New upstream version 2.1.3.1+dfsg

*.plist

tests/*log

snakemake/.snakemake/

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/

The MIT License (MIT)

Copyright (c) 2013,2014 Genome Institute of Singapore

Copyright (c) 2013-2017 Genome Institute of Singapore

Permission is hereby granted, free of charge, to any person obtaining a copy

of this software and associated documentation files (the "Software"), to deal

You will need:

- a C compiler (e.g. gcc or clang)

- a Python 2.7 interpreter

- a Python 2.7 or Python 3 interpreter

- zlib developer files

- a compiled version of [samtools (>=1.1)]((http://sourceforge.net/projects/samtools/files/samtools/1.1/samtools-1.1.tar.bz2/download))

- a compiled version of htslib (>= 1.1; use the one that comes bundled with samtools!)

- a compiled version of [samtools 1.1]((http://sourceforge.net/projects/samtools/files/samtools/1.1/samtools-1.1.tar.bz2/download))

- a compiled version of htslib 1.1; use the one that comes bundled with samtools!)

### Compilation

# 2.64 which allows to define a URL as well

# 2.68 seems to have updated ax_pthread

AC_INIT([LoFreq_Star], [2.1.2], [wilma@gis.a-star.edu.sg])

AC_INIT([LoFreq_Star], [2.1.3.1], [wilma@gis.a-star.edu.sg])

# The AC_INIT macro can take any source file as an argument. It just

# checks that the file is there, which should, in turn, mean that the