago. based on code collected about 1 year ago.
Jan 18, 2023 — Jan 18, 2024
Commit Message Contributor Files Modified Lines Added Lines Removed Code Location Date
minor spelling changes in formats.cas
tanghaibao
as Haibao Tang
More... over 13 years ago
add formats.gff.split(), extract(), merge()
tanghaibao
as Haibao Tang
More... over 13 years ago
version up trimmomatic; fix flaw in formats.fastq.guessoffset()
tanghaibao
as Haibao Tang
More... over 13 years ago
Merge branch 'master' of https://github.com/tanghaibao/jcvi
Jingping Li
More... over 13 years ago
add --distmode for pairs() function per vkrishna's suggestion (thanks)
tanghaibao
as Haibao Tang
More... over 13 years ago
Merge branch 'master' of https://github.com/tanghaibao/jcvi
Jingping Li
More... over 13 years ago
add apps.command.less() to augment unix less; make formats.base.split() use batch mode when splitting; make default fasta qual 21 when preparing for CA
tanghaibao
as Haibao Tang
More... over 13 years ago
regular
Jingping Li
More... over 13 years ago
add HTG_POOLED_MULTICLONE to apps.gbsubmit.htg()
tanghaibao
as Haibao Tang
More... over 13 years ago
add fasta.filter() to filter fasta records by size
tanghaibao
as Haibao Tang
More... over 13 years ago
missing choices option in graphics.base.set_format()
tanghaibao
as Haibao Tang
More... over 13 years ago
move vivekkrish's option to graphics.base to set_format()
tanghaibao
as Haibao Tang
More... over 13 years ago
Included a command line option to specify output file format for the chromosome image generated by graphics.chromosome()
vivekkrish
as Vivek Krishnakumar
More... over 13 years ago
add option --batchsize in apps.entrez to speed up download
tanghaibao
as Haibao Tang
More... over 13 years ago
Fixed error in caluclating block size for bed12 line; Modified color choices for BAC phases and gap features
vivekkrish
as Vivek Krishnakumar
More... over 13 years ago
modify agp.bed() to optionally print bed12 formatted output. caveat: bed12 file stores the BAC phase (ODF) or designates a gap (N) in the score column
vivekkrish
as Vivek Krishnakumar
More... over 13 years ago
add file based set operations
tanghaibao
as Haibao Tang
More... over 13 years ago
make assembly.goldenpath.tpf download singleton BACs as well
tanghaibao
as Haibao Tang
More... over 13 years ago
modify graphics.chromosome to use an optional id_mappings file
tanghaibao
as Haibao Tang
More... over 13 years ago
add --full option to apps.restriction
tanghaibao
as Haibao Tang
More... over 13 years ago
make --ignore_N also ignore X's in formats.fasta.diff()
tanghaibao
as Haibao Tang
More... over 13 years ago
add formats.blast.sort() and formats.gff.note()
tanghaibao
as Haibao Tang
More... over 13 years ago
add formats.blast.cscore()
tanghaibao
as Haibao Tang
More... over 13 years ago
add Ks calculation to apps.ks
tanghaibao
as Haibao Tang
More... over 13 years ago
modify formats.fasta.diff() to take --ignore_stop when checking proteins; output Problems.ids for any mismatches seen.
tanghaibao
as Haibao Tang
More... over 13 years ago
warn user if adjacent components do not share good overlap in assembly.goldenpath
tanghaibao
as Haibao Tang
More... over 13 years ago
remove hard-coded cutoffs in assembly.goldenpath
tanghaibao
as Haibao Tang
More... over 13 years ago
add README; replace list slicing with iterators in AGP adjacent clone lookups
tanghaibao
as Haibao Tang
More... over 13 years ago
refactor formats.blast.chain() and called by assembly.goldenpath.overlap()
tanghaibao
as Haibao Tang
More... over 13 years ago
significantly improve runtime of assembly.goldenpath.certificate(); add formats.blast.chain() to chain adjacent HSPs
tanghaibao
as Haibao Tang
More... over 13 years ago