| add apps.entrez.phytozome to download data for a list of plant species |
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almost 12 years ago
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| Use output file prefix instead of output file name in apps.entrez.fetch() |
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almost 12 years ago
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| simplify calling to apps.grid.kill by guessing the method |
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almost 12 years ago
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| Move email parameters to apps.base.OptionParser. Add `outfile` parameter to apps.entrez.fetch() |
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almost 12 years ago
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| Remove hardcoded cpu settings in assembly.preprocess.trim(); use apps.base.OptionParser.set_cpus() instead |
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almost 12 years ago
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| does not expose GridOpts any more |
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almost 12 years ago
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| add class GridOpts in apps.grid |
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almost 12 years ago
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| Add `--nouniq` option to formats.base.group() to avoid uniqifying grouped elements. Update apps.grid.GridProcess() to now allow specifying a job dependency for regular and array grid jobs |
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almost 12 years ago
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| simplify apps.bwa.bwasw(); remove samfile after running formats.sam.mapped in apps.bwa.align() |
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almost 12 years ago
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| add argument mapped to formats.sam.get_samfile(); simplify calling to formats.sam.output_bam() |
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almost 12 years ago
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| Minor fix to the apps.base.waitpid() notifier |
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almost 12 years ago
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| Added option `--chaindup` to formats.gff.format() to allow chaining of specific `type` of duplicate feature (normally used to chain parent level features such as `gene`); cannot be used in conjunction with `--unique` |
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almost 12 years ago
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| Added formats.sam.mapped() to extract mapped and/or unmapped reads from input SAM/BAM. Updated formats.sam.output_bam() to always output SAM if `--unmapped` is requested and then call the formats.sam.mapped() |
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almost 12 years ago
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| add assembly.automaton.contamination() |
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almost 12 years ago
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| bowtie.align() now writes out a file with suffix "fastq" |
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almost 12 years ago
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| enable grid log folder regardless of whether outfile or errfile is set |
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almost 12 years ago
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| add brewer2mpl in graphics.base |
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almost 12 years ago
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| allow changing cpus in apps.bwa.bwasw() |
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almost 12 years ago
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| reduce code dup in apps.bowtie and apps.bwa |
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almost 12 years ago
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| Fix incorrect file name extension for unmapped reads in apps.bwa.align() |
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almost 12 years ago
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| correct output counting in formats.bed.flanking(); allow pctid to be float in apps.base.set_align() |
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almost 12 years ago
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| Fix formats.sam.output_bam() so that `/dev/null` redirection happens only when `tee` is used to redirect the stream to two separate `samtools` commands |
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almost 12 years ago
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| Fixed logic of formats.sam.output_bam(); action varies based on the `app` making the fn call. Changed default method to `pattern` for apps.grid.kill() |
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almost 12 years ago
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| add assembly.automaton.pairs() to automatically determine insert sizes |
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almost 12 years ago
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| modify apps.bowtie to use output_bam() |
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almost 12 years ago
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| Added apps.grid.kill() to kill grid jobs based on SGE job ID or job name pattern (case-sensitive) |
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almost 12 years ago
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| add --append to assembly.deconvolute.split() |
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almost 12 years ago
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| route Popen calls to apps.base.Popen so that default is bufsize=1 (line buffered) |
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almost 12 years ago
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| add --cpus in annotation.pasa.prepare() |
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almost 12 years ago
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| add default vcode to valid_pcodes to avoid failure on non-JCVI servers |
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almost 12 years ago
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