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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
Merge branch 'master' of github.com:tanghaibao/jcvi
vivekkrish
as Vivek Krishnakumar
More... about 13 years ago
print more useful information in formats.vcf.summary()
tanghaibao
as Haibao Tang
More... about 13 years ago
Merge branch 'master' of github.com:tanghaibao/jcvi
vivekkrish
as Vivek Krishnakumar
More... about 13 years ago
add assembly.syntenypath.happy to parse HAPPY mapping data
tanghaibao
as Haibao Tang
More... about 13 years ago
use need_update in formats.sam
tanghaibao
as Haibao Tang
More... about 13 years ago
implement optical map parser
tanghaibao
as Haibao Tang
More... about 13 years ago
add --cpus to apps.bwa
tanghaibao
as Haibao Tang
More... about 13 years ago
Merge branch 'master' of github.com:tanghaibao/jcvi
vivekkrish
as Vivek Krishnakumar
More... about 13 years ago
report stats after formats.fasta.translate()
tanghaibao
as Haibao Tang
More... about 13 years ago
report stats after formats.fasta.translate()
tanghaibao
as Haibao Tang
More... about 13 years ago
add formats.fasta.translate() to translate CDS to proteins
tanghaibao
as Haibao Tang
More... about 13 years ago
allow algorithms.graph to dump graph; minor code fixes
tanghaibao
as Haibao Tang
More... about 13 years ago
Modified formats.gff.bed() and formats.gff.extendbed() to be able to produce GFF3 formatted output by invoking these functions using the --gff cmd line parameter.
vivekkrish
as Vivek Krishnakumar
More... about 13 years ago
Added wrapper for cap3 (jcvi.assembly.cap3) for batch jobs. Accepts input file name, folder with input files or file list. Allows tweaking of some important cap3 parameters. Added module specific to preparing files for per-clone assembly for FL-cDNA project.
vivekkrish
as Vivek Krishnakumar
More... about 13 years ago
add formats.vcf.summary() to summarize the genotype calls and tabulate all combinations
tanghaibao
as Haibao Tang
More... about 13 years ago
add algorithms.synteny.depth()
tanghaibao
as Haibao Tang
More... about 13 years ago
add formats.sam.bcf()
tanghaibao
as Haibao Tang
More... about 13 years ago
add offset checking when running bwa
tanghaibao
as Haibao Tang
More... about 13 years ago
add bam output for bwa wrapper
tanghaibao
as Haibao Tang
More... about 13 years ago
add formats.bed.refine()
tanghaibao
as Haibao Tang
More... about 13 years ago
make fragsdedup the default behavior for assembly.preprocess.correct()
tanghaibao
as Haibao Tang
More... about 13 years ago
add --fragdup option to assembly.preprocess.correct
tanghaibao
as Haibao Tang
More... about 13 years ago
bump up LICENSE year
tanghaibao
as Haibao Tang
More... about 13 years ago
add --horizontalbar to graphics.heatmap
tanghaibao
as Haibao Tang
More... about 13 years ago
add --rowgroups option to graphics.heatmap
tanghaibao
as Haibao Tang
More... about 13 years ago
add formats.bed.distance() and utils.cbook.SummaryStats()
tanghaibao
as Haibao Tang
More... about 13 years ago
add option --log to graphics.histogram
tanghaibao
as Haibao Tang
More... about 13 years ago
add --log in graphics.histogram() to plot logarithm axis
tanghaibao
as Haibao Tang
More... about 13 years ago
add formats.bed.sample() to sample down the bed file
tanghaibao
as Haibao Tang
More... about 13 years ago
minor options for apps.cdhit and apps.setop
tanghaibao
as Haibao Tang
More... about 13 years ago