ChangeLog

+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

-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)

README

@@ -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

@@ -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
 

configure

 #! /bin/sh
 # Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.63 for Stacks 1.46.
+# Generated by GNU Autoconf 2.63 for Stacks 2.0Beta8c.
 #
 # Copyright (C) 1992, 1993, 1994, 1995, 1996, 1998, 1999, 2000, 2001,
 # 2002, 2003, 2004, 2005, 2006, 2007, 2008 Free Software Foundation, Inc.
@@ -594,8 +594,8 @@ SHELL=${CONFIG_SHELL-/bin/sh}
 # Identity of this package.
 PACKAGE_NAME='Stacks'
 PACKAGE_TARNAME='stacks'
-PACKAGE_VERSION='1.46'
-PACKAGE_STRING='Stacks 1.46'
+PACKAGE_VERSION='2.0Beta8c'
+PACKAGE_STRING='Stacks 2.0Beta8c'
 PACKAGE_BUGREPORT=''
 
 ac_unique_file="src/ustacks.cc"
@@ -643,6 +643,7 @@ OPENMP_CFLAGS
 EGREP
 GREP
 CPP
+RANLIB
 HAVE_CXX11
 am__fastdepCC_FALSE
 am__fastdepCC_TRUE
@@ -666,7 +667,6 @@ CPPFLAGS
 LDFLAGS
 CXXFLAGS
 CXX
-SPARSEHASH_CFLAGS
 BAM_LIBS
 BAM_CFLAGS
 am__untar
@@ -733,8 +733,6 @@ ac_subst_files=''
 ac_user_opts='
 enable_option_checking
 enable_bam
-enable_sparsehash
-with_sparsehash_include_path
 enable_dependency_tracking
 enable_openmp
 '
@@ -1302,7 +1300,7 @@ if test "$ac_init_help" = "long"; then
   # Omit some internal or obsolete options to make the list less imposing.
   # This message is too long to be a string in the A/UX 3.1 sh.
   cat <<_ACEOF
-\`configure' configures Stacks 1.46 to adapt to many kinds of systems.
+\`configure' configures Stacks 2.0Beta8c to adapt to many kinds of systems.
 
 Usage: $0 [OPTION]... [VAR=VALUE]...
 
@@ -1368,7 +1366,7 @@ fi
 
 if test -n "$ac_init_help"; then
   case $ac_init_help in
-     short | recursive ) echo "Configuration of Stacks 1.46:";;
+     short | recursive ) echo "Configuration of Stacks 2.0Beta8c:";;
    esac
   cat <<\_ACEOF
 
@@ -1377,18 +1375,10 @@ Optional Features:
   --disable-FEATURE       do not include FEATURE (same as --enable-FEATURE=no)
   --enable-FEATURE[=ARG]  include FEATURE [ARG=yes]
   --disable-bam           Disable use of BAM files through HTSLib.
-  --enable-sparsehash     Enable the use of Google Sparsehash (must be
-                          installed).
   --disable-dependency-tracking  speeds up one-time build
   --enable-dependency-tracking   do not reject slow dependency extractors
   --disable-openmp        do not use OpenMP
 
-Optional Packages:
-  --with-PACKAGE[=ARG]    use PACKAGE [ARG=yes]
-  --without-PACKAGE       do not use PACKAGE (same as --with-PACKAGE=no)
-  --with-sparsehash-include-path
-                          location of Google Sparsehash headers
-
 Some influential environment variables:
   CXX         C++ compiler command
   CXXFLAGS    C++ compiler flags
@@ -1466,7 +1456,7 @@ fi
 test -n "$ac_init_help" && exit $ac_status
 if $ac_init_version; then
   cat <<\_ACEOF
-Stacks configure 1.46
+Stacks configure 2.0Beta8c
 generated by GNU Autoconf 2.63
 
 Copyright (C) 1992, 1993, 1994, 1995, 1996, 1998, 1999, 2000, 2001,
@@ -1480,7 +1470,7 @@ cat >config.log <<_ACEOF
 This file contains any messages produced by compilers while
 running configure, to aid debugging if configure makes a mistake.
 
-It was created by Stacks $as_me 1.46, which was
+It was created by Stacks $as_me 2.0Beta8c, which was
 generated by GNU Autoconf 2.63.  Invocation command line was
 
   $ $0 $@
@@ -2329,7 +2319,7 @@ fi
 
 # Define the identity of the package.
  PACKAGE='stacks'
- VERSION='1.46'
+ VERSION='2.0Beta8c'
 
 
 cat >>confdefs.h <<_ACEOF
@@ -2397,36 +2387,6 @@ BAM_LIBS='./htslib/libhts.a'
 
 
 
-fi
-
-
-#
-# Enable use of Google Sparsehash and get include location if requested.
-#
-# Check whether --enable-sparsehash was given.
-if test "${enable_sparsehash+set}" = set; then
-  enableval=$enable_sparsehash;
-fi
-
-
-if test "x$enable_sparsehash" = "xyes"; then
-
-
-cat >>confdefs.h <<\_ACEOF
-#define HAVE_SPARSEHASH 1
-_ACEOF
-
-
-# Check whether --with-sparsehash-include-path was given.
-if test "${with_sparsehash_include_path+set}" = set; then
-  withval=$with_sparsehash_include_path; SPARSEHASH_CFLAGS="-I$withval"
-else
-  SPARSEHASH_CFLAGS=""
-fi
-
-
-
-
 fi
 
 
@@ -5245,6 +5205,101 @@ _ACEOF
 
 
 
+# Checks for ar-based static libs.
+if test -n "$ac_tool_prefix"; then
+  # Extract the first word of "${ac_tool_prefix}ranlib", so it can be a program name with args.
+set dummy ${ac_tool_prefix}ranlib; ac_word=$2
+{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_RANLIB+set}" = set; then
+  $as_echo_n "(cached) " >&6
+else
+  if test -n "$RANLIB"; then
+  ac_cv_prog_RANLIB="$RANLIB" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+  IFS=$as_save_IFS
+  test -z "$as_dir" && as_dir=.
+  for ac_exec_ext in '' $ac_executable_extensions; do
+  if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+    ac_cv_prog_RANLIB="${ac_tool_prefix}ranlib"
+    $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
+    break 2
+  fi
+done
+done
+IFS=$as_save_IFS
+
+fi
+fi
+RANLIB=$ac_cv_prog_RANLIB
+if test -n "$RANLIB"; then
+  { $as_echo "$as_me:$LINENO: result: $RANLIB" >&5
+$as_echo "$RANLIB" >&6; }
+else
+  { $as_echo "$as_me:$LINENO: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+fi
+if test -z "$ac_cv_prog_RANLIB"; then
+  ac_ct_RANLIB=$RANLIB
+  # Extract the first word of "ranlib", so it can be a program name with args.
+set dummy ranlib; ac_word=$2
+{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_ac_ct_RANLIB+set}" = set; then
+  $as_echo_n "(cached) " >&6
+else
+  if test -n "$ac_ct_RANLIB"; then
+  ac_cv_prog_ac_ct_RANLIB="$ac_ct_RANLIB" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+  IFS=$as_save_IFS
+  test -z "$as_dir" && as_dir=.
+  for ac_exec_ext in '' $ac_executable_extensions; do
+  if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+    ac_cv_prog_ac_ct_RANLIB="ranlib"
+    $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
+    break 2
+  fi
+done
+done
+IFS=$as_save_IFS
+
+fi
+fi
+ac_ct_RANLIB=$ac_cv_prog_ac_ct_RANLIB
+if test -n "$ac_ct_RANLIB"; then
+  { $as_echo "$as_me:$LINENO: result: $ac_ct_RANLIB" >&5
+$as_echo "$ac_ct_RANLIB" >&6; }
+else
+  { $as_echo "$as_me:$LINENO: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+  if test "x$ac_ct_RANLIB" = x; then
+    RANLIB=":"
+  else
+    case $cross_compiling:$ac_tool_warned in
+yes:)
+{ $as_echo "$as_me:$LINENO: WARNING: using cross tools not prefixed with host triplet" >&5
+$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
+ac_tool_warned=yes ;;
+esac
+    RANLIB=$ac_ct_RANLIB
+  fi
+else
+  RANLIB="$ac_cv_prog_RANLIB"
+fi
+
+
+
 # Checks for libraries.
 
 
@@ -6431,6 +6486,152 @@ fi
 done
 
 
+for ac_header in unistd.h
+do
+as_ac_Header=`$as_echo "ac_cv_header_$ac_header" | $as_tr_sh`
+if { as_var=$as_ac_Header; eval "test \"\${$as_var+set}\" = set"; }; then
+  { $as_echo "$as_me:$LINENO: checking for $ac_header" >&5
+$as_echo_n "checking for $ac_header... " >&6; }
+if { as_var=$as_ac_Header; eval "test \"\${$as_var+set}\" = set"; }; then
+  $as_echo_n "(cached) " >&6
+fi
+ac_res=`eval 'as_val=${'$as_ac_Header'}
+		 $as_echo "$as_val"'`
+	       { $as_echo "$as_me:$LINENO: result: $ac_res" >&5
+$as_echo "$ac_res" >&6; }
+else
+  # Is the header compilable?
+{ $as_echo "$as_me:$LINENO: checking $ac_header usability" >&5
+$as_echo_n "checking $ac_header usability... " >&6; }
+cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+$ac_includes_default
+#include <$ac_header>
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+  (eval "$ac_compile") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest.$ac_objext; then
+  ac_header_compiler=yes
+else
+  $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+	ac_header_compiler=no
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+{ $as_echo "$as_me:$LINENO: result: $ac_header_compiler" >&5
+$as_echo "$ac_header_compiler" >&6; }
+
+# Is the header present?
+{ $as_echo "$as_me:$LINENO: checking $ac_header presence" >&5
+$as_echo_n "checking $ac_header presence... " >&6; }
+cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+#include <$ac_header>
+_ACEOF
+if { (ac_try="$ac_cpp conftest.$ac_ext"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+  (eval "$ac_cpp conftest.$ac_ext") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } >/dev/null && {
+	 test -z "$ac_c_preproc_warn_flag$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       }; then
+  ac_header_preproc=yes
+else
+  $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+  ac_header_preproc=no
+fi
+
+rm -f conftest.err conftest.$ac_ext
+{ $as_echo "$as_me:$LINENO: result: $ac_header_preproc" >&5
+$as_echo "$ac_header_preproc" >&6; }
+
+# So?  What about this header?
+case $ac_header_compiler:$ac_header_preproc:$ac_c_preproc_warn_flag in
+  yes:no: )
+    { $as_echo "$as_me:$LINENO: WARNING: $ac_header: accepted by the compiler, rejected by the preprocessor!" >&5
+$as_echo "$as_me: WARNING: $ac_header: accepted by the compiler, rejected by the preprocessor!" >&2;}
+    { $as_echo "$as_me:$LINENO: WARNING: $ac_header: proceeding with the compiler's result" >&5
+$as_echo "$as_me: WARNING: $ac_header: proceeding with the compiler's result" >&2;}
+    ac_header_preproc=yes
+    ;;
+  no:yes:* )
+    { $as_echo "$as_me:$LINENO: WARNING: $ac_header: present but cannot be compiled" >&5
+$as_echo "$as_me: WARNING: $ac_header: present but cannot be compiled" >&2;}
+    { $as_echo "$as_me:$LINENO: WARNING: $ac_header:     check for missing prerequisite headers?" >&5
+$as_echo "$as_me: WARNING: $ac_header:     check for missing prerequisite headers?" >&2;}
+    { $as_echo "$as_me:$LINENO: WARNING: $ac_header: see the Autoconf documentation" >&5
+$as_echo "$as_me: WARNING: $ac_header: see the Autoconf documentation" >&2;}
+    { $as_echo "$as_me:$LINENO: WARNING: $ac_header:     section \"Present But Cannot Be Compiled\"" >&5
+$as_echo "$as_me: WARNING: $ac_header:     section \"Present But Cannot Be Compiled\"" >&2;}
+    { $as_echo "$as_me:$LINENO: WARNING: $ac_header: proceeding with the preprocessor's result" >&5
+$as_echo "$as_me: WARNING: $ac_header: proceeding with the preprocessor's result" >&2;}
+    { $as_echo "$as_me:$LINENO: WARNING: $ac_header: in the future, the compiler will take precedence" >&5
+$as_echo "$as_me: WARNING: $ac_header: in the future, the compiler will take precedence" >&2;}
+
+    ;;
+esac
+{ $as_echo "$as_me:$LINENO: checking for $ac_header" >&5
+$as_echo_n "checking for $ac_header... " >&6; }
+if { as_var=$as_ac_Header; eval "test \"\${$as_var+set}\" = set"; }; then
+  $as_echo_n "(cached) " >&6
+else
+  eval "$as_ac_Header=\$ac_header_preproc"
+fi
+ac_res=`eval 'as_val=${'$as_ac_Header'}
+		 $as_echo "$as_val"'`
+	       { $as_echo "$as_me:$LINENO: result: $ac_res" >&5
+$as_echo "$ac_res" >&6; }
+
+fi
+as_val=`eval 'as_val=${'$as_ac_Header'}
+		 $as_echo "$as_val"'`
+   if test "x$as_val" = x""yes; then
+  cat >>confdefs.h <<_ACEOF
+#define `$as_echo "HAVE_$ac_header" | $as_tr_cpp` 1
+_ACEOF
+
+fi
+
+done
+
+
 # Check for OpenMP parallel execution support
 
   OPENMP_CFLAGS=
@@ -7650,6 +7851,186 @@ fi
 done
 
 
+for ac_func in clock_gettime
+do
+as_ac_var=`$as_echo "ac_cv_func_$ac_func" | $as_tr_sh`
+{ $as_echo "$as_me:$LINENO: checking for $ac_func" >&5
+$as_echo_n "checking for $ac_func... " >&6; }
+if { as_var=$as_ac_var; eval "test \"\${$as_var+set}\" = set"; }; then
+  $as_echo_n "(cached) " >&6
+else
+  cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+/* Define $ac_func to an innocuous variant, in case <limits.h> declares $ac_func.
+   For example, HP-UX 11i <limits.h> declares gettimeofday.  */
+#define $ac_func innocuous_$ac_func
+
+/* System header to define __stub macros and hopefully few prototypes,
+    which can conflict with char $ac_func (); below.
+    Prefer <limits.h> to <assert.h> if __STDC__ is defined, since
+    <limits.h> exists even on freestanding compilers.  */
+
+#ifdef __STDC__
+# include <limits.h>
+#else
+# include <assert.h>
+#endif
+
+#undef $ac_func
+
+/* Override any GCC internal prototype to avoid an error.
+   Use char because int might match the return type of a GCC
+   builtin and then its argument prototype would still apply.  */
+#ifdef __cplusplus
+extern "C"
+#endif
+char $ac_func ();
+/* The GNU C library defines this for functions which it implements
+    to always fail with ENOSYS.  Some functions are actually named
+    something starting with __ and the normal name is an alias.  */
+#if defined __stub_$ac_func || defined __stub___$ac_func
+choke me
+#endif
+
+int
+main ()
+{
+return $ac_func ();
+  ;
+  return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext conftest$ac_exeext
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+  (eval "$ac_link") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest$ac_exeext && {
+	 test "$cross_compiling" = yes ||
+	 $as_test_x conftest$ac_exeext
+       }; then
+  eval "$as_ac_var=yes"
+else
+  $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+	eval "$as_ac_var=no"
+fi
+
+rm -rf conftest.dSYM
+rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
+      conftest$ac_exeext conftest.$ac_ext
+fi
+ac_res=`eval 'as_val=${'$as_ac_var'}
+		 $as_echo "$as_val"'`
+	       { $as_echo "$as_me:$LINENO: result: $ac_res" >&5
+$as_echo "$ac_res" >&6; }
+as_val=`eval 'as_val=${'$as_ac_var'}
+		 $as_echo "$as_val"'`
+   if test "x$as_val" = x""yes; then
+  cat >>confdefs.h <<_ACEOF
+#define `$as_echo "HAVE_$ac_func" | $as_tr_cpp` 1
+_ACEOF
+
+fi
+done
+
+
+# `clock_gettime()`, declared in unistd.h, may be in librt (e.g. for glibc).
+if test $ac_cv_func_clock_gettime = no; then
+	{ $as_echo "$as_me:$LINENO: checking for clock_gettime in -lrt" >&5
+$as_echo_n "checking for clock_gettime in -lrt... " >&6; }
+if test "${ac_cv_lib_rt_clock_gettime+set}" = set; then
+  $as_echo_n "(cached) " >&6
+else
+  ac_check_lib_save_LIBS=$LIBS
+LIBS="-lrt  $LIBS"
+cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h.  */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h.  */
+
+/* Override any GCC internal prototype to avoid an error.
+   Use char because int might match the return type of a GCC
+   builtin and then its argument prototype would still apply.  */
+#ifdef __cplusplus
+extern "C"
+#endif
+char clock_gettime ();
+int
+main ()
+{
+return clock_gettime ();
+  ;
+  return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext conftest$ac_exeext
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+  (eval "$ac_link") 2>conftest.er1
+  ac_status=$?
+  grep -v '^ *+' conftest.er1 >conftest.err
+  rm -f conftest.er1
+  cat conftest.err >&5
+  $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+  (exit $ac_status); } && {
+	 test -z "$ac_c_werror_flag" ||
+	 test ! -s conftest.err
+       } && test -s conftest$ac_exeext && {
+	 test "$cross_compiling" = yes ||
+	 $as_test_x conftest$ac_exeext
+       }; then
+  ac_cv_lib_rt_clock_gettime=yes
+else
+  $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+	ac_cv_lib_rt_clock_gettime=no
+fi
+
+rm -rf conftest.dSYM
+rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
+      conftest$ac_exeext conftest.$ac_ext
+LIBS=$ac_check_lib_save_LIBS
+fi
+{ $as_echo "$as_me:$LINENO: result: $ac_cv_lib_rt_clock_gettime" >&5
+$as_echo "$ac_cv_lib_rt_clock_gettime" >&6; }
+if test "x$ac_cv_lib_rt_clock_gettime" = x""yes; then
+  LIBS="-lrt $LIBS"
+
+cat >>confdefs.h <<\_ACEOF
+#define HAVE_CLOCK_GETTIME 1
+_ACEOF
+
+
+fi
+
+fi
+
 #
 # Test if regular expressions are functional. Early regex implementations have nonfunctional stubs,
 # so the check for C++11 succeeds, but the compiled code will throw an exception.
@@ -8235,7 +8616,7 @@ exec 6>&1
 # report actual input values of CONFIG_FILES etc. instead of their
 # values after options handling.
 ac_log="
-This file was extended by Stacks $as_me 1.46, which was
+This file was extended by Stacks $as_me 2.0Beta8c, which was
 generated by GNU Autoconf 2.63.  Invocation command line was
 
   CONFIG_FILES    = $CONFIG_FILES
@@ -8298,7 +8679,7 @@ Report bugs to <bug-autoconf@gnu.org>."
 _ACEOF
 cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
 ac_cs_version="\\
-Stacks config.status 1.46
+Stacks config.status 2.0Beta8c
 configured by $0, generated by GNU Autoconf 2.63,
   with options \\"`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`\\"
 

configure.ac

@@ -2,7 +2,7 @@
 # Process this file with autoconf to produce a configure script.
 
 AC_PREREQ(2.59)
-AC_INIT([Stacks], [1.46])
+AC_INIT([Stacks], [2.0Beta8c])
 AC_CONFIG_AUX_DIR([config])
 AM_INIT_AUTOMAKE([-Wall -Werror foreign parallel-tests subdir-objects])
 AC_CONFIG_SRCDIR([src/ustacks.cc])
@@ -25,28 +25,15 @@ AC_SUBST([BAM_LIBS])
 
 ])
 
-#
-# Enable use of Google Sparsehash and get include location if requested.
-#
-AC_ARG_ENABLE([sparsehash],
-    AS_HELP_STRING([--enable-sparsehash], [Enable the use of Google Sparsehash (must be installed).]))
-
-AS_IF([test "x$enable_sparsehash" = "xyes"], [
-AC_DEFINE([HAVE_SPARSEHASH], [1], [Enable compilation with Google Sparsehash])
-AC_ARG_WITH([sparsehash-include-path],
-  [AS_HELP_STRING([--with-sparsehash-include-path],
-    [location of Google Sparsehash headers])],
-  [SPARSEHASH_CFLAGS="-I$withval"],
-  [SPARSEHASH_CFLAGS=""])
-AC_SUBST([SPARSEHASH_CFLAGS])
-
-])
-
 # Checks for programs.
 AC_PROG_CXX
 AM_PROG_CC_C_O
 AX_CXX_COMPILE_STDCXX(11,, [mandatory])
 
+# Checks for ar-based static libs.
+AC_PROG_RANLIB
+m4_ifdef([AM_PROG_AR], [AM_PROG_AR])
+
 # Checks for libraries.
 AC_CHECK_LIB([gomp], [omp_set_num_threads],, [AC_MSG_WARN([Unable to locate OpenMP library, you should probably specify '--disable-openmp'.])])
 AC_CHECK_LIB([z], [gzread],, [AC_MSG_ERROR([Zlib not found, reading gzipped files will not be possible.])]) 
@@ -55,6 +42,7 @@ AC_CHECK_LIB([z], [gzread],, [AC_MSG_ERROR([Zlib not found, reading gzipped file
 AC_HEADER_DIRENT
 AC_HEADER_STDC
 AC_CHECK_HEADERS([float.h limits.h stdlib.h string.h])
+AC_CHECK_HEADERS([unistd.h])
 
 # Check for OpenMP parallel execution support
 AC_OPENMP
@@ -69,6 +57,15 @@ AC_FUNC_CLOSEDIR_VOID
 AC_FUNC_MALLOC
 AC_FUNC_REALLOC
 AC_CHECK_FUNCS([floor memset pow sqrt])
+AC_CHECK_FUNCS([clock_gettime])
+
+# `clock_gettime()`, declared in unistd.h, may be in librt (e.g. for glibc).
+if test $ac_cv_func_clock_gettime = no; then
+	AC_CHECK_LIB(rt, clock_gettime,
+		[LIBS="-lrt $LIBS"
+		AC_DEFINE(HAVE_CLOCK_GETTIME, 1, [Define to 1 if you have the `clock_gettime' function.])
+		])
+fi
 
 #
 # Test if regular expressions are functional. Early regex implementations have nonfunctional stubs,

debian/changelog

+stacks (2.0Beta8c+dfsg-1) unstable; urgency=medium
+
+  * New upstream version
+  * Remove code copy of htslib and use Debian packaged version of htslib
+    instead
+  * Standards-Version: 4.1.3
+  * debhelper 11
+
+ -- Andreas Tille <tille@debian.org>  Sun, 18 Feb 2018 17:15:06 +0100
+
 stacks (1.46-1) unstable; urgency=medium
 
   * New upstream version

debian/compat

-10
+11

debian/control

@@ -4,13 +4,14 @@ Uploaders: Tim Booth <tbooth@ceh.ac.uk>,
            Andreas Tille <tille@debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 10),
+Build-Depends: debhelper (>= 11~),
                python,
                zlib1g-dev,
                libbam-dev,
                libsparsehash-dev (>= 2.0),
-               samtools
-Standards-Version: 4.0.0
+               samtools,
+               libhts-dev
+Standards-Version: 4.1.3
 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/stacks.git
 Vcs-Git: https://anonscm.debian.org/git/debian-med/stacks.git
 Homepage: http://creskolab.uoregon.edu/stacks/

debian/copyright

@@ -2,6 +2,7 @@ Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Upstream-Name: Stacks
 Upstream-Contact: Julian Catchen <jcatchen@uoregon.edu>
 Source: http://creskolab.uoregon.edu/stacks/
+Files-Excluded: */htslib
 
 Files: *
 Copyright: © Julian Catchen <jcatchen@uoregon.edu>

debian/patches/script-exe-paths

@@ -9,8 +9,8 @@ Last-Update: 2016-10-21
 This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
 --- a/Makefile.am
 +++ b/Makefile.am
-@@ -175,10 +175,10 @@
- 	$(MAKE) all "CXXFLAGS=-g -Wall -DDEBUG -std=gnu++0x"
+@@ -148,10 +148,10 @@ debug:
+ 	$(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
@@ -22,7 +22,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
  	mv $(DESTDIR)$(bindir)/ref_map.pl.subst $(DESTDIR)$(bindir)/ref_map.pl
  	chmod +x $(DESTDIR)$(bindir)/ref_map.pl
  	sed -e 's,_VERSION_,$(VERSION),' -e 's,_PKGDATADIR_,$(pkgdatadir)/,g' $(DESTDIR)$(bindir)/export_sql.pl > $(DESTDIR)$(bindir)/export_sql.pl.subst
-@@ -199,11 +199,11 @@
+@@ -172,11 +172,11 @@ install-data-hook:
  	sed -e 's,_VERSION_,$(VERSION),' -e 's,_PKGDATADIR_,$(pkgdatadir)/,g' $(DESTDIR)$(bindir)/load_sequences.pl > $(DESTDIR)$(bindir)/load_sequences.pl.subst
  	mv $(DESTDIR)$(bindir)/load_sequences.pl.subst $(DESTDIR)$(bindir)/load_sequences.pl
  	chmod +x $(DESTDIR)$(bindir)/load_sequences.pl

debian/patches/series

 constants.php.patch
 email-settings.patch
 script-exe-paths
+use_debian_packaged_htslib.patch

debian/patches/use_debian_packaged_htslib.patch

+Description: Use Debian packaged version of htslib
+Author: Andreas Tille <tille@debian.org>
+Last-Update: Sun, 18 Feb 2018 17:00:11 +0100
+
+--- a/Makefile.am
++++ b/Makefile.am
+@@ -142,7 +142,7 @@ EXTRA_DIST = $(nobase_pkgdata_DATA) LICE
+ 
+ pkglocalstatedir = $(localstatedir)/$(PACKAGE)
+ 
+-SUBDIRS = htslib .
++SUBDIRS = .
+ 
+ debug:
+ 	$(MAKE) all "CXXFLAGS=-g -Wall -DDEBUG -std=gnu++11"
+--- a/configure.ac
++++ b/configure.ac
+@@ -18,9 +18,9 @@ AC_ARG_ENABLE([bam],
+ AS_IF([test "x$enable_bam" != "xno"], [
+ AC_DEFINE([HAVE_BAM], [1], [Enable compilation with Samtools BAM library])
+ 
+-BAM_CFLAGS='-I./htslib/htslib'
++BAM_CFLAGS='-I/usr/include/htslib'
+ AC_SUBST([BAM_CFLAGS])
+-BAM_LIBS='./htslib/libhts.a'
++BAM_LIBS='-lhts'
+ AC_SUBST([BAM_LIBS])
+ 
+ ])

debian/watch

 version=4
 
-http://creskolab.uoregon.edu/stacks/ (?:.*/|)source/stacks-([0-9.]+).tar.[gzb2x]+
+opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,repack,compression=xz" \
+  https://creskolab.uoregon.edu/stacks/ (?:.*/|)source/stacks-(\d[0-9.Betac]+).tar.[gzb2x]+

htslib/INSTALL

-Basic Installation
-==================
-
-To build and install HTSlib, 'cd' to the htslib-1.x directory containing
-the package's source and type the following commands:
-
-    ./configure
-    make
-    make install
-
-The './configure' command checks your build environment and allows various
-optional functionality to be enabled (see Configuration below).  If you
-don't want to select any optional functionality, you may wish to omit
-configure and just type 'make; make install' as for previous versions
-of HTSlib.  However if the build fails you should run './configure' as
-it can diagnose the common reasons for build failures.
-
-The 'make' command builds the HTSlib library and and various useful
-utilities: bgzip, htsfile, and tabix.  If compilation fails you should
-run './configure' as it can diagnose problems with your build environment
-that cause build failures.
-
-The 'make install' command installs the libraries, library header files,
-utilities, several manual pages, and a pkgconfig file to /usr/local.
-The installation location can be changed by configuring with --prefix=DIR
-or via 'make prefix=DIR install' (see Installation Locations below).
-
-
-Configuration
-=============
-
-By default, './configure' examines your build environment, checking for
-requirements such as the zlib development files, and arranges for a plain
-HTSlib build.  The following configure options can be used to enable
-various features and specify further optional external requirements:
-
---enable-plugins
-    Use plugins to implement exotic file access protocols and other
-    specialised facilities.  This enables such facilities to be developed
-    and packaged outwith HTSlib, and somewhat isolates HTSlib-using programs
-    from their library dependencies.  By default, any enabled pluggable
-    facilities (such as iRODS and libcurl file access) are built directly
-    within HTSlib.
-
---with-plugin-dir=DIR
-    Specifies the directory into which plugins built while building HTSlib
-    should be installed; by default, LIBEXECDIR/htslib.
-
---with-plugin-path=DIR:DIR:DIR...
-    Specifies the list of directories that HTSlib will search for plugins.
-    By default, only the directory specified via --with-plugin-dir will be
-    searched; you can use --with-plugin-path='DIR:$(plugindir):DIR' and so
-    on to cause additional directories to be searched.
-
---with-irods[=DIR]
-    Specifies the location of the iRODS client library to use to enable
-    access to data objects stored in iRODS (<http://irods.org/>) via file
-    paths like 'irods:DATAOBJ'.  DIR is the base of an iRODS source tree
-    such that the library is present as DIR/lib/core/obj/libRodsAPI.* and
-    headers are present under DIR/lib/api/include and so on.  If '=DIR' is
-    omitted, $IRODS_HOME will be used as a base directory.
-
---enable-libcurl
-    Use libcurl (<http://curl.haxx.se/>) to implement network access to
-    remote files via FTP, HTTP, HTTPS, S3, etc.  By default, HTSlib uses
-    its own simple networking code to provide access via FTP and HTTP only.
-
-The configure script also accepts the usual options and environment variables
-for tuning installation locations and compilers: type './configure --help'
-for details.  For example,
-
-    ./configure CC=icc --prefix=/opt/icc-compiled
-
-would specify that HTSlib is to be built with icc and installed into bin,
-lib, etc subdirectories under /opt/icc-compiled.
-
-
-Installation Locations
-======================
-
-By default, 'make install' installs HTSlib libraries under /usr/local/lib,
-HTSlib header files under /usr/local/include, utility programs under
-/usr/local/bin, etc.  (To be precise, the header files are installed within
-a fixed 'htslib' subdirectory under the specified .../include location.)
-
-You can specify a different location to install HTSlib by configuring
-with --prefix=DIR or specify locations for particular parts of HTSlib by
-configuring with --libdir=DIR and so on.  Type './configure --help' for
-the full list of such install directory options.
-
-Alternatively you can specify different locations at install time by
-typing 'make prefix=DIR install' or 'make libdir=DIR install' and so on.
-Consult the list of prefix/exec_prefix/etc variables near the top of the
-Makefile for the full list of such variables that can be overridden.
-
-You can also specify a staging area by typing 'make DESTDIR=DIR install',
-possibly in conjunction with other --prefix or prefix=DIR settings.
-For example,
-
-    make DESTDIR=/tmp/staging prefix=/opt
-
-would install into bin, lib, etc subdirectories under /tmp/staging/opt.

htslib/LICENSE

-[Files in this distribution outwith the cram/ subdirectory are distributed
-according to the terms of the following MIT/Expat license.]
-
-The MIT/Expat License
-
-Copyright (C) 2012-2014 Genome Research Ltd.
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in
-all copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
-THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
-FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
-DEALINGS IN THE SOFTWARE.
-
-
-[Files within the cram/ subdirectory in this distribution are distributed
-according to the terms of the following Modified 3-Clause BSD license.]
-
-The Modified-BSD License
-
-Copyright (C) 2012-2014 Genome Research Ltd.
-
-Redistribution and use in source and binary forms, with or without
-modification, are permitted provided that the following conditions are met:
-
-1. Redistributions of source code must retain the above copyright notice,
-   this list of conditions and the following disclaimer.
-
-2. Redistributions in binary form must reproduce the above copyright notice,
-   this list of conditions and the following disclaimer in the documentation
-   and/or other materials provided with the distribution.
-
-3. Neither the names Genome Research Ltd and Wellcome Trust Sanger Institute
-   nor the names of its contributors may be used to endorse or promote products
-   derived from this software without specific prior written permission.
-
-THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS"
-AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR ITS CONTRIBUTORS BE LIABLE
-FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
-OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
-OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
-
-[The use of a range of years within a copyright notice in this distribution
-should be interpreted as being equivalent to a list of years including the
-first and last year specified and all consecutive years between them.
-
-For example, a copyright notice that reads "Copyright (C) 2005, 2007-2009,
-2011-2012" should be interpreted as being identical to a notice that reads
-"Copyright (C) 2005, 2007, 2008, 2009, 2011, 2012" and a copyright notice
-that reads "Copyright (C) 2005-2012" should be interpreted as being identical
-to a notice that reads "Copyright (C) 2005, 2006, 2007, 2008, 2009, 2010,
-2011, 2012".]

htslib/Makefile

-# Makefile for htslib, a C library for high-throughput sequencing data formats.
-#
-#    Copyright (C) 2013-2015 Genome Research Ltd.
-#
-#    Author: John Marshall <jm18@sanger.ac.uk>
-#
-# Permission is hereby granted, free of charge, to any person obtaining a copy
-# of this software and associated documentation files (the "Software"), to deal
-# in the Software without restriction, including without limitation the rights
-# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-# copies of the Software, and to permit persons to whom the Software is
-# furnished to do so, subject to the following conditions:
-#
-# The above copyright notice and this permission notice shall be included in
-# all copies or substantial portions of the Software.
-#
-# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
-# THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
-# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
-# DEALINGS IN THE SOFTWARE.
-
-CC     = gcc
-AR     = ar
-RANLIB = ranlib
-
-CPPFLAGS =
-# TODO: probably update cram code to make it compile cleanly with -Wc++-compat
-CFLAGS   = -g -Wall -O2
-EXTRA_CFLAGS_PIC = -fpic
-LDFLAGS  =
-LIBS     =
-
-# For now these don't work too well as samtools also needs to know to
-# add -lbz2 and -llzma if linking against the static libhts.a library.
-# TODO This needs configury and adding to htslib.pc.in.
-#
-# # Bzip2 support; optionally used by CRAM.
-# HAVE_LIBBZ2 := $(shell echo -e "\#include <bzlib.h>\012int main(void){return 0;}" > .test.c && $(CC) $(CFLAGS) $(CPPFLAGS) -o .test .test.c -lbz2 2>/dev/null && echo yes)
-# ifeq "$(HAVE_LIBBZ2)" "yes"
-# CPPFLAGS += -DHAVE_LIBBZ2
-# LIBS     += -lbz2
-# endif
-#
-# # Lzma support; optionally used by CRAM.
-# HAVE_LIBLZMA := $(shell echo -e "\#include <lzma.h>\012int main(void){return 0;}" > .test.c && $(CC) $(CFLAGS) $(CPPFLAGS) -o .test .test.c -llzma 2>/dev/null && echo yes)
-# ifeq "$(HAVE_LIBLZMA)" "yes"
-# CPPFLAGS += -DHAVE_LIBLZMA
-# LIBS     += -llzma
-# endif
-
-prefix      = /usr/local
-exec_prefix = $(prefix)
-bindir      = $(exec_prefix)/bin
-includedir  = $(prefix)/include
-libdir      = $(exec_prefix)/lib
-libexecdir  = $(exec_prefix)/libexec
-datarootdir = $(prefix)/share
-mandir      = $(datarootdir)/man
-man1dir     = $(mandir)/man1
-man5dir     = $(mandir)/man5
-pkgconfigdir= $(libdir)/pkgconfig
-
-MKDIR_P = mkdir -p
-INSTALL = install -p
-INSTALL_PROGRAM = $(INSTALL)
-INSTALL_DATA    = $(INSTALL) -m 644
-INSTALL_DIR     = $(MKDIR_P) -m 755
-
-# Set by config.mk if plugins are enabled
-plugindir =
-
-BUILT_PROGRAMS = \
-	bgzip \
-	htsfile \
-	tabix
-
-BUILT_TEST_PROGRAMS = \
-	test/fieldarith \
-	test/hfile \
-	test/sam \
-	test/test-regidx \
-	test/test_view \
-	test/test-vcf-api \
-	test/test-vcf-sweep
-
-# all: lib-static lib-shared $(BUILT_PROGRAMS) plugins $(BUILT_TEST_PROGRAMS)
-all: lib-static
-
-HTSPREFIX =
-include htslib_vars.mk
-
-
-PACKAGE_VERSION  = 1.3.1
-LIBHTS_SOVERSION = 1
-
-
-# $(NUMERIC_VERSION) is for items that must have a numeric X.Y.Z string
-# even if this is a dirty or untagged Git working tree.
-NUMERIC_VERSION = $(PACKAGE_VERSION)
-
-# If building from a Git repository, replace $(PACKAGE_VERSION) with the Git
-# description of the working tree: either a release tag with the same value
-# as $(PACKAGE_VERSION) above, or an exact description likely based on a tag.
-# Much of this is also GNU Make-specific.  If you don't have GNU Make and/or
-# are not building from a Git repository, comment out this conditional.
-ifneq "$(wildcard .git)" ""
-original_version := $(PACKAGE_VERSION)
-PACKAGE_VERSION := $(shell git describe --always --dirty)
-
-# Unless the Git description matches /\d*\.\d*(\.\d*)?/, i.e., is exactly a tag
-# with a numeric name, revert $(NUMERIC_VERSION) to the original version number
-# written above, but with the patchlevel field bumped to 255.
-ifneq "$(subst ..,.,$(subst 0,,$(subst 1,,$(subst 2,,$(subst 3,,$(subst 4,,$(subst 5,,$(subst 6,,$(subst 7,,$(subst 8,,$(subst 9,,$(PACKAGE_VERSION))))))))))))" "."
-empty :=
-NUMERIC_VERSION := $(subst $(empty) ,.,$(wordlist 1,2,$(subst ., ,$(original_version))) 255)
-endif
-
-# Force version.h to be remade if $(PACKAGE_VERSION) has changed.
-version.h: $(if $(wildcard version.h),$(if $(findstring "$(PACKAGE_VERSION)",$(shell cat version.h)),,force))
-endif
-
-version.h:
-	echo '#define HTS_VERSION "$(PACKAGE_VERSION)"' > $@
-
-print-version:
-	@echo $(PACKAGE_VERSION)
-
-
-.SUFFIXES: .bundle .c .o .pico .so
-
-.c.o:
-	$(CC) $(CFLAGS) -I. $(CPPFLAGS) -c -o $@ $<
-
-.c.pico:
-	$(CC) $(CFLAGS) -I. $(CPPFLAGS) $(EXTRA_CFLAGS_PIC) -c -o $@ $<
-
-
-LIBHTS_OBJS = \
-	kfunc.o \
-	knetfile.o \
-	kstring.o \
-	bgzf.o \
-	faidx.o \
-	hfile.o \
-	hfile_net.o \
-	hts.o \
-	md5.o \
-	regidx.o \
-	sam.o \
-	synced_bcf_reader.o \
-	vcf_sweep.o \
-	tbx.o \
-	vcf.o \
-	vcfutils.o \
-	cram/cram_codecs.o \
-	cram/cram_decode.o \
-	cram/cram_encode.o \
-	cram/cram_external.o \
-	cram/cram_index.o \
-	cram/cram_io.o \
-	cram/cram_samtools.o \
-	cram/cram_stats.o \
-	cram/files.o \
-	cram/mFILE.o \
-	cram/open_trace_file.o \
-	cram/pooled_alloc.o \
-	cram/rANS_static.o \
-	cram/sam_header.o \
-	cram/string_alloc.o \
-	cram/thread_pool.o \
-	cram/vlen.o \
-	cram/zfio.o
-
-PLUGIN_OBJS =
-
-cram_h = cram/cram.h $(cram_samtools_h) $(cram_sam_header_h) $(cram_structs_h) $(cram_io_h) cram/cram_encode.h cram/cram_decode.h cram/cram_stats.h cram/cram_codecs.h cram/cram_index.h $(htslib_cram_h)
-cram_io_h = cram/cram_io.h $(cram_misc_h)
-cram_misc_h = cram/misc.h cram/os.h
-cram_sam_header_h = cram/sam_header.h cram/string_alloc.h cram/pooled_alloc.h $(htslib_khash_h) $(htslib_kstring_h)
-cram_samtools_h = cram/cram_samtools.h $(htslib_sam_h) $(cram_sam_header_h)
-cram_structs_h = cram/cram_structs.h cram/thread_pool.h cram/string_alloc.h $(htslib_khash_h)
-cram_open_trace_file_h = cram/open_trace_file.h cram/mFILE.h
-hfile_internal_h = hfile_internal.h $(htslib_hfile_h)
-hts_internal_h = hts_internal.h $(htslib_hts_h)
-
-
-# To be effective, config.mk needs to appear after most Makefile variables are
-# set but before most rules appear, so that it can both use previously-set
-# variables in its own rules' prerequisites and also update variables for use
-# in later rules' prerequisites.
-
-# If your make doesn't accept -include, change this to 'include' if you are
-# using the configure script or just comment the line out if you are not.
--include config.mk
-
-# Usually config.h is generated by running configure or config.status,
-# but if those aren't used create a default config.h here.
-config.h:
-	echo '/* Empty config.h generated by Makefile */' > $@
-
-
-lib-static: libhts.a
-
-# $(shell), :=, and ifeq/.../endif are GNU Make-specific.  If you don't have
-# GNU Make, comment out the parts of this conditional that don't apply.
-PLATFORM := $(shell uname -s)
-ifeq "$(PLATFORM)" "Darwin"
-SHLIB_FLAVOUR = dylib
-lib-shared: libhts.dylib
-BUILT_PLUGINS = $(PLUGIN_OBJS:.o=.bundle)
-else
-SHLIB_FLAVOUR = so
-lib-shared: libhts.so
-BUILT_PLUGINS = $(PLUGIN_OBJS:.o=.so)
-endif
-
-plugins: $(BUILT_PLUGINS)
-
-
-libhts.a: $(LIBHTS_OBJS)
-	@-rm -f $@
-	$(AR) -rc $@ $(LIBHTS_OBJS)
-	-$(RANLIB) $@
-
-
-# The target here is libhts.so, as that is the built file that other rules
-# depend upon and that is used when -lhts appears in other program's recipes.
-# As a byproduct invisible to make, libhts.so.NN is also created, as it is the
-# file used at runtime (when $LD_LIBRARY_PATH includes the build directory).
-
-libhts.so: $(LIBHTS_OBJS:.o=.pico)
-	$(CC) -shared -Wl,-soname,libhts.so.$(LIBHTS_SOVERSION) -pthread $(LDFLAGS) -o $@ $(LIBHTS_OBJS:.o=.pico) -lz -lm $(LIBS)
-	ln -sf $@ libhts.so.$(LIBHTS_SOVERSION)
-
-# Similarly this also creates libhts.NN.dylib as a byproduct, so that programs
-# when run can find this uninstalled shared library (when $DYLD_LIBRARY_PATH
-# includes this project's build directory).
-
-libhts.dylib: $(LIBHTS_OBJS)
-	$(CC) -dynamiclib -install_name $(libdir)/libhts.$(LIBHTS_SOVERSION).dylib -current_version $(NUMERIC_VERSION) -compatibility_version $(LIBHTS_SOVERSION) $(LDFLAGS) -o $@ $(LIBHTS_OBJS) -lz $(LIBS)
-	ln -sf $@ libhts.$(LIBHTS_SOVERSION).dylib
-
-
-.pico.so:
-	$(CC) -shared -Wl,-E -pthread $(LDFLAGS) -o $@ $< $(LIBS)
-
-.o.bundle:
-	$(CC) -bundle -Wl,-undefined,dynamic_lookup $(LDFLAGS) -o $@ $< $(LIBS)
-
-
-bgzf.o bgzf.pico: bgzf.c config.h $(htslib_hts_h) $(htslib_bgzf_h) $(htslib_hfile_h) $(htslib_khash_h)
-kstring.o kstring.pico: kstring.c config.h $(htslib_kstring_h)
-knetfile.o knetfile.pico: knetfile.c config.h $(htslib_knetfile_h)
-hfile.o hfile.pico: hfile.c config.h $(htslib_hfile_h) $(hfile_internal_h) $(hts_internal_h) $(htslib_khash_h)
-hfile_irods.o hfile_irods.pico: hfile_irods.c config.h $(hfile_internal_h) $(htslib_hts_h) $(htslib_kstring_h)
-hfile_libcurl.o hfile_libcurl.pico: hfile_libcurl.c config.h $(hfile_internal_h) $(htslib_hts_h) $(htslib_kstring_h)
-hfile_net.o hfile_net.pico: hfile_net.c config.h $(hfile_internal_h) $(htslib_knetfile_h)
-hts.o hts.pico: hts.c config.h version.h $(htslib_hts_h) $(htslib_bgzf_h) $(cram_h) $(htslib_hfile_h) $(htslib_khash_h) $(htslib_kseq_h) $(htslib_ksort_h) $(hts_internal_h)
-vcf.o vcf.pico: vcf.c config.h $(htslib_vcf_h) $(htslib_bgzf_h) $(htslib_tbx_h) $(htslib_hfile_h) $(hts_internal_h) $(htslib_khash_h) $(htslib_kseq_h) $(htslib_kstring_h) $(htslib_khash_str2int_h)
-sam.o sam.pico: sam.c config.h $(htslib_sam_h) $(htslib_bgzf_h) $(cram_h) $(hts_internal_h) $(htslib_hfile_h) $(htslib_khash_h) $(htslib_kseq_h) $(htslib_kstring_h)
-tbx.o tbx.pico: tbx.c config.h $(htslib_tbx_h) $(htslib_bgzf_h) $(htslib_khash_h)
-faidx.o faidx.pico: faidx.c config.h $(htslib_bgzf_h) $(htslib_faidx_h) $(htslib_hfile_h) $(htslib_khash_h) $(htslib_kstring_h)
-synced_bcf_reader.o synced_bcf_reader.pico: synced_bcf_reader.c config.h $(htslib_synced_bcf_reader_h) $(htslib_kseq_h) $(htslib_khash_str2int_h) $(htslib_bgzf_h)
-vcf_sweep.o vcf_sweep.pico: vcf_sweep.c config.h $(htslib_vcf_sweep_h) $(htslib_bgzf_h)
-vcfutils.o vcfutils.pico: vcfutils.c config.h $(htslib_vcfutils_h) $(htslib_kbitset_h)
-kfunc.o kfunc.pico: kfunc.c config.h $(htslib_kfunc_h)
-regidx.o regidx.pico: regidx.c config.h $(htslib_hts_h) $(htslib_kstring_h) $(htslib_kseq_h) $(htslib_khash_str2int_h) $(htslib_regidx_h)
-md5.o md5.pico: md5.c config.h $(htslib_hts_h)
-plugin.o plugin.pico: plugin.c config.h $(hts_internal_h) $(htslib_kstring_h)
-
-cram/cram_codecs.o cram/cram_codecs.pico: cram/cram_codecs.c config.h $(cram_h)
-cram/cram_decode.o cram/cram_decode.pico: cram/cram_decode.c config.h $(cram_h) cram/os.h $(htslib_hts_h)
-cram/cram_encode.o cram/cram_encode.pico: cram/cram_encode.c config.h $(cram_h) cram/os.h $(htslib_hts_h)
-cram/cram_external.o cram/cram_external.pico: cram/cram_external.c config.h $(htslib_hfile_h) $(cram_h)
-cram/cram_index.o cram/cram_index.pico: cram/cram_index.c config.h $(htslib_hfile_h) $(cram_h) cram/os.h cram/zfio.h $(hts_internal_h)
-cram/cram_io.o cram/cram_io.pico: cram/cram_io.c config.h $(cram_h) cram/os.h $(htslib_hts_h) $(cram_open_trace_file_h) cram/rANS_static.h $(htslib_hfile_h) $(htslib_bgzf_h) $(htslib_faidx_h)
-cram/cram_samtools.o cram/cram_samtools.pico: cram/cram_samtools.c config.h $(cram_h) $(htslib_sam_h)
-cram/cram_stats.o cram/cram_stats.pico: cram/cram_stats.c config.h $(cram_h) cram/os.h
-cram/files.o cram/files.pico: cram/files.c config.h $(cram_misc_h)
-cram/mFILE.o cram/mFILE.pico: cram/mFILE.c config.h cram/os.h cram/mFILE.h cram/vlen.h
-cram/open_trace_file.o cram/open_trace_file.pico: cram/open_trace_file.c config.h cram/os.h $(cram_open_trace_file_h) $(cram_misc_h) $(htslib_hfile_h)
-cram/pooled_alloc.o cram/pooled_alloc.pico: cram/pooled_alloc.c config.h cram/pooled_alloc.h
-cram/rANS_static.o cram/rANS_static.pico: cram/rANS_static.c config.h cram/rANS_static.h cram/rANS_byte.h
-cram/sam_header.o cram/sam_header.pico: cram/sam_header.c config.h $(cram_sam_header_h) cram/string_alloc.h
-cram/string_alloc.o cram/string_alloc.pico: cram/string_alloc.c config.h cram/string_alloc.h
-cram/thread_pool.o cram/thread_pool.pico: cram/thread_pool.c config.h cram/thread_pool.h
-cram/vlen.o cram/vlen.pico: cram/vlen.c config.h cram/vlen.h cram/os.h
-cram/zfio.o cram/zfio.pico: cram/zfio.c config.h cram/os.h cram/zfio.h
-
-
-bgzip: bgzip.o libhts.a
-	$(CC) -pthread $(LDFLAGS) -o $@ bgzip.o libhts.a -lz $(LIBS)
-
-htsfile: htsfile.o libhts.a
-	$(CC) -pthread $(LDFLAGS) -o $@ htsfile.o libhts.a -lz $(LIBS)
-
-tabix: tabix.o libhts.a
-	$(CC) -pthread $(LDFLAGS) -o $@ tabix.o libhts.a -lz $(LIBS)
-
-bgzip.o: bgzip.c config.h $(htslib_bgzf_h) $(htslib_hts_h)
-htsfile.o: htsfile.c config.h $(htslib_hfile_h) $(htslib_hts_h) $(htslib_sam_h) $(htslib_vcf_h)
-tabix.o: tabix.c config.h $(htslib_tbx_h) $(htslib_sam_h) $(htslib_vcf_h) $(htslib_kseq_h) $(htslib_bgzf_h) $(htslib_hts_h) $(htslib_regidx_h)
-
-
-# For tests that might use it, set $REF_PATH explicitly to use only reference
-# areas within the test suite (or set it to ':' to use no reference areas).
-check test: htsfile $(BUILT_TEST_PROGRAMS)
-	test/fieldarith test/fieldarith.sam
-	test/hfile
-	test/sam test/ce.fa test/faidx.fa
-	test/test-regidx
-	cd test && REF_PATH=: ./test.pl
-
-test/fieldarith: test/fieldarith.o libhts.a
-	$(CC) -pthread $(LDFLAGS) -o $@ test/fieldarith.o libhts.a -lz $(LIBS)
-
-test/hfile: test/hfile.o libhts.a
-	$(CC) -pthread $(LDFLAGS) -o $@ test/hfile.o libhts.a -lz $(LIBS)
-
-test/sam: test/sam.o libhts.a
-	$(CC) -pthread $(LDFLAGS) -o $@ test/sam.o libhts.a -lz $(LIBS)
-
-test/test-regidx: test/test-regidx.o libhts.a
-	$(CC) -pthread $(LDFLAGS) -o $@ test/test-regidx.o libhts.a -lz $(LIBS)
-
-test/test_view: test/test_view.o libhts.a
-	$(CC) -pthread $(LDFLAGS) -o $@ test/test_view.o libhts.a -lz $(LIBS)
-
-test/test-vcf-api: test/test-vcf-api.o libhts.a
-	$(CC) -pthread $(LDFLAGS) -o $@ test/test-vcf-api.o libhts.a -lz $(LIBS)
-
-test/test-vcf-sweep: test/test-vcf-sweep.o libhts.a
-	$(CC) -pthread $(LDFLAGS) -o $@ test/test-vcf-sweep.o libhts.a -lz $(LIBS)
-
-test/fieldarith.o: test/fieldarith.c config.h $(htslib_sam_h)
-test/hfile.o: test/hfile.c config.h $(htslib_hfile_h) $(htslib_hts_defs_h)
-test/sam.o: test/sam.c config.h $(htslib_hts_defs_h) $(htslib_sam_h) $(htslib_faidx_h) $(htslib_kstring_h)
-test/test-regidx.o: test/test-regidx.c config.h $(htslib_regidx_h)
-test/test_view.o: test/test_view.c config.h $(cram_h) $(htslib_sam_h)
-test/test-vcf-api.o: test/test-vcf-api.c config.h $(htslib_hts_h) $(htslib_vcf_h) $(htslib_kstring_h) $(htslib_kseq_h)
-test/test-vcf-sweep.o: test/test-vcf-sweep.c config.h $(htslib_vcf_sweep_h)
-
-
-# install: libhts.a $(BUILT_PROGRAMS) $(BUILT_PLUGINS) installdirs install-$(SHLIB_FLAVOUR) install-pkgconfig
-# 	$(INSTALL_PROGRAM) $(BUILT_PROGRAMS) $(DESTDIR)$(bindir)
-# 	if test -n "$(BUILT_PLUGINS)"; then $(INSTALL_PROGRAM) $(BUILT_PLUGINS) $(DESTDIR)$(plugindir); fi
-# 	$(INSTALL_DATA) htslib/*.h $(DESTDIR)$(includedir)/htslib
-# 	$(INSTALL_DATA) libhts.a $(DESTDIR)$(libdir)/libhts.a
-# 	$(INSTALL_DATA) htsfile.1 tabix.1 $(DESTDIR)$(man1dir)
-# 	$(INSTALL_DATA) faidx.5 sam.5 vcf.5 $(DESTDIR)$(man5dir)
-
-installdirs:
-	$(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(includedir) $(DESTDIR)$(includedir)/htslib $(DESTDIR)$(libdir) $(DESTDIR)$(man1dir) $(DESTDIR)$(man5dir) $(DESTDIR)$(pkgconfigdir)
-	if test -n "$(plugindir)"; then $(INSTALL_DIR) $(DESTDIR)$(plugindir); fi
-
-# After installation, the real file in $(libdir) will be libhts.so.X.Y.Z,
-# with symlinks libhts.so (used via -lhts during linking of client programs)
-# and libhts.so.NN (used by client executables at runtime).
-
-install-so: libhts.so installdirs
-	$(INSTALL_DATA) libhts.so $(DESTDIR)$(libdir)/libhts.so.$(PACKAGE_VERSION)
-	ln -sf libhts.so.$(PACKAGE_VERSION) $(DESTDIR)$(libdir)/libhts.so
-	ln -sf libhts.so.$(PACKAGE_VERSION) $(DESTDIR)$(libdir)/libhts.so.$(LIBHTS_SOVERSION)
-
-install-dylib: libhts.dylib installdirs
-	$(INSTALL_PROGRAM) libhts.dylib $(DESTDIR)$(libdir)/libhts.$(PACKAGE_VERSION).dylib
-	ln -sf libhts.$(PACKAGE_VERSION).dylib $(DESTDIR)$(libdir)/libhts.dylib
-	ln -sf libhts.$(PACKAGE_VERSION).dylib $(DESTDIR)$(libdir)/libhts.$(LIBHTS_SOVERSION).dylib
-
-# Substitute these pseudo-autoconf variables only at install time
-# so that "make install prefix=/prefix/path" etc continue to work.
-install-pkgconfig: installdirs
-	sed -e 's#@includedir@#$(includedir)#g;s#@libdir@#$(libdir)#g;s#@PACKAGE_VERSION@#$(PACKAGE_VERSION)#g' htslib.pc.in > $(DESTDIR)$(pkgconfigdir)/htslib.pc
-	chmod 644 $(DESTDIR)$(pkgconfigdir)/htslib.pc
-
-# A pkg-config file (suitable for copying to $PKG_CONFIG_PATH) that provides
-# flags for building against the uninstalled library in this build directory.
-htslib-uninstalled.pc: htslib.pc.in
-	sed -e 's#@includedir@#'`pwd`'#g;s#@libdir@#'`pwd`'#g' htslib.pc.in > $@
-
-
-testclean:
-	-rm -f test/*.tmp test/*.tmp.*
-
-mostlyclean: testclean
-	-rm -f *.o *.pico cram/*.o cram/*.pico test/*.o test/*.dSYM version.h
-
-clean: mostlyclean clean-$(SHLIB_FLAVOUR)
-	-rm -f libhts.a $(BUILT_PROGRAMS) $(BUILT_PLUGINS) $(BUILT_TEST_PROGRAMS)
-
-distclean maintainer-clean: clean
-	-rm -f config.cache config.h config.log config.mk config.status
-	-rm -f TAGS *-uninstalled.pc
-
-clean-so:
-	-rm -f libhts.so libhts.so.*
-
-clean-dylib:
-	-rm -f libhts.dylib libhts.*.dylib
-
-
-tags TAGS:
-	ctags -f TAGS *.[ch] cram/*.[ch] htslib/*.h
-
-# We recommend libhts-using programs be built against a separate htslib
-# installation.  However if you feel that you must bundle htslib source
-# code with your program, this hook enables Automake-style "make dist"
-# for this subdirectory.  If you do bundle an htslib snapshot, please
-# add identifying information to $(PACKAGE_VERSION) as appropriate.
-# (The wildcards attempt to omit non-exported files (.git*, README.md,
-# etc) and other detritus that might be in the top-level directory.)
-distdir:
-	tar -c *.[ch15] [ILMNRcht]*[ELSbcekmnt] | (cd $(distdir) && tar -x)
-	+cd $(distdir) && $(MAKE) distclean
-
-force:
-
-
-.PHONY: all check clean distclean distdir force
-.PHONY: install install-pkgconfig installdirs lib-shared lib-static
-.PHONY: maintainer-clean mostlyclean plugins print-version tags test testclean
-.PHONY: clean-so install-so
-.PHONY: clean-dylib install-dylib

htslib/NEWS

-Noteworthy changes in release 1.3.1 (22 April 2016)
-
-* Improved error checking and reporting, especially of I/O errors when
-  writing output files (#17, #315, PR #271, PR #317).
-
-* Build fixes for 32-bit systems; be sure to run configure to enable
-  large file support and access to 2GiB+ files.
-
-* Numerous VCF parsing fixes (#321, #322, #323, #324, #325; PR #370).
-  Particular thanks to Kostya Kortchinsky of the Google Security Team
-  for testing and numerous input parsing bug reports.
-
-* HTSlib now prints an informational message when initially creating a
-  CRAM reference cache in the default location under your $HOME directory.
-  (No message is printed if you are using $REF_CACHE to specify a location.)
-
-* Avoided rare race condition when caching downloaded CRAM reference sequence
-  files, by using distinctive names for temporary files (in addition to O_EXCL,
-  which has always been used).  Occasional corruption would previously occur
-  when multiple tools were simultaneously caching the same reference sequences
-  on an NFS filesystem that did not support O_EXCL (PR #320).
-
-* Prevented race condition in file access plugin loading (PR #341).
-
-* Fixed mpileup memory leak, so no more "[bam_plp_destroy] memory leak [...]
-  Continue anyway" warning messages (#299).
-
-* Various minor CRAM fixes.
-
-* Fixed documentation problems #348 and #358.
-
-
-Noteworthy changes in release 1.3  (15 December 2015)
-
-* Files can now be accessed via HTTPS and Amazon S3 in addition to HTTP
-  and FTP, when HTSlib is configured to use libcurl for network file access
-  rather than the included basic knetfile networking.
-
-* HTSlib can be built to use remote access hFILE backends (such as iRODS
-  and libcurl) via a plugin mechanism.  This allows other backends to be
-  easily added and facilitates building tools that use HTSlib, as they
-  don't need to be linked with the backends' various required libraries.
-
-* When writing CRAM output, sam_open() etc now default to writing CRAM v3.0
-  rather than v2.1.
-
-* fai_build() and samtools faidx now accept initial whitespace in ">"
-  headers (e.g., "> chr1 description" is taken to refer to "chr1").
-
-* tabix --only-header works again (was broken in 1.2.x; #249).
-
-* HTSlib's configure script and Makefile now fully support the standard
-  convention of allowing CC/CPPFLAGS/CFLAGS/LDFLAGS/LIBS to be overridden
-  as needed.  Previously the Makefile listened to $(LDLIBS) instead; if you
-  were overriding that, you should now override LIBS rather than LDLIBS.
-
-* Fixed bugs #168, #172, #176, #197, #206, #225, #245, #265, #295, and #296.
-
-
-Noteworthy changes in release 1.2.1  (3 February 2015)
-
-* Reinstated hts_file_type() and FT_* macros, which were available until 1.1
-  but briefly removed in 1.2.  This function is deprecated and will be removed
-  in a future release -- you should use hts_detect_format() etc instead
-
-
-Noteworthy changes in release 1.2  (2 February 2015)
-
-* HTSlib now has a configure script which checks your build environment
-  and allows for selection of optional extras.  See INSTALL for details
-
-* By default, reference sequences are fetched from the EBI CRAM Reference
-  Registry and cached in your $HOME cache directory.  This behaviour can
-  be controlled by setting REF_PATH and REF_CACHE enviroment variables
-  (see the samtools(1) man page for details)
-
-* Numerous CRAM improvements:
-  - Support for CRAM v3.0, an upcoming revision to CRAM supporting
-    better compression and per-container checksums
-  - EOF checking for v2.1 and v3.0 (similar to checking BAM EOF blocks)
-  - Non-standard values for PNEXT and TLEN fields are now preserved
-  - hts_set_fai_filename() now provides a reference file when encoding
-  - Generated read names are now numbered from 1, rather than being
-    labelled 'slice:record-in-slice'
-  - Multi-threading and speed improvements
-
-* New htsfile command for identifying file formats, and corresponding
-  file format detection APIs
-
-* New tabix --regions FILE, --targets FILE options for filtering via BED files
-
-* Optional iRODS file access, disabled by default.  Configure with --with-irods
-  to enable accessing iRODS data objects directly via 'irods:DATAOBJ'
-
-* All occurences of 2^29 in the source have been eliminated, so indexing
-  and querying against reference sequences larger than 512Mbp works (when
-  using CSI indices)
-
-* Support for plain GZIP compression in various places
-
-* VCF header editing speed improvements
-
-* Added seq_nt16_int[] (equivalent to the samtools API's bam_nt16_nt4_table)
-
-* Reinstated faidx_fetch_nseq(), which was accidentally removed from 1.1.
-  Now faidx_fetch_nseq() and faidx_nseq() are equivalent; eventually
-  faidx_fetch_nseq() will be deprecated and removed [#156]
-
-* Fixed bugs #141, #152, #155, #158, #159, and various memory leaks

htslib/README

-HTSlib is an implementation of a unified C library for accessing common file
-formats, such as SAM, CRAM, VCF, and BCF, used for high-throughput sequencing
-data.  It is the core library used by samtools and bcftools.
-
-See INSTALL for building and installation instructions.