Commit 8c824c31 authored by Andreas Tille's avatar Andreas Tille
Browse files

New upstream version 2.0Beta8c+dfsg

parent 5eedfd97

ChangeLog

+117 −1
Original line number Diff line number Diff line 
Stacks 2.0 Beta 8 - Feb 03, 2018

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

    Feature: populations: Now calculated deviation from Hardy-Weinberg equilibrium at the SNP level

             (using an exact test), and at the haplotype level (using Guo+Thompson's MCMC algorithm).

    Feature: populations: Added an export type for FineRADStructure.

    Feature: populations: Added the GQ/GL fields in the VCF SNPs output.

    Feature: gstacks: Made the default behavior regarding paired-end reads more logical (in

             reference-based mode --paired has been replaced with --unpaired).

    Feature: gstacks: Added details about samples and coverages to the log outputs.

    Feautre: Added enzymes NspI, BbvCI, fixed BfuCI.

    Bugfix:  corrected a major performance bottleneck in populations when smoothing population statistics

             across the genome.

    Bugfix:  populations: The VCF output now preserves the input sample order.

    Bugfix:  gstacks: Fixed the handling of a rare special case in the PCR duplicates code.

    Bugfix:  gstacks: Fixed 100% being added to all per-thread timings.



Stacks 2.0 Beta 7 - Dec 29, 2017

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

    Feature: gstacks: Added an option to remove PCR duplicates based on insert

             size (--rm-pcr-duplicates, plus the related --rm-unpaired-reads).

    Feature: populations: Added a haplotype Genepop export.

    Feature: populations: improved the help; changed the output names for SNP

             files to 'populations.snps.EXT'; added option --no_hap_exports.

    Feature: gstacks and populations: Clarified the logs; moved distributions

             to a separate '.xlog' file and added script stacks-xlog-extract.

    Feature: gstacks: Tweaked the help/interface; especially, replaced --spacer

             with --suffix (for BAM directory input).

    Feature: Added enzymes BfuI and HinP1.

    Feature: Added option --inline_null to clone_filter.

    Bugfix: gstacks: Fixed a typo preventing the paired reads from being merged.

    Bugfix: populations: Fixed a segfault that occurred with some large datasets.

    Bugfix: Made VCF outputs more standard compliant.

    Bugfix: populations: Repaired --fasta_samples and --fasta_samples_raw.

    Bugfix: populations: Fixed population aborting at the end of the run

            when an export option was specified multiple times.

    Bugfix: gstacks: Adjusted progression report for catalog asymmetry.

    Bugfix: Fixed installation of stacks-integrate-alignments on MacOS.



Stacks 2.0 Beta 6 - Dec 02, 2017

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

    Feature: Implmented the VCF haplotypes output.

    Bugfix:  Corrected asset failure in populations when exporting data for genepop or structure output. 



Stacks 2.0 Beta 5 - Nov 27, 2017

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

    Feature: Reimplemented structure, phylip, and phylip_var exports.

    Bugfix: Tightened up the overlap algorithm to require 80% of overlapping sequence to be 

            aligned and of the aligned sequence, 80% must be identities.

    Bugfix: Fixed segfault in gstacks when compiled with CLANG on OS X.

    Bugfix: gstacks: Fixed how misphasings are reported.



Stacks 2.0 Beta 4 - Nov 07, 2017

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

    Bugfix: Continued improving overlap algorithm to join SE and PE contigs.

    Bugfix: Improved build system to handle new timing functions in gstacks.



Stacks 2.0 Beta 3 - Nov 01, 2017

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

    Feature: Added output to populations describing mean PE contig size and mean number of

             genotyped sites per locus, which reflects the current filtering paramters.

    Feature: Improved the output of gstacks and populations.

    Feature: Added script `stacks-integrate-alignments`.

    Bugfix: made further improvements to the single-end/paired-end locus overlapping algorithm.

    Bugfix: fixed all depths being null in populations' VCF output.

    Bugfix: Numerically tweaked the marukilow model to remove a limit case.



Stacks 2.0 Beta 2 - Oct 19, 2017

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

    Feature: gstacks: Made it possible to read from multiple BAM files at the same time; modified the

             interface accordingly.

    Feature: gstacks: Parallelized the reference-based mode.

    Feature: gstacks: Added various statistics & improvements to the log output.

    Feature: gstacks: Improved how the forward & paired-end reads are merged (in denovo mode; no more trimming).

    Feature: populations: Added code to calculate the overlap between RAD loci when a reference is available.

    Feature: populations: Added VCF ouput (--vcf).

    Feature: Updated the denovo_map.pl and ref_map.pl wrappers, samples must now be specified using --samples and --popmap.

    Bugfix: Fixed three memory leaks in populations; improved reference-aligned batch logic.

    Bugfix: Improved overlapping code in gstacks to merge more single and paired-end contigs together.

    Bugfix: Now compiles on Apple OS X.

    Bugfix: Fixed a bug that skewed the fixed-site (no-SNP) likelihood in the marukilow model.



Stacks 2.0 Beta 1 - Oct 09, 2017

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

    Feature: Paired-end sequencing data can be utilized fully. In particular, when the shearing-based

             protocol is used, the software will assemble a local contig from the paired reads across

             the population, possibly overlap it with the forward-reads region, then align all reads to the

             assembled contig. This new approach also fully supports double-digest protocols.

    Feature: Haplotype calling and diploidy-violation dectection now rely on a novel, more powerful algorithm.

    Feature: SNP and genotype-calling now uses the diploid models of Maruki and Lynch (2017).

    Feature: The rxstacks program has been replaced with the gstacks program, and there is no need to re-run

	     some of the earlier steps of the pipeline anymore.

    Feature: The memory footprint of the populations program has been considerably reduced and can be scaled

	     for any size data set.

    Feature: The reference-based pipeline has been simplified, and now only comprises two steps: gstacks and populations.

    Feature: Added --null_inline mode to clone_filter (and process_radtags) for previously unseen type

             of oligo combination.



Stacks 1.48 - Nov 20, 2017

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

    Feature: Added HinP1I restriction enzyme.

    Feature: Added --null_inline mode to clone_filter (and process_radtags) for previously unseen type 

             of oligo combination.



Stacks 1.47 - Sept 06, 2017

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

    Feature: Improved populations's fasta output options (especially,

             added a option to export locus consensus sequences).

    Feature: denovo_map.pl and red_map.pl now stop if a component

             of the pipeline fails.

    Feature: Improved the output of denovo_map.pl and ref_map.pl.

    Bugfix: Added a format check in Fasta/GzFasta to avoid a potential

            segfault when working on FastQ files.

    Bugfix: Fixed a bug in count_fixed_catalog_snps.py that could cause

            overwrites when working with uncompressed files.



Stacks 1.46 - Apr 17, 2017

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

    Feature: Added HaeIII enzyme.

    Bugfix: Corrected memory leaks in rxstacks.

    Bugfix: Corrected non-functioning --min_mapq parameter for pstacks.

    Bugfix: Corrected segfault when combining a VCF input file to populations, with genomic output and masking a restriction enzyme.

    Bugfix: Corrected segfault when combining a VCF input file to populations,

            with genomic output and masking a restriction enzyme.



Stacks 1.45 - Feb 24, 2017

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

Makefile.am

+113 −138
Original line number Diff line number Diff line 
bin_PROGRAMS = ustacks pstacks estacks cstacks sstacks rxstacks hstacks process_radtags process_shortreads \

	kmer_filter clone_filter genotypes populations phasedstacks



ustacks_SOURCES = src/ustacks.h src/ustacks.cc src/stacks.h src/stacks.cc src/constants.h src/constants.cc \

	src/mstack.h src/mstack.cc src/mst.h src/mst.cc src/cmb.h src/cmb.cc \

	src/DNASeq.h src/DNASeq.cc src/DNANSeq.h src/DNANSeq.cc \

	src/models.h src/models.cc src/utils.h src/utils.cc \

	src/kmers.h src/kmers.cc src/GappedAln.h src/aln_utils.h src/aln_utils.cc \

	src/input.h src/input.cc src/Tsv.h src/BowtieI.h src/FastaI.h src/FastqI.h src/SamI.h \

	src/gzFasta.h src/gzFastq.h



pstacks_SOURCES = src/pstacks.h src/pstacks.cc src/stacks.h src/stacks.cc src/constants.h src/constants.cc \

	src/mstack.h src/mstack.cc src/log_utils.h src/log_utils.cc \

	src/DNANSeq.h src/DNANSeq.cc src/DNASeq.h src/DNASeq.cc \

	src/models.h src/models.cc src/utils.h src/utils.cc src/aln_utils.h src/aln_utils.cc \

	src/input.h src/input.cc src/Tsv.h src/BowtieI.h src/FastaI.h src/FastqI.h src/SamI.h \

	src/BamI.h



estacks_SOURCES = src/estacks.h src/estacks.cc src/stacks.h src/stacks.cc src/constants.h src/constants.cc \

	src/mstack.h src/mstack.cc \

        src/models.h src/models.cc src/utils.h src/utils.cc src/aln_utils.h src/aln_utils.cc \

	src/DNASeq.h src/DNASeq.cc src/DNANSeq.h src/DNANSeq.cc \

        src/input.h src/input.cc src/Tsv.h src/BowtieI.h src/FastaI.h src/FastqI.h src/SamI.h



cstacks_SOURCES = src/cstacks.h src/cstacks.cc src/constants.h src/constants.cc \

	src/stacks.h src/stacks.cc src/locus.h src/locus.cc \

	src/kmers.h src/kmers.cc src/utils.h src/utils.cc \

	src/GappedAln.h src/aln_utils.h src/aln_utils.cc \

	src/DNASeq.h src/DNASeq.cc src/DNANSeq.h src/DNANSeq.cc \

	src/input.h src/input.cc src/sql_utilities.h src/sql_utilities.cc \

	src/MetaPopInfo.h src/MetaPopInfo.cc



hstacks_SOURCES = src/hstacks.h src/hstacks.cc src/constants.h src/constants.cc \

	src/stacks.h src/stacks.cc src/locus.h src/locus.cc \

	src/kmers.h src/kmers.cc \

	src/DNASeq.h src/DNASeq.cc src/DNANSeq.h src/DNANSeq.cc \

	src/utils.h src/utils.cc \

	src/input.h src/input.cc src/sql_utilities.h src/sql_utilities.cc

bin_PROGRAMS = ustacks cstacks sstacks process_radtags process_shortreads \

	kmer_filter clone_filter populations phasedstacks \

	tsv2bam gstacks



sstacks_SOURCES = src/sstacks.h src/sstacks.cc src/constants.h src/constants.cc \

	src/stacks.h src/stacks.cc src/locus.h src/locus.cc \

noinst_LIBRARIES = libcore.a libclean.a libpop.a



libcore_a_SOURCES = \

	src/aln_utils.h src/aln_utils.cc \

	src/BamI.h src/BamI.cc \

	src/BamUnalignedI.h \

	src/BowtieI.h \

	src/BustardI.h \

	src/catalog_utils.h src/catalog_utils.cc \

	src/cmb.h src/cmb.cc \

	src/constants.h src/constants.cc \

	src/DNANSeq.h src/DNANSeq.cc \

	src/DNASeq4.h src/DNASeq4.cc \

	src/DNASeq.h src/DNASeq.cc \

	src/FastaI.h \

	src/FastqI.h \

	src/GappedAln.h \

	src/gzFasta.h src/gzFasta.cc \

	src/gzFastq.h \

	src/input.h src/input.cc \

	src/kmers.h src/kmers.cc \

	src/GappedAln.h src/aln_utils.h src/aln_utils.cc \

	src/DNASeq.h src/DNASeq.cc src/DNANSeq.h src/DNANSeq.cc src/utils.h src/utils.cc \

	src/input.h src/input.cc src/sql_utilities.h src/sql_utilities.cc src/catalog_utils.cc \

	src/MetaPopInfo.h src/MetaPopInfo.cc



rxstacks_SOURCES = src/rxstacks.h src/rxstacks.cc src/constants.h src/constants.cc \

	src/stacks.h src/stacks.cc src/locus.h src/locus.cc \

	src/DNANSeq.h src/DNANSeq.cc src/DNASeq.h src/DNASeq.cc \

	src/mst.h src/mst.cc \

	src/locus.h src/locus.cc \

	src/locus_readers.h \

	src/log_utils.h src/log_utils.cc \

	src/MetaPopInfo.h src/MetaPopInfo.cc \

	src/models.h src/models.cc \

	src/aln_utils.h src/aln_utils.cc src/utils.h src/utils.cc \

	src/input.h src/input.cc src/sql_utilities.h src/sql_utilities.cc src/catalog_utils.cc \

	src/MetaPopInfo.h src/MetaPopInfo.cc

	src/mstack.h src/mstack.cc \

	src/mst.h src/mst.cc \

	src/nucleotides.h src/nucleotides.cc \

	src/renz.h src/renz.cc \

	src/SamI.h \

	src/Seq.h src/Seq.cc \

	src/sql_utilities.h src/sql_utilities.cc \

	src/stacks.h src/stacks.cc \

	src/Tsv.h \

	src/utils.h src/utils.cc \

	src/Vcf.h src/Vcf.cc



process_radtags_SOURCES = src/process_radtags.h src/process_radtags.cc src/constants.h src/constants.cc \

	src/utils.h src/utils.cc src/log_utils.h src/log_utils.cc \

	src/write.h src/write.cc \

libclean_a_SOURCES = \

	src/clean.h src/clean.cc \

	src/file_io.h src/file_io.cc \

	src/input.h src/input.cc src/BustardI.h src/BamUnalignedI.h src/FastqI.h src/gzFastq.h \

	src/renz.h src/renz.cc

	src/write.h src/write.cc



process_shortreads_SOURCES = src/process_shortreads.h src/process_shortreads.cc src/constants.h src/constants.cc \

	src/clean.h src/clean.cc \

	src/file_io.h src/file_io.cc \

	src/utils.h src/utils.cc src/log_utils.h src/log_utils.cc \

	src/write.h src/write.cc \

	src/kmers.h src/kmers.cc \

	src/input.h src/input.cc src/BustardI.h src/BamUnalignedI.h src/FastqI.h src/gzFastq.h 

libpop_a_SOURCES = \

	src/bootstrap.h \

	src/export_formats.h src/export_formats.cc \

	src/genotype_dictionaries.h src/genotype_dictionaries.cc \

	src/ordered.h \

	src/PopMap.h \

	src/PopSum.h src/PopSum.cc \

	src/smoothing.h \

	src/smoothing_utils.h \

	src/Hwp.h src/Hwp.cc



kmer_filter_SOURCES = src/kmer_filter.h src/kmer_filter.cc src/constants.h src/constants.cc \

	src/utils.h src/utils.cc \

	src/write.h src/write.cc \

	src/kmers.h src/kmers.cc \

	src/input.h src/input.cc src/BustardI.h src/FastqI.h src/FastaI.h \

	src/gzFastq.h src/gzFasta.h

libcore_a_CXXFLAGS = $(OPENMP_CFLAGS) $(BAM_CFLAGS)

libpop_a_CXXFLAGS  = $(OPENMP_CFLAGS) $(BAM_CFLAGS)



clone_filter_SOURCES = src/clone_filter.h src/clone_filter.cc src/constants.h src/constants.cc \

	src/kmers.h src/kmers.cc \

	src/utils.h src/utils.cc \

	src/write.h src/write.cc \

	src/clean.h src/clean.cc src/file_io.h src/file_io.cc \

	src/input.h src/input.cc src/BustardI.h src/FastqI.h src/FastaI.h \

	src/gzFastq.h src/gzFasta.h

phasedstacks_SOURCES = libcore.a src/phasedstacks.h src/phasedstacks.cc



genotypes_SOURCES = src/genotypes.h src/genotypes.cc src/constants.h src/constants.cc \

	src/utils.h src/utils.cc src/catalog_utils.h src/catalog_utils.cc \

	src/log_utils.h src/log_utils.cc \

	src/stacks.h src/stacks.cc src/locus.h src/locus.cc \

	src/DNASeq.h src/DNASeq.cc src/DNANSeq.h src/DNANSeq.cc \

	src/aln_utils.h src/aln_utils.cc \

	src/PopMap.h src/genotype_dictionaries.h src/genotype_dictionaries.cc\

	src/input.h src/input.cc src/sql_utilities.h src/sql_utilities.cc src/renz.h src/renz.cc \

	src/MetaPopInfo.h src/MetaPopInfo.cc

process_radtags_SOURCES    = libcore.a libclean.a src/process_radtags.h src/process_radtags.cc

process_shortreads_SOURCES = libcore.a libclean.a src/process_shortreads.h src/process_shortreads.cc

kmer_filter_SOURCES        = libcore.a libclean.a src/kmer_filter.h src/kmer_filter.cc

clone_filter_SOURCES       = libcore.a libclean.a src/clone_filter.h src/clone_filter.cc



populations_SOURCES = src/populations.h src/populations.cc src/constants.h src/constants.cc \

	src/utils.h src/utils.cc src/catalog_utils.h src/catalog_utils.cc \

	src/log_utils.h src/log_utils.cc \

	src/stacks.h src/stacks.cc src/locus.h src/locus.cc \

	src/DNASeq.h src/DNASeq.cc src/DNANSeq.h src/DNANSeq.cc \

	src/PopMap.h src/PopSum.h src/aln_utils.h src/aln_utils.cc src/genotype_dictionaries.h src/genotype_dictionaries.cc \

	src/input.h src/input.cc src/sql_utilities.h src/sql_utilities.cc src/renz.h src/renz.cc \

	src/bootstrap.h src/ordered.h src/smoothing.h src/smoothing_utils.h \

	src/export_formats.h src/export_formats.cc \

	src/MetaPopInfo.h src/MetaPopInfo.cc src/Vcf.h src/Vcf.cc

ustacks_SOURCES = libcore.a src/ustacks.h src/ustacks.cc

cstacks_SOURCES = libcore.a src/cstacks.h src/cstacks.cc

sstacks_SOURCES = libcore.a src/sstacks.h src/sstacks.cc



phasedstacks_SOURCES = src/phasedstacks.h src/phasedstacks.cc src/constants.h src/constants.cc \

	src/locus.h src/locus.cc \

	src/input.h src/input.cc src/sql_utilities.h src/sql_utilities.cc \

	src/log_utils.h src/log_utils.cc \

	src/utils.h src/utils.cc src/catalog_utils.h src/catalog_utils.cc 

populations_SOURCES = libcore.a libpop.a src/populations.h src/populations.cc



# tsv2bam & gstacks

tsv2bam_SOURCES = libcore.a src/tsv2bam.cc

gstacks_SOURCES = libcore.a src/gstacks.h src/gstacks.cc src/debruijn.h src/debruijn.cc src/Alignment.h src/SuffixTree.h src/SuffixTree.cc



ustacks_CXXFLAGS  = $(OPENMP_CFLAGS) $(SPARSEHASH_CFLAGS)

phasedstacks_CXXFLAGS = $(OPENMP_CFLAGS)

phasedstacks_LDFLAGS  = $(OPENMP_CFLAGS)

phasedstacks_LDADD    = libcore.a $(BAM_LIBS)



ustacks_CXXFLAGS = $(OPENMP_CFLAGS)

ustacks_LDFLAGS  = $(OPENMP_CFLAGS)

pstacks_CXXFLAGS = $(OPENMP_CFLAGS) $(BAM_CFLAGS) $(SPARSEHASH_CFLAGS)

pstacks_LDFLAGS   = $(OPENMP_CFLAGS)

pstacks_LDADD     = $(BAM_LIBS)

estacks_CXXFLAGS = $(OPENMP_CFLAGS) $(SPARSEHASH_CFLAGS) $(BAM_CFLAGS)

estacks_LDFLAGS   = $(OPENMP_CFLAGS)

estacks_LDADD = $(BAM_LIBS)

cstacks_CXXFLAGS  = $(OPENMP_CFLAGS) $(SPARSEHASH_CFLAGS)

ustacks_LDADD    = libcore.a $(BAM_LIBS)

cstacks_CXXFLAGS = $(OPENMP_CFLAGS)

cstacks_LDFLAGS  = $(OPENMP_CFLAGS)

hstacks_CXXFLAGS = $(OPENMP_CFLAGS) $(SPARSEHASH_CFLAGS)

hstacks_LDFLAGS   = $(OPENMP_CFLAGS)

sstacks_CXXFLAGS = $(OPENMP_CFLAGS) $(SPARSEHASH_CFLAGS)

cstacks_LDADD    = libcore.a $(BAM_LIBS)

sstacks_CXXFLAGS = $(OPENMP_CFLAGS) $(BAM_CFLAGS)

sstacks_LDFLAGS  = $(OPENMP_CFLAGS)

rxstacks_CXXFLAGS = $(OPENMP_CFLAGS) $(SPARSEHASH_CFLAGS)

rxstacks_LDFLAGS  = $(OPENMP_CFLAGS)

process_radtags_CXXFLAGS = $(OPENMP_CFLAGS) $(SPARSEHASH_CFLAGS) $(BAM_CFLAGS) 

sstacks_LDADD    = libcore.a $(BAM_LIBS)



process_radtags_CXXFLAGS = $(OPENMP_CFLAGS) $(BAM_CFLAGS)

process_radtags_LDFLAGS  = $(OPENMP_CFLAGS)

process_radtags_LDADD    = $(BAM_LIBS)

process_shortreads_CXXFLAGS = $(OPENMP_CFLAGS) $(SPARSEHASH_CFLAGS) $(BAM_CFLAGS) 

process_radtags_LDADD    =  libcore.a libclean.a $(BAM_LIBS)

process_shortreads_CXXFLAGS = $(OPENMP_CFLAGS) $(BAM_CFLAGS)

process_shortreads_LDFLAGS  = $(OPENMP_CFLAGS)

process_shortreads_LDADD    = $(BAM_LIBS)

kmer_filter_CXXFLAGS  = $(OPENMP_CFLAGS) $(SPARSEHASH_CFLAGS)

process_shortreads_LDADD    =  libcore.a libclean.a $(BAM_LIBS)

clone_filter_CXXFLAGS = $(OPENMP_CFLAGS) $(BAM_CFLAGS)

clone_filter_LDFLAGS  = $(OPENMP_CFLAGS)

clone_filter_LDADD    = libcore.a libclean.a $(BAM_LIBS)

kmer_filter_CXXFLAGS = $(OPENMP_CFLAGS)

kmer_filter_LDFLAGS  = $(OPENMP_CFLAGS)

genotypes_CXXFLAGS    = $(OPENMP_CFLAGS) $(SPARSEHASH_CFLAGS)

genotypes_LDFLAGS     = $(OPENMP_CFLAGS)

populations_CXXFLAGS  = $(OPENMP_CFLAGS) $(SPARSEHASH_CFLAGS)

kmer_filter_LDADD    = libcore.a libclean.a $(BAM_LIBS)



populations_CXXFLAGS = $(OPENMP_CFLAGS) $(BAM_CFLAGS)

populations_LDFLAGS  = $(OPENMP_CFLAGS)

phasedstacks_CXXFLAGS = $(OPENMP_CFLAGS) $(SPARSEHASH_CFLAGS)

phasedstacks_LDFLAGS  = $(OPENMP_CFLAGS)

clone_filter_CXXFLAGS = $(OPENMP_CFLAGS) $(SPARSEHASH_CFLAGS) $(BAM_CFLAGS)

clone_filter_LDFLAGS  = $(OPENMP_CFLAGS)

clone_filter_LDADD    = $(BAM_LIBS)

populations_LDADD    = libcore.a libpop.a $(BAM_LIBS)



# tsv2bam & gstacks

tsv2bam_CXXFLAGS = $(OPENMP_CFLAGS) $(BAM_CFLAGS)

tsv2bam_LDFLAGS  = $(OPENMP_CFLAGS)

tsv2bam_LDADD    = libcore.a $(BAM_LIBS)

gstacks_CXXFLAGS = $(OPENMP_CFLAGS) $(BAM_CFLAGS)

gstacks_LDFLAGS  = $(OPENMP_CFLAGS)

gstacks_LDADD    = libcore.a $(BAM_LIBS)



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

	scripts/sort_read_pairs.pl scripts/exec_velvet.pl scripts/load_sequences.pl \

	scripts/index_radtags.pl scripts/load_radtags.pl scripts/stacks_export_notify.pl \

	scripts/integrate_alignments.py scripts/count_fixed_catalog_snps.py

	scripts/integrate_alignments.py scripts/count_fixed_catalog_snps.py \

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



dist_noinst_SCRIPTS = autogen.sh scripts/extract_interpop_chars.pl scripts/convert_stacks.pl
@@ -170,12 +140,12 @@ TESTS = tests/process_radtags.t tests/kmer_filter.t tests/ustacks.t tests/pstack 


EXTRA_DIST = $(nobase_pkgdata_DATA) LICENSE INSTALL README ChangeLog $(TESTS)



SUBDIRS = htslib .



pkglocalstatedir = $(localstatedir)/$(PACKAGE)



SUBDIRS = htslib .



debug:

	$(MAKE) all "CXXFLAGS=-g -Wall -DDEBUG -std=gnu++0x"

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



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
@@ -211,6 +181,11 @@ install-data-hook: 
	mv $(DESTDIR)$(pkgdatadir)/php/constants.php.dist.subst $(DESTDIR)$(pkgdatadir)/php/constants.php.dist

	echo $(VERSION) > $(DESTDIR)$(pkgdatadir)/php/version.php

	$(install_sh) -d -m 755 $(DESTDIR)$(pkgdatadir)/php/export

	sed -i.bkp -e 's,_VERSION_,$(VERSION),' $(DESTDIR)$(bindir)/stacks-integrate-alignments

	rm -f $(DESTDIR)$(bindir)/stacks-integrate-alignments.bkp

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

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

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



uninstall-hook:

	rm -rf $(DESTDIR)$(pkglocalstatedir)

Makefile.in

+694 −2848

File changed.

Preview size limit exceeded, changes collapsed.

README

+2 −10
Original line number Diff line number Diff line
@@ -17,23 +17,15 @@ external software. 
     Stacks, you can install GCC by hand, or using a package system such as 

     Homebrew (http://brew.sh/) or MacPorts (http://www.macports.org/).



1. Install optional components for wrapper programs:



Several Perl scripts are distributed with Stacks to run the pipeline components and

upload pipeline output to the MySQL database serer. For these to work, you must have

the Perl DBI module installed with the MySQL driver. Most Linux distributions will

include the Perl DBI module, but if not Perl modules are easily installed with the

cpan tool.



1. Install optional components:



If you would like to lower memory usage install Google's SparseHash class.



    http://code.google.com/p/sparsehash/



If you are running a version of Linux, the above software can be installed via the 

package manager. If you are using Ubuntu, you can install the following packages:



% sudo apt-get install libdbd-mysql-perl

% sudo apt-get install libsparsehash-dev



A similar set of commands can be executed on Debian using apt-get, or on a RedHat derived Linux

system using yum, or another package manager on other Linux distributions.

config.h.in

+3 −3
Original line number Diff line number Diff line
@@ -6,6 +6,9 @@ 
/* Enable compilation with Samtools BAM library */

#undef HAVE_BAM



/* Define to 1 if you have the `clock_gettime' function. */

#undef HAVE_CLOCK_GETTIME



/* define if the compiler supports basic C++11 syntax */

#undef HAVE_CXX11
@@ -51,9 +54,6 @@ 
   and to 0 otherwise. */

#undef HAVE_REALLOC



/* Enable compilation with Google Sparsehash */

#undef HAVE_SPARSEHASH



/* Define to 1 if you have the `sqrt' function. */

#undef HAVE_SQRT