| allow stdin and stdout to process .gz files in apps.base.sh() |
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over 12 years ago
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| remove redundant options in soap pregraph |
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over 12 years ago
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| add formats.agp.format() and add --splitcomponent to formats.agp.mask() |
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over 12 years ago
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| add option --haploidify in assembly.preprocess.correct() |
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over 12 years ago
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| minor parameter adjustment in assembly.soap.clean() |
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over 12 years ago
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| implement SOAPdenovo v2 pipeline |
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over 12 years ago
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| add apps.base.mdownload() to allow parallel downloads; add formats.html.links() to extract a list of links from a web page. |
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over 12 years ago
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| Updated annotation.ahrd() to now account for InterProScan results to be intergrated with the AHRD pipeline. Updated BLAST -m8 format sorting to now do general numeric sort. Added in option to extract score from GFF attribute and place in BED file score column. |
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over 12 years ago
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| add utils.data to store external data like adapters FASTA sequences |
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over 12 years ago
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| add formats.sam.pairs() to plot insert size distribution given BAM output |
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over 12 years ago
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| add option --bam in apps.bwa.bwasw() |
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over 12 years ago
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| move seqid_parse() to utils.cbook |
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over 12 years ago
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| add formats.base.seqid_parse() to attempt to split seqid into prefix, numerical ID, and suffix |
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over 12 years ago
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| add algorithms.fractionation.napus() |
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over 12 years ago
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| add algorithms.fractionation to assess gene loss, bites, etc. |
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over 12 years ago
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| add apps.gbsubmit.fcs() to handle Genbank FCS qc failures |
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over 12 years ago
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| make intreefile optional in apps.phylo.run_ffitch(); add 'minsize' arg in algorithms.synteny.read_anchors() |
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over 12 years ago
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| add apps.base.expand() to expand subfolder files into current |
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over 12 years ago
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| add option --dir in assembly.preprocess.count() |
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over 12 years ago
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| add more descriptions in formats.sbt.names() |
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over 12 years ago
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| add option --plot in apps.ks.gc3(); allow float output in utils.cbook.SummaryStats(); update some codes |
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over 12 years ago
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| modify K-mer ceiling in KmerSpectrum.analyze() |
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over 12 years ago
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| add assembly.gaps.annotate() to annotate AGP with gap linkages; various modifications for AGP v2 compatibility |
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over 12 years ago
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| change default mapping parameters in apps.clc.map() |
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over 12 years ago
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| add formats.fastq.first() to extract first N reads from file |
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over 12 years ago
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| add graphics.logo to design logo and three free ttf fonts from urbanfonts.com |
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over 12 years ago
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| adjust plotting parameters in graphics.karyotype |
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over 12 years ago
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| allow bcf as input to formats.vcf.mstmap() |
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over 12 years ago
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| move formats.fastq.deconvolute to assembly.deconvolute.split() |
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over 12 years ago
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| allow ambiguous dna codes in barcode file in formats.fastq.deconvolute() |
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over 12 years ago
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