HenrikBengtsson aroma.seq issues

HenrikBengtsson / aroma.seq

🔬 R package: aroma.seq: High-Throughput Sequence Analysis using the Aroma Framework

https://github.com/HenrikBengtsson/aroma.seq

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ROBUSTNESS: Add explicit 'stringsAsFactors' arguments [rbind]

#51 HenrikBengtsson opened 4 years ago
1
ROBUSTNESS: Add explicit 'stringsAsFactors' arguments [data.frame]

#52 HenrikBengtsson opened 4 years ago
0
ROBUSTNESS: Add explicit 'stringsAsFactors' arguments [read.table]

#50 HenrikBengtsson opened 4 years ago
0
pileup2seqz() requires sequenza (<= 2.1.2)

#48 HenrikBengtsson opened 4 years ago
0
TIPCC: sequenza 3.0.0 fails to install on TIPCC

#49 HenrikBengtsson opened 4 years ago
0
mpileup(): Assert that BAM files have been indexed

#47 HenrikBengtsson closed 5 years ago
0
ROBUSTNESS: Detect when a gzip'ed FASTA file is trying to be used with samtools

#46 HenrikBengtsson opened 7 years ago
0
OUTPUT NOISE: In interactive mode, output sessionDetails() as verbose message

#45 HenrikBengtsson closed 5 years ago
1
Analogue to *.gz files, add basic support for *.bgz files (bgzip)

#44 HenrikBengtsson opened 7 years ago
0
ROBUSTNESS: Protect against non-sense parsing of paths

#43 HenrikBengtsson opened 7 years ago
0
REPRODUCIBILITY: Report on versions for external tools used in verbose output

#42 HenrikBengtsson opened 7 years ago
2
getIndexFile() should check file time stamps too

#41 HenrikBengtsson closed 7 years ago
1
TESTS: Realign BAM files through BWA

#40 HenrikBengtsson opened 7 years ago
0
CLEANUP: Rename argument absolutePath -> absolute

#39 HenrikBengtsson closed 7 years ago
1
FASTA stats: Report on length and MD5 checksum per sequence

#38 HenrikBengtsson opened 8 years ago
1
Add clean=TRUE to getSeqLengths()

#37 HenrikBengtsson closed 7 years ago
0
SPEED: Store BAM index and flag stats on file

#36 HenrikBengtsson opened 8 years ago
0
GcBaseFile: Add getBinWidth() and report it with print()

#35 HenrikBengtsson opened 8 years ago
0
Add isCompatibleWith() for BamDataSet:s

#34 HenrikBengtsson closed 7 years ago
1
Assert that BwaIndexSet is compatible with FastaReferenceFile

#33 HenrikBengtsson closed 8 years ago
2
FUTURE: Use do.call(fcn, ...) - not do.call("fcn", ...)

#32 HenrikBengtsson closed 8 years ago
0
Add MPileupFile and MPileupFileSet

#31 HenrikBengtsson closed 7 years ago
1
Java 8: [Samtools-devel] HTSJDK Moving to Java 8

#30 HenrikBengtsson opened 8 years ago
0
tests/Bowtie2Alignment,SE.R: assertion error

#29 HenrikBengtsson closed 8 years ago
2
TopHat2 requires Python v 2.7.x - does not work with Python 3

#28 HenrikBengtsson opened 8 years ago
0
Call GATK with Java (<= 1.7.x)

#27 HenrikBengtsson opened 8 years ago
0
Replace all dsApply() with for loops with futures

#26 HenrikBengtsson closed 7 years ago
1
REPRODUCIBILITY: Call external tools with <md5 checksum>.<ext> to make file headers stable

#25 HenrikBengtsson opened 8 years ago
1
print() on a "missing" BamDataFile gives "Error in Rsamtools::BamFile(pathname, ..."

#24 HenrikBengtsson closed 8 years ago
1
Bug report: 4 arguments passed to .Internal(nchar)

#23 HenrikBengtsson closed 9 years ago
3
organism(): Genus species. With and without underscore

#22 HenrikBengtsson opened 9 years ago
0
Add findCNVkit()

#21 HenrikBengtsson closed 9 years ago
0
Is genome assembly important enough to become first class citizen?

#20 HenrikBengtsson opened 9 years ago
0
Add getDefaultOrganism(), getOrganism(), and setOrganism()

#19 HenrikBengtsson opened 9 years ago
0
Use Ensembl-flavored organism names, e.g. Homo_sapiens (instead of HomoSapiens)

#18 HenrikBengtsson closed 9 years ago
1
DESIGN: Add SequenceContigsInterface class

#17 HenrikBengtsson closed 9 years ago
1
BamDataFile should report on whether there are paired end reads or not

#16 HenrikBengtsson opened 9 years ago
1
Add TabixIndexFile class

#15 HenrikBengtsson opened 9 years ago
0
Support countNucleotides() for [m]pileup and VCF files too

#14 HenrikBengtsson opened 9 years ago
1
WISH: FastqDataFile and BamDataFile report on read lengths

#13 HenrikBengtsson opened 9 years ago
1
Deprecated function Biostrings::fasta.info() - use fasta.seqlengths() instead

#12 HenrikBengtsson closed 9 years ago
2
process() for TotalCnBinnedCounting uses a stray 'next' inside dsApply()

#11 HenrikBengtsson closed 9 years ago
0
findHTSeq() fails to identify version and gives a warning

#10 HenrikBengtsson closed 9 years ago
1
Make FastaReferenceFile, BamDataFile, ... more informative on sequences/targets

#9 HenrikBengtsson closed 9 years ago
3
BamDataFile reports Mb when it should be Gb

#8 HenrikBengtsson closed 9 years ago
0
BamDataFileSet should report on number of unique BAM header target lengths finger prints

#7 HenrikBengtsson closed 9 years ago
3
Add FastaReferenceIndexFile (*.fai)

#6 HenrikBengtsson closed 9 years ago
2
CNVkit: Add file classes for CNVkit file formats

#5 HenrikBengtsson opened 9 years ago
0
Add hasIndex() to FastaReferenceFile

#4 HenrikBengtsson closed 9 years ago
1
Harmonize getSeqNames(), getSequenceNames() and getTargetNames()

#3 HenrikBengtsson closed 9 years ago
2