Changelog

2020-06-15      Changes in 2.1.5        Andreas Wilm <andreas.wilm@gmail.com>
    * Fixed a long-standing Heisenbug related to indel formatting (closes #89)

2020-01-04      Changes in 2.1.4        Andreas Wilm <andreas.wilm@gmail.com>
    * Now using htslib API thanks to John Marshall. Requires htslib >= 1.4. New configure flags
	replacing SAMTOOLS and HTSLIB: --with-htslib
	* Minor fixes in parallel caller closing #85
	* Fixed #58
	* Enhancements to lofreq2_add_fake_gt.py

2017-06-21	Changes in 2.1.3.1	Andreas Wilm <wilma@gis.a-star.edu.sg>
	* Fixed bug introduced last minute in 2.1.3 that creates segfault if call is used without -o

2017-06-21	Changes in 2.1.3	Andreas Wilm <wilma@gis.a-star.edu.sg>
	* Maintenance release before major rewrite
	* Added Python3 support
	* Added best practices snakemake workflow
	* Little easier on memory in high coverage situations
	* Added --force-overwrite option to 'call'

2015-05-19	Changes in 2.1.2	Andreas Wilm <wilma@gis.a-star.edu.sg>
	* 'indelqual' now allows to read bam from stdin
	* Fixed bug in 'call' which resulted in negative phred quality
 	filter, when pvalue alpha was above 1 and number of tests was low
	* 'indelqual' dindel now deletes BI/BD before inserting
	* remove unnecessary dependency on kaln.h (not present in samtools
	1.2)
	* 'uniq' now closing output vcf filehandle on error, thus always
	writing at least a header (reported by DNANexus)
	* Added HRUN info field to output vcf
	* Fixed calling of indel consvars
	* Removed options (and use of) cons-as-ref and skip-n. now reference
	is always used by default to call against and n's are always
	skipped. also means the consensus variants (CONSVAR) concept
	disappeared
	* Set DEFAULT_MIN_PLP_IDQ to zero
	* Caught yet another variant of the reference sequence name
	mismatch problem
	* 'viterbi': memory allocation now mainly dynamic.
	fixes observed segfault on pacbio reads (unclear why though)
	*  Low AF false positive multi-allelic 1bp indel adjacent to
	poly-AT now filtered by default.
	* 'indelqual': added support for adding uniform insertion and
	deletion qualities (instead of just indel qualities)
	* indel calling: fixed index violation while accessing pdi[u] in
	idaq happening while processing pacbio reads. added bound check as
	hack (idaq() mostly illumina specific anyway)
	* Removed MAX_READ_LEN globally
	* 'call': added special case for SB test: if ref is entirely missing
	and we have alts on only one strand fisher's exact test will
	return 0, which is most certainly not what we want. setting to
	INT_MAX instead
	* vcfset: only-[type] now correctly dealt with in vcf2 on top of vcf1.
	* vcfset: fixed bug which match vars even if they only overlapped
	partially (now also checking position instead of relying on
	tabix iterator)
	* Reference sequences now converted to uppercase after fetching to be safe.
	This also addresses the "AQ-bug" where low AQ values were reported
	because of a lower-case reference
	* 'pparallel': made bed reading function standard conform and more
	fault tolerant. e.g. now allowing browser and track lines
	* 'somatic': now also producing germline indels
	* 'somatic': min cov lowered to 7
	* 'somatic': normal stringent now has separate parameters, i.e. independent of
	tumor stringent (set to fdr 1%)
	* 'somatic': sq ignore normal now ignoring indels and snvs
	* 'somatic': Added support for multiple ignore vcf files
	* 'filter': corrected wrong info about default sb mtc method
	* Changed MQ0 prob to a generic 0.5
	* Fixed bug in fdr application in filter: previous versions
	called more tests significant than actually true. Fixed by setting
	all values to not significant right after calling fdr()
	* 'somatic': added --min-cov option

Changes in versions before 2.1.2: See http://csb5.github.io/lofreq/blog/