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Commits : Listings

Analyzed about 11 hours ago. based on code collected about 11 hours ago.
Jul 18, 2024 — Jul 18, 2025
Commit Message Contributor Files Modified Lines Added Lines Removed Code Location Date
add --writecolors in apps.phylo.prepare()
Jingping Li
More... almost 13 years ago
add --leafcolorfile in graphics.tree
Jingping Li
More... almost 13 years ago
support phred64 fastqfiles in assembly.allpaths.prepare()
tanghaibao
as Haibao Tang
More... almost 13 years ago
add --pctid in formats.coords.bed()
tanghaibao
as Haibao Tang
More... almost 13 years ago
suppress Gblocks editing in apps.phylo.build() if too few positions are retained
Jingping Li
More... almost 13 years ago
parallelize convert() in assembly.soap.clean(); deprecate formats.fastq.unpair()
tanghaibao
as Haibao Tang
More... almost 13 years ago
bug fix gff.load(): initialize missing variables
vivekkrish
as Vivek Krishnakumar
More... almost 13 years ago
invert query and ref in graphics.mummerplot()
tanghaibao
as Haibao Tang
More... almost 13 years ago
add assembly.preprocess.hetsmooth()
tanghaibao
as Haibao Tang
More... almost 13 years ago
add assembly.kmer.jellyfish()
tanghaibao
as Haibao Tang
More... almost 13 years ago
increase stringency to report tandems in algorithms.catalog.tandem() --not_self; add --barcode in graphics.tree
Jingping Li
More... almost 13 years ago
add formats.fasta.longestorf() and formats.gff.orient()
tanghaibao
as Haibao Tang
More... almost 13 years ago
fix reverse_complement() bug in formats.fasta.ORFFinder
tanghaibao
as Haibao Tang
More... almost 13 years ago
allow formats.coords.summary() to accept delta file as well
tanghaibao
as Haibao Tang
More... almost 13 years ago
Refactored formats.gff.load(). Moved code to calculate upstream start/end coordinates to a subroutine. Also created new subroutine to parse the `--feature` param which encodes the requested upstream sequence start site and length
vivekkrish
as Vivek Krishnakumar
More... almost 13 years ago
Added functionality to formats.gff.load() to allow extracting sequence upstream of transcription or translation start site (TSS or TrSS)
vivekkrish
as Vivek Krishnakumar
More... almost 13 years ago
change label position in graphics.landscape.heatmap()
tanghaibao
as Haibao Tang
More... almost 13 years ago
add option --scutoff in graphics.tree.draw_tree() for support display
Jingping Li
More... almost 13 years ago
add assembly.soap.clean() and assembly.soap.correct()
tanghaibao
as Haibao Tang
More... almost 13 years ago
add option --norbh in algorithms.catalog.omgprepare()
tanghaibao
as Haibao Tang
More... almost 13 years ago
make some drawing changes (minor)
Jingping Li
More... almost 13 years ago
revert two recent changes in graphics.tree
tanghaibao
as Haibao Tang
More... almost 13 years ago
add --SH in apps.phylo.build() for alt topology testing
Jingping Li
More... almost 13 years ago
fix index bug in algorithms.reconstruct.zipbed()
tanghaibao
as Haibao Tang
More... almost 13 years ago
add option --trunc_name in graphics.tree
Jingping Li
More... almost 13 years ago
add algorithms.reconstruct.pairs() to add block ids to anchorsfile
tanghaibao
as Haibao Tang
More... almost 13 years ago
add algorithms.reconstruct.zipbed() to automate the Bowers' and Tang bottom-up approach
tanghaibao
as Haibao Tang
More... almost 13 years ago
Added in a new class `Fastqheader` in formats.fastq to handle different FASTQ header dialects. Added formats.fastq.format() which currently allows converting Illumina 1.8+ header to an older format.
vivekkrish
as Vivek Krishnakumar
More... almost 13 years ago
make some compatibility related changes
Jingping Li
More... almost 13 years ago
add --minsize and --seqpairs in algorithms.synteny.screen()
tanghaibao
as Haibao Tang
More... almost 13 years ago