ngslib/RELEASE at master · tsznxx/ngslib · GitHub

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ngslib 1.1.19 update:
	Utils:
		add naturalkeys to sort strings with numbers. For chroms: sort to "chr1 chr2 ... chr10 chr11 ..." instead of "chr1 chr10 chr11 ... chr19 chr2 chr20"
		modify touchtime function by adding the default output stream to "sys.stderr", and touchtime function will print it, instead of returning the string.
	GeneBed:
		toBed12 add txstart and txstop columns
	misc.py:
		ExcelWriter to return a writer object for pandas to write in. Append is enabled.
	setup.py:
		check os.system('make') return code. Stop installation if it is not 0.
	wGetTSS.py:
		set ftype to 'guess'
	wplot.py:
		Add Algorithms class. Add getCTable to Algorithms class.
	wplot.py:
		Add fourWayVenn plot class to generate 4 way Venn diagram.
	genome:
		Add hg38 chrom sizes
	Bed3:
		add __or__, __and__ function for operators | and &.
		update __sub__ function to return left and right parts after substraction.

ngslib 1.1.18 update:
	GeneBed:
		getUTR5/3 bug fix.
	wXLS2TXT.py:
		basename bug fix.
	mFile:
		add flush() function

ngslib 1.1.17 update:
	ngslib 1.1.15 and 1.1.16 are deleted for submission bugs.

ngslib 1.1.16 update:(deleted)
	Wrong submission.

ngslib 1.1.15 update:(deleted)
    Add __eq__ function to Bed3 class. Note __eq__ only checks the chrom, start and stop.
	Set default converter as IO.converters[self.ftype] in TabixFile.
	GeneBed:
		Add functions: genomic_position(pos) and transcript_position(pos) to convert genomic position from/to transcriptomic position.
	GeneBed:
		Add function: toBed12(self)
	Utils:
		Add non-canonical TIS table in transTables.

ngslib 1.1.14 update:
	wBedToFasta.py:
		when 'stdin' is used, input file format should be specified.
	IO.guess:
		raise error when stdin is used and file type is not specified, or input file has no extension.
	BedList.merge:
		fix bugs. Allow merge for adjacent beds.
	GeneBed.truncate:
		Allow gene trucation to fit a genomic region.

ngslib 1.1.13 update:
	wBedToFasta.py:
		By default, the program will guess the file format instead of using 'bed' as default.
	wSamToWig.py:
		Allow SAM/BAM format input. Sorting is not necessary.
	wBamToWig.py:
		Replaced by wSamToWig.py

ngslib 1.1.12 update:
	BigWigFile can fetch items using generator. This avoids huge memory consumption when fetching the whole chromosome.

ngslib 1.1.11 update:
	GeneBed.fetchDB() returns a DNA instead of string object if fetch from Fasta file. To be consisitent with Bed.fetchDB()
	Fix bugs in Pipeline.ChIP_Project.

ngslib 1.1.10 update:
	test if issubclass before adding objects with Bed3 or its derived classes.