New upstream version 2.2+dfsg

Stacks 2.2 - Aug 22, 2018

--------------------------

    Feature: Added the --bestrad flag to process_radtags. When used it will look for reads that need transposed

             before they are processed.

    Feature: gstacks: New option --max-debrujin-reads to control the construction of the de Bruijn graph; replaces 

             --min-kmer-freq which is now deprecated

    Bugfix: Added run number to output FASTQ headers in process_radtags to make sure read IDs are always unique.

Stacks 2.1 - June 25, 2018

--------------------------

    Bugfix: Fixed a performance regression in sstacks. Recent changes in sstacks made it more likely to

            invoke the gapped algorithm to match to the catalog. In some cases, matches to the catalog

            would be marked as ambiguous alignments and dropped from the next stages of analysis due to 

            differences in CIGAR strings from the gapped alignment. 

    Feature: ustacks Changed --high_cov_thres default value from 2.0 to 3.0.

    Feature: gstacks: Changed --min-kmer-freq default value from 0.05 to 0.01.

    Feature: Added further checks on zlib calls.

Stacks 2.0 - Apr 23, 2018

-------------------------

    Feature: modified cstacks and ustacks gapped alignment algorithms to always align the two stacks/alleles

             with the most k-mers in common, removed the previous minimum k-mer limit.

    Feature: modified cstacks so that when a sample locus matches two or more catalog loci, those catalog

             loci are combined, or rolled-up, reducing undermerged loci that generate excess homozygote calls.

    Feature: modified tsv2bam so that when two loci from the same sample match the same catalog locus, those

             loci are combined.

    Bugfix: corrected BbvCI restriction enzyme to add the missing negative strand sequence.

    Bugfix: corrected the catalog writing routines for unzipped output files to include missing column.

    Bugfix: populations: Fixed the filtering of monomorphic loci.

    Bugfix: populations: Now preserving sample ordering in all outputs.

    Bugfix: Fixed ICPC compilation.

    2.0b - May 1, 2018

    Feature: gstacks: Removed the assertion that the first basepair of each locus should

             be part of a cutsite (now a warning).

    Feature: gstacks: The reported effective coverage is now a more realistic weighted mean.

    Bugfix: populations: Fixed STRUCTURE output being corrupted for some unordereds population maps.

Stacks 2.0 Beta 10 - Apr 10, 2018

---------------------------------

    Feature: Improved gapped alignment for secondary reads in ustacks.

    Feature: Improved populations performance.

    Feature: Added enzymes Cac8I, MslI.

    Feature: Made population maps more tolerant to spurious extra spaces and lines.

    Feature: populations: VCF output: changed the format of the catalog locus field and made the column 1-based.

    Feature: gstacks: increased haplotyping rates by adding a filtering of spurious SNPs step.

    Bugfix:  Fixed populations dramatric slow-down on datasets with more than several hundred samples.

    Bugfix:  Restored the NS/locus distribution in populations's distributions log.

    Bugfix:  Fixed the populations --radpainter export.

    Bugfix:  stacks-dist-extract: Fixed OSX compatibility.

    Bugfix:  Fixed breaking bug in populations --in-vcf mode filtering statistics.

Stacks 2.0 Beta 9 - Mar 12, 2018

--------------------------------

    Feature: Cleaned up tags/snps/alleles/matches files. We removed the batch ID from ustacks and cstacks

dist_bin_SCRIPTS = scripts/denovo_map.pl scripts/ref_map.pl \

	scripts/integrate_alignments.py scripts/count_fixed_catalog_snps.py \

	scripts/stacks-integrate-alignments scripts/stacks-dist-extract scripts/stacks-gdb

	scripts/stacks-integrate-alignments scripts/stacks-dist-extract scripts/stacks-gdb # scripts/denovo_map.py

dist_noinst_SCRIPTS = autogen.sh scripts/extract_interpop_chars.pl scripts/convert_stacks.pl

pkglocalstatedir = $(localstatedir)/$(PACKAGE)

debug:

	$(MAKE) all "CXXFLAGS=-g -Wall -DDEBUG -std=gnu++11"

	$(MAKE) all "CXXFLAGS=-g -Wall -DDEBUG -O0"

install-data-hook:

	sed -e 's,_VERSION_,$(VERSION),' -e 's,_BINDIR_,$(bindir)/,g' -e 's,_PKGDATADIR_,$(pkgdatadir)/,g' $(DESTDIR)$(bindir)/denovo_map.pl > $(DESTDIR)$(bindir)/denovo_map.pl.subst

	chmod +x $(DESTDIR)$(bindir)/stacks-integrate-alignments

	chmod +x $(DESTDIR)$(bindir)/stacks-dist-extract

	chmod +x $(DESTDIR)$(bindir)/stacks-gdb

	##sed -e 's,_VERSION_,$(VERSION),' -e 's,_BINDIR_,$(DESTDIR)$(bindir)/,g' -e 's,_PKGDATADIR_,$(pkgdatadir)/,g' $(DESTDIR)$(bindir)/denovo_map.py > $(DESTDIR)$(bindir)/denovo_map.py.subst

	##mv $(DESTDIR)$(bindir)/denovo_map.py.subst $(DESTDIR)$(bindir)/denovo_map.py

	##chmod +x $(DESTDIR)$(bindir)/denovo_map.py

uninstall-hook:

	rm -rf $(DESTDIR)$(pkglocalstatedir)

/* Define to 1 if the system has the type `_Bool'. */

#undef HAVE__BOOL

/* Define to 1 if your C compiler doesn't accept -c and -o together. */

#undef NO_MINUS_C_MINUS_O

/* Name of package */

#undef PACKAGE

/* Define to the one symbol short name of this package. */

#undef PACKAGE_TARNAME

/* Define to the home page for this package. */

#undef PACKAGE_URL

/* Define to the version of this package. */

#undef PACKAGE_VERSION