[med-svn] [freebayes] 01/01: Mass commit of freebayes 1.1.0 packaging, the Git archive is quite spoiled but I do not think that the history is really interesting.
Andreas Tille
tille at debian.org
Sat Sep 2 12:46:23 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository freebayes.
commit 150a1f16a337a1ab4bc093c74bfdd6aafa6f9d41
Author: Andreas Tille <tille at debian.org>
Date: Sat Sep 2 14:00:23 2017 +0200
Mass commit of freebayes 1.1.0 packaging, the Git archive is quite spoiled but I do not think that the history is really interesting.
---
debian/README.source | 11 +
debian/bamleftalign.1 | 27 --
debian/changelog | 6 +
debian/control | 9 +-
debian/copyright | 428 +------------------
debian/createmanpages | 28 ++
debian/freebayes.1 | 459 ---------------------
debian/manpages | 1 -
debian/patches/fix_test.patch | 8 +
debian/patches/series | 3 +
debian/patches/use_debian_packaged_bamtools.patch | 68 +--
.../patches/use_debian_packaged_libjsoncpp.patch | 17 +
debian/patches/use_debian_packaged_seqlib.patch | 87 ++++
debian/patches/use_debian_packaged_vcflib.patch | 271 ++----------
debian/patches/vcffirstheader.patch | 29 ++
debian/rules | 6 +-
debian/test-simple-bash/lib/test-simple.bash | 110 +++++
debian/test-simple-bash/test/basics.t | 26 ++
debian/test-simple-bash/test/doc.t | 15 +
debian/test-simple-bash/test/no-label.t | 25 ++
20 files changed, 444 insertions(+), 1190 deletions(-)
diff --git a/debian/README.source b/debian/README.source
new file mode 100644
index 0000000..26e4dc4
--- /dev/null
+++ b/debian/README.source
@@ -0,0 +1,11 @@
+To run the test suite some bash testing framework was used
+bu upstream as Git submodules. For the Git packaging these
+were downloaded separately
+
+Files: debian/bash-tap/*
+ Obtained from
+ https://github.com/illusori/bash-tap
+
+Files: debian/test-simple-bash/*
+ Obtained from
+ https://github.com/ingydotnet/test-simple-bash/tree/master/lib
diff --git a/debian/bamleftalign.1 b/debian/bamleftalign.1
deleted file mode 100644
index db395a7..0000000
--- a/debian/bamleftalign.1
+++ /dev/null
@@ -1,27 +0,0 @@
-.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4.
-.TH BAMLEFTALIGN "1" "January 2017" "bamleftalign 1.0.2" "User Commands"
-.SH NAME
-bamleftalign \- Left\-aligns and merges the insertions and deletions in all alignments
-.SH SYNOPSIS
-[BAM data stream] | \fBbamleftalign\fR [options]
-.SH DESCRIPTION
-Left\-aligns and merges the insertions and deletions in all alignments in stdin.
-Iterates until each alignment is stable through a left\-realignment step.
-.SH OPTIONS
-.TP
-\fB\-f\fR \fB\-\-fasta\-reference\fR FILE
-FASTA reference file to use for realignment (required)
-.TP
-\fB\-d\fR \fB\-\-debug\fR
-Print debugging information about realignment process
-.TP
-\fB\-s\fR \fB\-\-suppress\-output\fR
-Don't write BAM output stream (for debugging)
-.TP
-\fB\-m\fR \fB\-\-max\-iterations\fR N
-Iterate the left\-realignment no more than this many times
-.TP
-\fB\-c\fR \fB\-\-compressed\fR
-Write compressed BAM on stdout, default is uncompressed
-.SH AUTHOR
-This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/changelog b/debian/changelog
index eaeaad5..8cf611a 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+freebayes (1.1.0-1) UNRELEASED; urgency=low
+
+ * New upstream version
+
+ -- Andreas Tille <tille at debian.org> Tue, 08 Nov 2016 11:40:28 +0100
+
freebayes (1.0.2-1) unstable; urgency=low
* Initial packaging (Closes: #851306)
diff --git a/debian/control b/debian/control
index 301577b..99d8397 100644
--- a/debian/control
+++ b/debian/control
@@ -7,12 +7,16 @@ Priority: optional
Build-Depends: debhelper (>= 9),
cmake,
pkg-config,
+ python,
zlib1g-dev,
libbamtools-dev,
- libvcflib-dev,
+ libvcflib-dev (>= 1.0.0~rc1+dfsg1-4),
libtabixpp-dev,
+ libseqlib-dev,
bc,
- samtools
+ samtools,
+ parallel,
+ libvcflib-tools
Standards-Version: 3.9.8
Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/freebayes.git
Vcs-Git: https://anonscm.debian.org/git/debian-med/freebayes.git
@@ -22,6 +26,7 @@ Package: freebayes
Architecture: any
Depends: ${shlibs:Depends},
${misc:Depends}
+Recommends: parallel
Description: Bayesian haplotype-based polymorphism discovery and genotyping
FreeBayes is a Bayesian genetic variant detector designed to find
small polymorphisms, specifically SNPs (single-nucleotide
diff --git a/debian/copyright b/debian/copyright
index 06830b0..6a31d5e 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -9,6 +9,14 @@ License: MIT
Files: debian/bash-tap/*
Copyright: 2012-2016 Sam Graham
License: MIT
+Comment: Files obtained from
+ https://github.com/illusori/bash-tap
+
+Files: debian/test-simple-bash
+Copyright: 2013 Ingy.Net
+License: MIT
+Comment: File obtained from
+ https://github.com/ingydotnet/test-simple-bash/tree/master/lib
Files: ttmath/*
Copyright: 2006-2012, Tomasz Sowa
@@ -39,426 +47,6 @@ License: BSD-3-clause
ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF
THE POSSIBILITY OF SUCH DAMAGE.
-Files: src/fastlz.*
-Copyright: 2005-2007 Ariya Hidayat <ariya at kde.org>
-License: MIT
-
-Files: paper/genome_research.bst
-Copyright: 1994-2007 Patrick W Daly
-License: LPPL-1+
- The LaTeX Project Public License
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- .
- LPPL Version 1.3c 2008-05-04
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Files: debian/*
Copyright: 2014 Brad Chapman <chapmanb at 50mail.com>
License: MIT
diff --git a/debian/createmanpages b/debian/createmanpages
new file mode 100755
index 0000000..edc2633
--- /dev/null
+++ b/debian/createmanpages
@@ -0,0 +1,28 @@
+#!/bin/sh
+MANDIR=debian
+mkdir -p $MANDIR
+
+VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'`
+
+AUTHOR=".SH AUTHOR\nThis manpage was written by $DEBFULLNAME for the Debian distribution and
+can be used for any other usage of the program.
+"
+
+progname=bamleftalign
+help2man --no-info --no-discard-stderr \
+ --name='<optional description of the program>' \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=freebayes
+help2man --no-info --no-discard-stderr --help-option=" " \
+ --name='<optional description of the program>' \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+cat <<EOT
+Please enhance the help2man output.
+The following web page might be helpful in doing so:
+ http://liw.fi/manpages/
+EOT
+
diff --git a/debian/freebayes.1 b/debian/freebayes.1
deleted file mode 100644
index 70b8157..0000000
--- a/debian/freebayes.1
+++ /dev/null
@@ -1,459 +0,0 @@
-.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4.
-.TH FREEBAYES "1" "January 2017" "freebayes 1.0.2" "User Commands"
-.SH NAME
-freebayes \- Bayesian haplotype\-based polymorphism discovery
-.SH SYNOPSIS
-.B freebayes
-\fB\-f\fR [REFERENCE] [OPTIONS] [BAM FILES] >[OUTPUT]
-.SH DESCRIPTION
-FreeBayes is a Bayesian genetic variant detector designed to find
-small polymorphisms, specifically SNPs (single-nucleotide
-polymorphisms), indels (insertions and deletions), MNPs
-(multi-nucleotide polymorphisms), and complex events (composite
-insertion and substitution events) smaller than the length of a
-short-read sequencing alignment.
-.SS Overview:
-To call variants from aligned short\-read sequencing data, supply BAM files and
-a reference. FreeBayes will provide VCF output on standard out describing SNPs,
-indels, and complex variants in samples in the input alignments.
-.PP
-By default, FreeBayes will consider variants supported by at least 2
-observations in a single sample (\fB\-C\fR) and also by at least 20% of the reads from
-a single sample (\fB\-F\fR). These settings are suitable to low to high depth
-sequencing in haploid and diploid samples, but users working with polyploid or
-pooled samples may wish to adjust them depending on the characteristics of
-their sequencing data.
-.IP
-FreeBayes is capable of calling variant haplotypes shorter than a read length
-where multiple polymorphisms segregate on the same read. The maximum distance
-between polymorphisms phased in this way is determined by the
-\fB\-\-max\-complex\-gap\fR, which defaults to 3bp. In practice, this can comfortably be
-set to half the read length.
-.IP
-Ploidy may be set to any level (\fB\-p\fR), but by default all samples are assumed to
-be diploid. FreeBayes can model per\-sample and per\-region variation in
-copy\-number (\fB\-A\fR) using a copy\-number variation map.
-.IP
-FreeBayes can act as a frequency\-based pooled caller and describe variants
-and haplotypes in terms of observation frequency rather than called genotypes.
-To do so, use \fB\-\-pooled\-continuous\fR and set input filters to a suitable level.
-Allele observation counts will be described by AO and RO fields in the VCF output.
-.SH Examples
-.TP
-# call variants assuming a diploid sample
-freebayes \fB\-f\fR ref.fa aln.bam >var.vcf
-.TP
-# call variants assuming a diploid sample, providing gVCF output
-freebayes \fB\-f\fR ref.fa \fB\-\-gvcf\fR aln.bam >var.gvcf
-.TP
-# require at least 5 supporting observations to consider a variant
-freebayes \fB\-f\fR ref.fa \fB\-C\fR 5 aln.bam >var.vcf
-.TP
-# use a different ploidy
-freebayes \fB\-f\fR ref.fa \fB\-p\fR 4 aln.bam >var.vcf
-.TP
-# assume a pooled sample with a known number of genome copies
-freebayes \fB\-f\fR ref.fa \fB\-p\fR 20 \fB\-\-pooled\-discrete\fR aln.bam >var.vcf
-.TP
-# generate frequency\-based calls for all variants passing input thresholds
-freebayes \fB\-f\fR ref.fa \fB\-F\fR 0.01 \fB\-C\fR 1 \fB\-\-pooled\-continuous\fR aln.bam >var.vcf
-.TP
-# use an input VCF (bgzipped + tabix indexed) to force calls at particular alleles
-freebayes \fB\-f\fR ref.fa \-@ in.vcf.gz aln.bam >var.vcf
-.TP
-# generate long haplotype calls over known variants
-freebayes \fB\-f\fR ref.fa \fB\-\-haplotype\-basis\-alleles\fR in.vcf.gz \fB\-\-haplotype\-length\fR 50 aln.bam
-.TP
-# naive variant calling: simply annotate observation counts of SNPs and indels
-freebayes \fB\-f\fR ref.fa \fB\-\-haplotype\-length\fR 0 \fB\-\-min\-alternate\-count\fR 1 \fB\-\-min\-alternate\-fraction\fR 0 \fB\-\-pooled\-continuous\fR \fB\-\-report\-monomorphic\fR >var.vcf
-.SH OPTIONS
-.TP
-\fB\-h\fR \fB\-\-help\fR
-Prints this help dialog.
-.TP
-\fB\-\-version\fR
-Prints the release number and the git commit id.
-.SS input
-.TP
-\fB\-b\fR \fB\-\-bam\fR FILE
-Add FILE to the set of BAM files to be analyzed.
-.HP
-\fB\-L\fR \fB\-\-bam\-list\fR FILE
-.IP
-A file containing a list of BAM files to be analyzed.
-.TP
-\fB\-c\fR \fB\-\-stdin\fR
-Read BAM input on stdin.
-.HP
-\fB\-f\fR \fB\-\-fasta\-reference\fR FILE
-.IP
-Use FILE as the reference sequence for analysis.
-An index file (FILE.fai) will be created if none exists.
-If neither \fB\-\-targets\fR nor \fB\-\-region\fR are specified, FreeBayes
-will analyze every position in this reference.
-.HP
-\fB\-t\fR \fB\-\-targets\fR FILE
-.IP
-Limit analysis to targets listed in the BED\-format FILE.
-.HP
-\fB\-r\fR \fB\-\-region\fR <chrom>:<start_position>\-<end_position>
-.IP
-Limit analysis to the specified region, 0\-base coordinates,
-end_position not included (same as BED format).
-Either '\-' or '..' maybe used as a separator.
-.HP
-\fB\-s\fR \fB\-\-samples\fR FILE
-.IP
-Limit analysis to samples listed (one per line) in the FILE.
-By default FreeBayes will analyze all samples in its input
-BAM files.
-.HP
-\fB\-\-populations\fR FILE
-.IP
-Each line of FILE should list a sample and a population which
-it is part of. The population\-based bayesian inference model
-will then be partitioned on the basis of the populations.
-.HP
-\fB\-A\fR \fB\-\-cnv\-map\fR FILE
-.IP
-Read a copy number map from the BED file FILE, which has
-the format:
-.IP
-reference sequence, start, end, sample name, copy number
-.IP
-\&... for each region in each sample which does not have the
-default copy number as set by \fB\-\-ploidy\fR.
-.SS output
-.TP
-\fB\-v\fR \fB\-\-vcf\fR FILE
-Output VCF\-format results to FILE. (default: stdout)
-.HP
-\fB\-\-gvcf\fR
-.IP
-Write gVCF output, which indicates coverage in uncalled regions.
-.HP
-\fB\-\-gvcf\-chunk\fR NUM
-.IP
-When writing gVCF output emit a record for every NUM bases.
-.HP
-\-@ \fB\-\-variant\-input\fR VCF
-.IP
-Use variants reported in VCF file as input to the algorithm.
-Variants in this file will included in the output even if
-there is not enough support in the data to pass input filters.
-.HP
-\fB\-l\fR \fB\-\-only\-use\-input\-alleles\fR
-.IP
-Only provide variant calls and genotype likelihoods for sites
-and alleles which are provided in the VCF input, and provide
-output in the VCF for all input alleles, not just those which
-have support in the data.
-.HP
-\fB\-\-haplotype\-basis\-alleles\fR VCF
-.IP
-When specified, only variant alleles provided in this input
-VCF will be used for the construction of complex or haplotype
-alleles.
-.HP
-\fB\-\-report\-all\-haplotype\-alleles\fR
-.IP
-At sites where genotypes are made over haplotype alleles,
-provide information about all alleles in output, not only
-those which are called.
-.HP
-\fB\-\-report\-monomorphic\fR
-.IP
-Report even loci which appear to be monomorphic, and report all
-considered alleles, even those which are not in called genotypes.
-Loci which do not have any potential alternates have '.' for ALT.
-.TP
-\fB\-P\fR \fB\-\-pvar\fR N
-Report sites if the probability that there is a polymorphism
-at the site is greater than N. default: 0.0. Note that postfiltering is generally recommended over the use of this parameter.
-.SS population model
-.TP
-\fB\-T\fR \fB\-\-theta\fR N
-The expected mutation rate or pairwise nucleotide diversity
-among the population under analysis. This serves as the
-single parameter to the Ewens Sampling Formula prior model
-default: 0.001
-.TP
-\fB\-p\fR \fB\-\-ploidy\fR N
-Sets the default ploidy for the analysis to N. default: 2
-.HP
-\fB\-J\fR \fB\-\-pooled\-discrete\fR
-.IP
-Assume that samples result from pooled sequencing.
-Model pooled samples using discrete genotypes across pools.
-When using this flag, set \fB\-\-ploidy\fR to the number of
-alleles in each sample or use the \fB\-\-cnv\-map\fR to define
-per\-sample ploidy.
-.HP
-\fB\-K\fR \fB\-\-pooled\-continuous\fR
-.IP
-Output all alleles which pass input filters, regardles of
-genotyping outcome or model.
-.SS reference allele
-.HP
-\fB\-Z\fR \fB\-\-use\-reference\-allele\fR
-.IP
-This flag includes the reference allele in the analysis as
-if it is another sample from the same population.
-.HP
-\fB\-\-reference\-quality\fR MQ,BQ
-.IP
-Assign mapping quality of MQ to the reference allele at each
-site and base quality of BQ. default: 100,60
-.SS allele scope
-.TP
-\fB\-I\fR \fB\-\-no\-snps\fR
-Ignore SNP alleles.
-.TP
-\fB\-i\fR \fB\-\-no\-indels\fR
-Ignore insertion and deletion alleles.
-.TP
-\fB\-X\fR \fB\-\-no\-mnps\fR
-Ignore multi\-nuceotide polymorphisms, MNPs.
-.HP
-\fB\-u\fR \fB\-\-no\-complex\fR Ignore complex events (composites of other classes).
-.HP
-\fB\-n\fR \fB\-\-use\-best\-n\-alleles\fR N
-.IP
-Evaluate only the best N SNP alleles, ranked by sum of
-supporting quality scores. (Set to 0 to use all; default: all)
-.HP
-\fB\-E\fR \fB\-\-max\-complex\-gap\fR N
-.HP
-\fB\-\-haplotype\-length\fR N
-.IP
-Allow haplotype calls with contiguous embedded matches of up
-to this length. (default: 3)
-.HP
-\fB\-\-min\-repeat\-size\fR N
-.IP
-When assembling observations across repeats, require the total repeat
-length at least this many bp. (default: 5)
-.HP
-\fB\-\-min\-repeat\-entropy\fR N
-.IP
-To detect interrupted repeats, build across sequence until it has
-entropy > N bits per bp. (default: 0, off)
-.HP
-\fB\-\-no\-partial\-observations\fR
-.IP
-Exclude observations which do not fully span the dynamically\-determined
-detection window. (default, use all observations, dividing partial
-support across matching haplotypes when generating haplotypes.)
-.SS indel realignment
-.HP
-\fB\-O\fR \fB\-\-dont\-left\-align\-indels\fR
-.IP
-Turn off left\-alignment of indels, which is enabled by default.
-.SS input filters
-.HP
-\fB\-4\fR \fB\-\-use\-duplicate\-reads\fR
-.IP
-Include duplicate\-marked alignments in the analysis.
-default: exclude duplicates marked as such in alignments
-.HP
-\fB\-m\fR \fB\-\-min\-mapping\-quality\fR Q
-.IP
-Exclude alignments from analysis if they have a mapping
-quality less than Q. default: 1
-.HP
-\fB\-q\fR \fB\-\-min\-base\-quality\fR Q
-.IP
-Exclude alleles from analysis if their supporting base
-quality is less than Q. default: 0
-.HP
-\fB\-R\fR \fB\-\-min\-supporting\-allele\-qsum\fR Q
-.IP
-Consider any allele in which the sum of qualities of supporting
-observations is at least Q. default: 0
-.HP
-\fB\-Y\fR \fB\-\-min\-supporting\-mapping\-qsum\fR Q
-.IP
-Consider any allele in which and the sum of mapping qualities of
-supporting reads is at least Q. default: 0
-.HP
-\fB\-Q\fR \fB\-\-mismatch\-base\-quality\-threshold\fR Q
-.IP
-Count mismatches toward \fB\-\-read\-mismatch\-limit\fR if the base
-quality of the mismatch is >= Q. default: 10
-.HP
-\fB\-U\fR \fB\-\-read\-mismatch\-limit\fR N
-.IP
-Exclude reads with more than N mismatches where each mismatch
-has base quality >= mismatch\-base\-quality\-threshold.
-default: ~unbounded
-.HP
-\fB\-z\fR \fB\-\-read\-max\-mismatch\-fraction\fR N
-.IP
-Exclude reads with more than N [0,1] fraction of mismatches where
-each mismatch has base quality >= mismatch\-base\-quality\-threshold
-default: 1.0
-.HP
-\-$ \fB\-\-read\-snp\-limit\fR N
-.IP
-Exclude reads with more than N base mismatches, ignoring gaps
-with quality >= mismatch\-base\-quality\-threshold.
-default: ~unbounded
-.HP
-\fB\-e\fR \fB\-\-read\-indel\-limit\fR N
-.IP
-Exclude reads with more than N separate gaps.
-default: ~unbounded
-.TP
-\fB\-0\fR \fB\-\-standard\-filters\fR
-Use stringent input base and mapping quality filters
-.IP
-Equivalent to \fB\-m\fR 30 \fB\-q\fR 20 \fB\-R\fR 0 \fB\-S\fR 0
-.HP
-\fB\-F\fR \fB\-\-min\-alternate\-fraction\fR N
-.IP
-Require at least this fraction of observations supporting
-an alternate allele within a single individual in the
-in order to evaluate the position. default: 0.2
-.HP
-\fB\-C\fR \fB\-\-min\-alternate\-count\fR N
-.IP
-Require at least this count of observations supporting
-an alternate allele within a single individual in order
-to evaluate the position. default: 2
-.HP
-\fB\-3\fR \fB\-\-min\-alternate\-qsum\fR N
-.IP
-Require at least this sum of quality of observations supporting
-an alternate allele within a single individual in order
-to evaluate the position. default: 0
-.HP
-\fB\-G\fR \fB\-\-min\-alternate\-total\fR N
-.IP
-Require at least this count of observations supporting
-an alternate allele within the total population in order
-to use the allele in analysis. default: 1
-.HP
-\fB\-\-min\-coverage\fR N
-.IP
-Require at least this coverage to process a site. default: 0
-.HP
-\fB\-\-max\-coverage\fR N
-.IP
-Do not process sites with greater than this coverage. default: no limit
-.SS population priors
-.HP
-\fB\-k\fR \fB\-\-no\-population\-priors\fR
-.IP
-Equivalent to \fB\-\-pooled\-discrete\fR \fB\-\-hwe\-priors\-off\fR and removal of
-Ewens Sampling Formula component of priors.
-.SS mappability priors
-.HP
-\fB\-w\fR \fB\-\-hwe\-priors\-off\fR
-.IP
-Disable estimation of the probability of the combination
-arising under HWE given the allele frequency as estimated
-by observation frequency.
-.HP
-\fB\-V\fR \fB\-\-binomial\-obs\-priors\-off\fR
-.IP
-Disable incorporation of prior expectations about observations.
-Uses read placement probability, strand balance probability,
-and read position (5'\-3') probability.
-.HP
-\fB\-a\fR \fB\-\-allele\-balance\-priors\-off\fR
-.IP
-Disable use of aggregate probability of observation balance between alleles
-as a component of the priors.
-.SS genotype likelihoods
-.HP
-\fB\-\-observation\-bias\fR FILE
-.IP
-Read length\-dependent allele observation biases from FILE.
-The format is [length] [alignment efficiency relative to reference]
-where the efficiency is 1 if there is no relative observation bias.
-.HP
-\fB\-\-base\-quality\-cap\fR Q
-.IP
-Limit estimated observation quality by capping base quality at Q.
-.HP
-\fB\-\-prob\-contamination\fR F
-.TP
-An estimate of contamination to use for all samples.
-default: 10e\-9
-.TP
-\fB\-\-legacy\-gls\fR
-Use legacy (polybayes equivalent) genotype likelihood calculations
-.HP
-\fB\-\-contamination\-estimates\fR FILE
-.IP
-A file containing per\-sample estimates of contamination, such as
-those generated by VerifyBamID. The format should be:
-.IP
-sample p(read=R|genotype=AR) p(read=A|genotype=AA)
-.IP
-Sample '*' can be used to set default contamination estimates.
-.SS algorithmic features
-.HP
-\fB\-\-report\-genotype\-likelihood\-max\fR
-.IP
-Report genotypes using the maximum\-likelihood estimate provided
-from genotype likelihoods.
-.HP
-\fB\-B\fR \fB\-\-genotyping\-max\-iterations\fR N
-.IP
-Iterate no more than N times during genotyping step. default: 1000.
-.HP
-\fB\-\-genotyping\-max\-banddepth\fR N
-.IP
-Integrate no deeper than the Nth best genotype by likelihood when
-genotyping. default: 6.
-.HP
-\fB\-W\fR \fB\-\-posterior\-integration\-limits\fR N,M
-.IP
-Integrate all genotype combinations in our posterior space
-which include no more than N samples with their Mth best
-data likelihood. default: 1,3.
-.HP
-\fB\-N\fR \fB\-\-exclude\-unobserved\-genotypes\fR
-.IP
-Skip sample genotypings for which the sample has no supporting reads.
-.HP
-\fB\-S\fR \fB\-\-genotype\-variant\-threshold\fR N
-.IP
-Limit posterior integration to samples where the second\-best
-genotype likelihood is no more than log(N) from the highest
-genotype likelihood for the sample. default: ~unbounded
-.HP
-\fB\-j\fR \fB\-\-use\-mapping\-quality\fR
-.IP
-Use mapping quality of alleles when calculating data likelihoods.
-.HP
-\fB\-H\fR \fB\-\-harmonic\-indel\-quality\fR
-.IP
-Use a weighted sum of base qualities around an indel, scaled by the
-distance from the indel. By default use a minimum BQ in flanking sequence.
-.HP
-\fB\-D\fR \fB\-\-read\-dependence\-factor\fR N
-.IP
-Incorporate non\-independence of reads by scaling successive
-observations by this factor during data likelihood
-calculations. default: 0.9
-.HP
-\fB\-=\fR \fB\-\-genotype\-qualities\fR
-.IP
-Calculate the marginal probability of genotypes and report as GQ in
-each sample field in the VCF output.
-.SS debugging
-.TP
-\fB\-d\fR \fB\-\-debug\fR
-Print debugging output.
-.TP
-\fB\-dd\fR
-Print more verbose debugging output (requires "make DEBUG")
-.SH SEE ALSO
-"Haplotype\-based variant detection from short\-read sequencing"
-arXiv:1207.3907 (http://arxiv.org/abs/1207.3907)
-.SH AUTHOR
-Erik Garrison <erik.garrison at bc.edu>, Marth Lab, Boston College, 2010\-2014, Gabor Marth
-.pp
-This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/manpages b/debian/manpages
deleted file mode 100644
index 0f65186..0000000
--- a/debian/manpages
+++ /dev/null
@@ -1 +0,0 @@
-debian/*.1
diff --git a/debian/patches/fix_test.patch b/debian/patches/fix_test.patch
index a5af80c..302ed80 100644
--- a/debian/patches/fix_test.patch
+++ b/debian/patches/fix_test.patch
@@ -13,3 +13,11 @@ Description: vcflib is in a different package - do not test this
prove -v t
$(freebayes):
+--- a/scripts/freebayes-parallel
++++ b/scripts/freebayes-parallel
+@@ -37,4 +37,4 @@ command=("freebayes" "$@")
+ # iterate over regions using gnu parallel to dispatch jobs
+ cat "$regionsfile" | parallel -k -j "$ncpus" "${command[@]}" --region {}
+ ) | ../vcflib/scripts/vcffirstheader \
+- | ../vcflib/bin/vcfstreamsort -w 1000 | vcfuniq # remove duplicates at region edges
++ | vcfstreamsort -w 1000 | vcfuniq # remove duplicates at region edges
diff --git a/debian/patches/series b/debian/patches/series
index e9ae68a..3052e50 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,3 +1,6 @@
use_debian_packaged_bamtools.patch
use_debian_packaged_vcflib.patch
+use_debian_packaged_seqlib.patch
+use_debian_packaged_libjsoncpp.patch
fix_test.patch
+vcffirstheader.patch
diff --git a/debian/patches/use_debian_packaged_bamtools.patch b/debian/patches/use_debian_packaged_bamtools.patch
index 23f035e..9155580 100644
--- a/debian/patches/use_debian_packaged_bamtools.patch
+++ b/debian/patches/use_debian_packaged_bamtools.patch
@@ -4,83 +4,83 @@ Description: Use Debian packaged bamtools
--- a/src/Makefile
+++ b/src/Makefile
-@@ -12,11 +12,10 @@ C=gcc
+@@ -12,14 +12,13 @@ C=gcc
CFLAGS=-O3 -D_FILE_OFFSET_BITS=64 -g
#CFLAGS=-O3 -static -D VERBOSE_DEBUG # enables verbose debugging via --debug2
-BAMTOOLS_ROOT=../bamtools
+ SEQLIB_ROOT=../SeqLib
VCFLIB_ROOT=../vcflib
+ TABIX_ROOT=$(VCFLIB_ROOT)/tabixpp
+ HTSLIB_ROOT=$(TABIX_ROOT)/htslib
--LIBS = -L./ -L$(VCFLIB_ROOT)/tabixpp/ -L$(BAMTOOLS_ROOT)/lib -ltabix -lz -lm
--INCLUDE = -I$(BAMTOOLS_ROOT)/src -I../ttmath -I$(VCFLIB_ROOT)/src -I$(VCFLIB_ROOT)/
-+LIBS = -L./ -L$(VCFLIB_ROOT)/tabixpp/ -lbamtools -ltabixpp -lz -lm
-+INCLUDE = -I/usr/include/bamtools -I../ttmath -I$(VCFLIB_ROOT)/src -I$(VCFLIB_ROOT)/
+-LIBS = -lz -lm -lpthread
+-INCLUDE = -I../ttmath -I$(BAMTOOLS_ROOT)/src/ -I$(VCFLIB_ROOT)/src/ -I$(TABIX_ROOT)/ -I$(VCFLIB_ROOT)/smithwaterman/ -I$(VCFLIB_ROOT)/multichoose/ -I$(VCFLIB_ROOT)/filevercmp/ -I$(HTSLIB_ROOT) -I$(SEQLIB_ROOT) -I$(SEQLIB_ROOT)/htslib
++LIBS = -lbamtools -ltabixpp -lz -lm -lpthread
++INCLUDE = -I../ttmath -I/usr/include/bamtools -I$(VCFLIB_ROOT)/src/ -I$(TABIX_ROOT)/ -I$(VCFLIB_ROOT)/smithwaterman/ -I$(VCFLIB_ROOT)/multichoose/ -I$(VCFLIB_ROOT)/filevercmp/ -I$(HTSLIB_ROOT) -I$(SEQLIB_ROOT) -I$(SEQLIB_ROOT)/htslib
all: autoversion ../bin/freebayes ../bin/bamleftalign
-@@ -34,10 +33,6 @@ gprof:
+@@ -37,9 +36,6 @@ gprof:
.PHONY: all static debug profiling gprof
-# builds bamtools static lib, and copies into root
-$(BAMTOOLS_ROOT)/lib/libbamtools.a:
- cd $(BAMTOOLS_ROOT) && mkdir -p build && cd build && cmake .. && $(MAKE)
--
+ $(HTSLIB_ROOT)/libhts.a:
+ cd $(HTSLIB_ROOT) && make
- OBJECTS=BedReader.o \
- CNV.o \
-@@ -70,8 +65,7 @@ OBJECTS=BedReader.o \
- ../vcflib/smithwaterman/LeftAlign.o \
+@@ -78,7 +74,6 @@ OBJECTS=BedReader.o \
../vcflib/smithwaterman/Repeats.o \
../vcflib/smithwaterman/IndelAllele.o \
-- Variant.o \
-- $(BAMTOOLS_ROOT)/lib/libbamtools.a
-+ Variant.o
-
- HEADERS=multichoose.h version_git.h
-
-@@ -86,10 +80,10 @@ alleles ../bin/alleles: alleles.o $(OBJE
+ Variant.o \
+- $(BAMTOOLS_ROOT)/lib/libbamtools.a \
+ $(SEQLIB_ROOT)/src/libseqlib.a \
+ $(SEQLIB_ROOT)/bwa/libbwa.a \
+ $(SEQLIB_ROOT)/fermi-lite/libfml.a \
+@@ -97,10 +92,10 @@ alleles ../bin/alleles: alleles.o $(OBJE
dummy ../bin/dummy: dummy.o $(OBJECTS) $(HEADERS)
$(CXX) $(CFLAGS) $(INCLUDE) dummy.o $(OBJECTS) -o ../bin/dummy $(LIBS)
--bamleftalign ../bin/bamleftalign: $(BAMTOOLS_ROOT)/lib/libbamtools.a bamleftalign.o Fasta.o LeftAlign.o IndelAllele.o split.o
-- $(CXX) $(CFLAGS) $(INCLUDE) bamleftalign.o Fasta.o LeftAlign.o IndelAllele.o split.o $(BAMTOOLS_ROOT)/lib/libbamtools.a -o ../bin/bamleftalign $(LIBS)
-+bamleftalign ../bin/bamleftalign: bamleftalign.o Fasta.o
-+ $(CXX) $(CFLAGS) $(INCLUDE) bamleftalign.o Fasta.o LeftAlign.o IndelAllele.o split.o -o ../bin/bamleftalign -lbamtools
+-bamleftalign ../bin/bamleftalign: $(BAMTOOLS_ROOT)/lib/libbamtools.a $(SEQLIB_ROOT)/src/libseqlib.a $(SEQLIB_ROOT)/htslib/libhts.a bamleftalign.o Fasta.o LeftAlign.o IndelAllele.o split.o
+- $(CXX) $(CFLAGS) $(INCLUDE) bamleftalign.o Fasta.o Utility.o LeftAlign.o IndelAllele.o split.o $(BAMTOOLS_ROOT)/lib/libbamtools.a $(SEQLIB_ROOT)/src/libseqlib.a $(SEQLIB_ROOT)/htslib/libhts.a -o ../bin/bamleftalign $(LIBS)
++bamleftalign ../bin/bamleftalign: $(SEQLIB_ROOT)/src/libseqlib.a $(SEQLIB_ROOT)/htslib/libhts.a bamleftalign.o Fasta.o LeftAlign.o IndelAllele.o split.o
++ $(CXX) $(CFLAGS) $(INCLUDE) bamleftalign.o Fasta.o Utility.o LeftAlign.o IndelAllele.o split.o $(SEQLIB_ROOT)/src/libseqlib.a $(SEQLIB_ROOT)/htslib/libhts.a -o ../bin/bamleftalign $(LIBS)
--bamfiltertech ../bin/bamfiltertech: $(BAMTOOLS_ROOT)/lib/libbamtools.a bamfiltertech.o $(OBJECTS) $(HEADERS)
-+bamfiltertech ../bin/bamfiltertech: bamfiltertech.o $(OBJECTS) $(HEADERS)
+-bamfiltertech ../bin/bamfiltertech: $(BAMTOOLS_ROOT)/lib/libbamtools.a $(SEQLIB_ROOT)/src/libseqlib.a $(SEQLIB_ROOT)/htslib/libhts.a bamfiltertech.o $(OBJECTS) $(HEADERS)
++bamfiltertech ../bin/bamfiltertech: $(SEQLIB_ROOT)/src/libseqlib.a $(SEQLIB_ROOT)/htslib/libhts.a bamfiltertech.o $(OBJECTS) $(HEADERS)
$(CXX) $(CFLAGS) $(INCLUDE) bamfiltertech.o $(OBJECTS) -o ../bin/bamfiltertech $(LIBS)
-@@ -104,7 +98,7 @@ alleles.o: alleles.cpp AlleleParser.o Al
+@@ -115,7 +110,7 @@ alleles.o: alleles.cpp AlleleParser.o Al
dummy.o: dummy.cpp AlleleParser.o Allele.o
$(CXX) $(CFLAGS) $(INCLUDE) -c dummy.cpp
--freebayes.o: freebayes.cpp TryCatch.h $(BAMTOOLS_ROOT)/lib/libbamtools.a
-+freebayes.o: freebayes.cpp TryCatch.h
+-freebayes.o: freebayes.cpp TryCatch.h $(HTSLIB_ROOT)/libhts.a $(BAMTOOLS_ROOT)/lib/libbamtools.a
++freebayes.o: freebayes.cpp TryCatch.h $(HTSLIB_ROOT)/libhts.a
$(CXX) $(CFLAGS) $(INCLUDE) -c freebayes.cpp
fastlz.o: fastlz.c fastlz.h
-@@ -125,7 +119,7 @@ Genotype.o: Genotype.cpp Genotype.h Alle
+@@ -136,7 +131,7 @@ Genotype.o: Genotype.cpp Genotype.h Alle
Ewens.o: Ewens.cpp Ewens.h
$(CXX) $(CFLAGS) $(INCLUDE) -c Ewens.cpp
--AlleleParser.o: AlleleParser.cpp AlleleParser.h multichoose.h Parameters.h $(BAMTOOLS_ROOT)/lib/libbamtools.a
-+AlleleParser.o: AlleleParser.cpp AlleleParser.h multichoose.h Parameters.h
+-AlleleParser.o: AlleleParser.cpp AlleleParser.h multichoose.h Parameters.h $(BAMTOOLS_ROOT)/lib/libbamtools.a $(HTSLIB_ROOT)/libhts.a
++AlleleParser.o: AlleleParser.cpp AlleleParser.h multichoose.h Parameters.h $(HTSLIB_ROOT)/libhts.a
$(CXX) $(CFLAGS) $(INCLUDE) -c AlleleParser.cpp
Utility.o: Utility.cpp Utility.h Sum.h Product.h
-@@ -173,7 +167,7 @@ bamleftalign.o: bamleftalign.cpp LeftAli
+@@ -184,7 +179,7 @@ bamleftalign.o: bamleftalign.cpp LeftAli
bamfiltertech.o: bamfiltertech.cpp
$(CXX) $(CFLAGS) $(INCLUDE) -c bamfiltertech.cpp
--LeftAlign.o: LeftAlign.h LeftAlign.cpp $(BAMTOOLS_ROOT)/lib/libbamtools.a
-+LeftAlign.o: LeftAlign.h LeftAlign.cpp
+-LeftAlign.o: LeftAlign.h LeftAlign.cpp $(BAMTOOLS_ROOT)/lib/libbamtools.a $(HTSLIB_ROOT)/libhts.a
++LeftAlign.o: LeftAlign.h LeftAlign.cpp $(HTSLIB_ROOT)/libhts.a
$(CXX) $(CFLAGS) $(INCLUDE) -c LeftAlign.cpp
IndelAllele.o: IndelAllele.cpp IndelAllele.h
-@@ -263,6 +257,5 @@ autoversion:
+@@ -275,6 +270,5 @@ autoversion:
clean:
rm -rf *.o *.cgh *~ freebayes alleles ../bin/freebayes ../bin/alleles ../vcflib/*.o ../vcflib/tabixpp/*.{o,a}
diff --git a/debian/patches/use_debian_packaged_libjsoncpp.patch b/debian/patches/use_debian_packaged_libjsoncpp.patch
new file mode 100644
index 0000000..5ded25a
--- /dev/null
+++ b/debian/patches/use_debian_packaged_libjsoncpp.patch
@@ -0,0 +1,17 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Wed, 28 May 2014 21:23:38 +0200
+Description: Use Debian packaged libjsoncpp
+
+--- a/src/Makefile
++++ b/src/Makefile
+@@ -12,8 +12,8 @@ C=gcc
+ CFLAGS=-O3 -D_FILE_OFFSET_BITS=64 -g
+ #CFLAGS=-O3 -static -D VERBOSE_DEBUG # enables verbose debugging via --debug2
+
+-LIBS = -lbamtools -ltabixpp -lz -lm -lpthread `pkg-config --libs libvcflib` `pkg-config --libs htslib` `pkg-config --libs libseqlib`
+-INCLUDE = -I../ttmath -I/usr/include/bamtools `pkg-config --cflags libvcflib` `pkg-config --cflags libseqlib` `pkg-config --cflags htslib`
++LIBS = -lbamtools -ltabixpp -lz -lm -lpthread `pkg-config --libs libvcflib` `pkg-config --libs htslib` `pkg-config --libs libseqlib` `pkg-config --libs jsoncpp`
++INCLUDE = -I../ttmath -I/usr/include/bamtools `pkg-config --cflags libvcflib` `pkg-config --cflags libseqlib` `pkg-config --cflags htslib` `pkg-config --cflags jsoncpp`
+
+ all: autoversion ../bin/freebayes ../bin/bamleftalign
+
diff --git a/debian/patches/use_debian_packaged_seqlib.patch b/debian/patches/use_debian_packaged_seqlib.patch
new file mode 100644
index 0000000..9e7a35b
--- /dev/null
+++ b/debian/patches/use_debian_packaged_seqlib.patch
@@ -0,0 +1,87 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Wed, 28 May 2014 21:23:38 +0200
+Description: Use Debian packaged htslib and seqlib
+ seqlib carries another copy of htslib - we replace both
+
+--- a/src/Makefile
++++ b/src/Makefile
+@@ -12,10 +12,8 @@ C=gcc
+ CFLAGS=-O3 -D_FILE_OFFSET_BITS=64 -g
+ #CFLAGS=-O3 -static -D VERBOSE_DEBUG # enables verbose debugging via --debug2
+
+-SEQLIB_ROOT=../SeqLib
+-
+-LIBS = -lbamtools -ltabixpp -lz -lm -lpthread `pkg-config --libs libvcflib`
+-INCLUDE = -I../ttmath -I/usr/include/bamtools `pkg-config --cflags libvcflib` -I$(SEQLIB_ROOT) -I$(SEQLIB_ROOT)/htslib
++LIBS = -lbamtools -ltabixpp -lz -lm -lpthread `pkg-config --libs libvcflib` `pkg-config --libs htslib` `pkg-config --libs libseqlib`
++INCLUDE = -I../ttmath -I/usr/include/bamtools `pkg-config --cflags libvcflib` `pkg-config --cflags libseqlib` `pkg-config --cflags htslib`
+
+ all: autoversion ../bin/freebayes ../bin/bamleftalign
+
+@@ -33,12 +31,6 @@ gprof:
+
+ .PHONY: all static debug profiling gprof
+
+-$(HTSLIB_ROOT)/libhts.a:
+- cd $(HTSLIB_ROOT) && make
+-
+-$(SEQLIB_ROOT)/src/libseqlib.a:
+- cd $(SEQLIB_ROOT) && ./configure && make
+-
+ OBJECTS=BedReader.o \
+ CNV.o \
+ fastlz.o \
+@@ -62,11 +54,7 @@ OBJECTS=BedReader.o \
+ Bias.o \
+ Contamination.o \
+ NonCall.o \
+- SegfaultHandler.o \
+- $(SEQLIB_ROOT)/src/libseqlib.a \
+- $(SEQLIB_ROOT)/bwa/libbwa.a \
+- $(SEQLIB_ROOT)/fermi-lite/libfml.a \
+- $(SEQLIB_ROOT)/htslib/libhts.a
++ SegfaultHandler.o
+
+ HEADERS=multichoose.h version_git.h
+
+@@ -81,10 +69,10 @@ alleles ../bin/alleles: alleles.o $(OBJE
+ dummy ../bin/dummy: dummy.o $(OBJECTS) $(HEADERS)
+ $(CXX) $(CFLAGS) $(INCLUDE) dummy.o $(OBJECTS) -o ../bin/dummy $(LIBS)
+
+-bamleftalign ../bin/bamleftalign: $(SEQLIB_ROOT)/src/libseqlib.a $(SEQLIB_ROOT)/htslib/libhts.a bamleftalign.o Fasta.o LeftAlign.o IndelAllele.o split.o
+- $(CXX) $(CFLAGS) $(INCLUDE) bamleftalign.o Fasta.o Utility.o LeftAlign.o IndelAllele.o split.o $(SEQLIB_ROOT)/src/libseqlib.a $(SEQLIB_ROOT)/htslib/libhts.a -o ../bin/bamleftalign $(LIBS)
++bamleftalign ../bin/bamleftalign: bamleftalign.o Fasta.o LeftAlign.o IndelAllele.o split.o
++ $(CXX) $(CFLAGS) $(INCLUDE) bamleftalign.o Fasta.o Utility.o LeftAlign.o IndelAllele.o split.o -o ../bin/bamleftalign $(LIBS)
+
+-bamfiltertech ../bin/bamfiltertech: $(SEQLIB_ROOT)/src/libseqlib.a $(SEQLIB_ROOT)/htslib/libhts.a bamfiltertech.o $(OBJECTS) $(HEADERS)
++bamfiltertech ../bin/bamfiltertech: bamfiltertech.o $(OBJECTS) $(HEADERS)
+ $(CXX) $(CFLAGS) $(INCLUDE) bamfiltertech.o $(OBJECTS) -o ../bin/bamfiltertech $(LIBS)
+
+
+@@ -99,7 +87,7 @@ alleles.o: alleles.cpp AlleleParser.o Al
+ dummy.o: dummy.cpp AlleleParser.o Allele.o
+ $(CXX) $(CFLAGS) $(INCLUDE) -c dummy.cpp
+
+-freebayes.o: freebayes.cpp TryCatch.h $(HTSLIB_ROOT)/libhts.a
++freebayes.o: freebayes.cpp TryCatch.h
+ $(CXX) $(CFLAGS) $(INCLUDE) -c freebayes.cpp
+
+ fastlz.o: fastlz.c fastlz.h
+@@ -120,7 +108,7 @@ Genotype.o: Genotype.cpp Genotype.h Alle
+ Ewens.o: Ewens.cpp Ewens.h
+ $(CXX) $(CFLAGS) $(INCLUDE) -c Ewens.cpp
+
+-AlleleParser.o: AlleleParser.cpp AlleleParser.h multichoose.h Parameters.h $(HTSLIB_ROOT)/libhts.a
++AlleleParser.o: AlleleParser.cpp AlleleParser.h multichoose.h Parameters.h
+ $(CXX) $(CFLAGS) $(INCLUDE) -c AlleleParser.cpp
+
+ Utility.o: Utility.cpp Utility.h Sum.h Product.h
+@@ -168,7 +156,7 @@ bamleftalign.o: bamleftalign.cpp LeftAli
+ bamfiltertech.o: bamfiltertech.cpp
+ $(CXX) $(CFLAGS) $(INCLUDE) -c bamfiltertech.cpp
+
+-LeftAlign.o: LeftAlign.h LeftAlign.cpp $(HTSLIB_ROOT)/libhts.a
++LeftAlign.o: LeftAlign.h LeftAlign.cpp
+ $(CXX) $(CFLAGS) $(INCLUDE) -c LeftAlign.cpp
+
+ IndelAllele.o: IndelAllele.cpp IndelAllele.h
diff --git a/debian/patches/use_debian_packaged_vcflib.patch b/debian/patches/use_debian_packaged_vcflib.patch
index dd907a8..dc36617 100644
--- a/debian/patches/use_debian_packaged_vcflib.patch
+++ b/debian/patches/use_debian_packaged_vcflib.patch
@@ -4,45 +4,46 @@ Description: vcflib needs to be packaged separately
--- a/src/Makefile
+++ b/src/Makefile
-@@ -12,10 +12,8 @@ C=gcc
- CFLAGS=-O3 -D_FILE_OFFSET_BITS=64 -g
+@@ -13,12 +13,9 @@ CFLAGS=-O3 -D_FILE_OFFSET_BITS=64 -g
#CFLAGS=-O3 -static -D VERBOSE_DEBUG # enables verbose debugging via --debug2
+ SEQLIB_ROOT=../SeqLib
-VCFLIB_ROOT=../vcflib
--
--LIBS = -L./ -L$(VCFLIB_ROOT)/tabixpp/ -lbamtools -ltabixpp -lz -lm
--INCLUDE = -I/usr/include/bamtools -I../ttmath -I$(VCFLIB_ROOT)/src -I$(VCFLIB_ROOT)/
-+LIBS = -lbamtools -ltabixpp -lz -lm -lvcflib `pkg-config --libs libsmithwaterman`
-+INCLUDE = -I/usr/include/bamtools -I../ttmath -I/usr/include/vcflib -I/usr/include/intervaltree `pkg-config --cflags libsmithwaterman` -ldisorder
+-TABIX_ROOT=$(VCFLIB_ROOT)/tabixpp
+-HTSLIB_ROOT=$(TABIX_ROOT)/htslib
+
+-LIBS = -lbamtools -ltabixpp -lz -lm -lpthread
+-INCLUDE = -I../ttmath -I/usr/include/bamtools -I$(VCFLIB_ROOT)/src/ -I$(TABIX_ROOT)/ -I$(VCFLIB_ROOT)/smithwaterman/ -I$(VCFLIB_ROOT)/multichoose/ -I$(VCFLIB_ROOT)/filevercmp/ -I$(HTSLIB_ROOT) -I$(SEQLIB_ROOT) -I$(SEQLIB_ROOT)/htslib
++LIBS = -lbamtools -ltabixpp -lz -lm -lpthread `pkg-config --libs libvcflib`
++INCLUDE = -I../ttmath -I/usr/include/bamtools `pkg-config --cflags libvcflib` -I$(SEQLIB_ROOT) -I$(SEQLIB_ROOT)/htslib
all: autoversion ../bin/freebayes ../bin/bamleftalign
-@@ -57,15 +55,7 @@ OBJECTS=BedReader.o \
- Bias.o \
+@@ -66,14 +63,6 @@ OBJECTS=BedReader.o \
Contamination.o \
NonCall.o \
-- SegfaultHandler.o \
+ SegfaultHandler.o \
- ../vcflib/tabixpp/tabix.o \
-- ../vcflib/tabixpp/bgzf.o \
+- ../vcflib/tabixpp/htslib/bgzf.o \
- ../vcflib/smithwaterman/SmithWatermanGotoh.o \
-- ../vcflib/smithwaterman/disorder.c \
+- ../vcflib/smithwaterman/disorder.cpp \
- ../vcflib/smithwaterman/LeftAlign.o \
- ../vcflib/smithwaterman/Repeats.o \
- ../vcflib/smithwaterman/IndelAllele.o \
-- Variant.o
-+ SegfaultHandler.o
-
- HEADERS=multichoose.h version_git.h
-
-@@ -173,17 +163,6 @@ LeftAlign.o: LeftAlign.h LeftAlign.cpp
+- Variant.o \
+ $(SEQLIB_ROOT)/src/libseqlib.a \
+ $(SEQLIB_ROOT)/bwa/libbwa.a \
+ $(SEQLIB_ROOT)/fermi-lite/libfml.a \
+@@ -185,18 +174,6 @@ LeftAlign.o: LeftAlign.h LeftAlign.cpp $
IndelAllele.o: IndelAllele.cpp IndelAllele.h
$(CXX) $(CFLAGS) $(INCLUDE) -c IndelAllele.cpp
-Variant.o: $(VCFLIB_ROOT)/src/Variant.h $(VCFLIB_ROOT)/src/Variant.cpp
- $(CXX) $(CFLAGS) $(INCLUDE) -c $(VCFLIB_ROOT)/src/Variant.cpp
-
--../vcflib/tabixpp/tabix.o: ../vcflib/tabixpp/tabix.hpp ../vcflib/tabixpp/tabix.cpp
--../vcflib/tabixpp/bgzf.o: ../vcflib/tabixpp/bgzf.c ../vcflib/tabixpp/bgzf.h
+-../vcflib/tabixpp/tabix.o:
+- cd $(TABIX_ROOT)/ && make
+-../vcflib/tabixpp/htslib/bgzf.o: ../vcflib/tabixpp/htslib/bgzf.c ../vcflib/tabixpp/htslib/htslib/bgzf.h
- cd ../vcflib/tabixpp && $(MAKE)
-
-../vcflib/smithwaterman/SmithWatermanGotoh.o: ../vcflib/smithwaterman/SmithWatermanGotoh.h ../vcflib/smithwaterman/SmithWatermanGotoh.cpp
@@ -52,11 +53,13 @@ Description: vcflib needs to be packaged separately
VERSION_FILE=./version_git.h
RELEASED_VERSION_FILE=./version_release.txt
-@@ -257,5 +236,4 @@ autoversion:
+@@ -269,6 +246,5 @@ autoversion:
+
clean:
- rm -rf *.o *.cgh *~ freebayes alleles ../bin/freebayes ../bin/alleles ../vcflib/*.o ../vcflib/tabixpp/*.{o,a}
+- rm -rf *.o *.cgh *~ freebayes alleles ../bin/freebayes ../bin/alleles ../vcflib/*.o ../vcflib/tabixpp/*.{o,a}
- cd ../vcflib/smithwaterman && make clean
++ rm -rf *.o *.cgh *~ freebayes alleles ../bin/freebayes ../bin/alleles
--- a/Makefile
+++ b/Makefile
@@ -66,227 +69,3 @@ Description: vcflib needs to be packaged separately
cd src && $(MAKE)
log: src/version_git.h
---- a/src/AlleleParser.cpp
-+++ b/src/AlleleParser.cpp
-@@ -485,7 +485,7 @@ void AlleleParser::setupVCFInput(void) {
- // variant input for analysis and targeting
- if (!parameters.variantPriorsFile.empty()) {
- variantCallInputFile.open(parameters.variantPriorsFile);
-- currentVariant = new vcf::Variant(variantCallInputFile);
-+ currentVariant = new vcflib::Variant(variantCallInputFile);
- usingVariantInputAlleles = true;
-
- // get sample names from VCF input file
-@@ -1108,7 +1108,7 @@ void AlleleParser::updateHaplotypeBasisA
- pos + referenceLength + CACHED_BASIS_HAPLOTYPE_WINDOW + 1)) {
- //cerr << "the vcf line " << haplotypeVariantInputFile.line << endl;
- // get the variants in the target region
-- vcf::Variant var(haplotypeVariantInputFile);
-+ vcflib::Variant var(haplotypeVariantInputFile);
- while (haplotypeVariantInputFile.getNextVariant(var)) {
- //cerr << "input variant: " << var << endl;
-
-@@ -1122,9 +1122,9 @@ void AlleleParser::updateHaplotypeBasisA
- }
- */
-
-- map<string, vector<vcf::VariantAllele> > variants = var.parsedAlternates();
-- for (map<string, vector<vcf::VariantAllele> >::iterator a = variants.begin(); a != variants.end(); ++a) {
-- for (vector<vcf::VariantAllele>::iterator v = a->second.begin(); v != a->second.end(); ++v) {
-+ map<string, vector<vcflib::VariantAllele> > variants = var.parsedAlternates();
-+ for (map<string, vector<vcflib::VariantAllele> >::iterator a = variants.begin(); a != variants.end(); ++a) {
-+ for (vector<vcflib::VariantAllele>::iterator v = a->second.begin(); v != a->second.end(); ++v) {
- //cerr << v->ref << "/" << v->alt << endl;
- if (v->ref != v->alt) {
- //cerr << "basis allele " << v->position << " " << v->ref << "/" << v->alt << endl;
-@@ -2107,7 +2107,7 @@ void AlleleParser::getInputVariantsInReg
- if (!usingVariantInputAlleles) return;
-
- // get the variants in the target region
-- vcf::Variant var(variantCallInputFile);
-+ vcflib::Variant var(variantCallInputFile);
- if (!seq.empty()) {
- variantCallInputFile.setRegion(seq, start, end);
- }
-@@ -2117,10 +2117,10 @@ void AlleleParser::getInputVariantsInReg
- long int pos = currentVariant->position - 1;
- // get alternate alleles
- bool includePreviousBaseForIndels = true;
-- map<string, vector<vcf::VariantAllele> > variantAlleles = currentVariant->parsedAlternates();
-+ map<string, vector<vcflib::VariantAllele> > variantAlleles = currentVariant->parsedAlternates();
- // TODO this would be a nice option: why does it not work?
-- //map<string, vector<vcf::VariantAllele> > variantAlleles = currentVariant->flatAlternates();
-- vector< vector<vcf::VariantAllele> > orderedVariantAlleles;
-+ //map<string, vector<vcflib::VariantAllele> > variantAlleles = currentVariant->flatAlternates();
-+ vector< vector<vcflib::VariantAllele> > orderedVariantAlleles;
- for (vector<string>::iterator a = currentVariant->alt.begin(); a != currentVariant->alt.end(); ++a) {
- orderedVariantAlleles.push_back(variantAlleles[*a]);
- }
-@@ -2128,14 +2128,14 @@ void AlleleParser::getInputVariantsInReg
- vector<Allele> genotypeAlleles;
- set<long int> alternatePositions;
-
-- for (vector< vector<vcf::VariantAllele> >::iterator g = orderedVariantAlleles.begin(); g != orderedVariantAlleles.end(); ++g) {
-+ for (vector< vector<vcflib::VariantAllele> >::iterator g = orderedVariantAlleles.begin(); g != orderedVariantAlleles.end(); ++g) {
-
-- vector<vcf::VariantAllele>& altAllele = *g;
-+ vector<vcflib::VariantAllele>& altAllele = *g;
-
- vector<Allele> alleles;
-
-- for (vector<vcf::VariantAllele>::iterator v = altAllele.begin(); v != altAllele.end(); ++v) {
-- vcf::VariantAllele& variant = *v;
-+ for (vector<vcflib::VariantAllele>::iterator v = altAllele.begin(); v != altAllele.end(); ++v) {
-+ vcflib::VariantAllele& variant = *v;
- long int allelePos = variant.position - 1;
- AlleleType type;
- string alleleSequence = variant.alt;
-@@ -2240,7 +2240,7 @@ void AlleleParser::updateInputVariants(l
- if (gotRegion) {
-
- // get the variants in the target region
-- vcf::Variant var(variantCallInputFile);
-+ vcflib::Variant var(variantCallInputFile);
- bool ok;
- while (ok = variantCallInputFile.getNextVariant(*currentVariant)) {
-
-@@ -2248,10 +2248,10 @@ void AlleleParser::updateInputVariants(l
- long int pos = currentVariant->position - 1;
- // get alternate alleles
- bool includePreviousBaseForIndels = true;
-- map<string, vector<vcf::VariantAllele> > variantAlleles = currentVariant->parsedAlternates();
-+ map<string, vector<vcflib::VariantAllele> > variantAlleles = currentVariant->parsedAlternates();
- // TODO this would be a nice option: why does it not work?
-- //map<string, vector<vcf::VariantAllele> > variantAlleles = currentVariant->flatAlternates();
-- vector< vector<vcf::VariantAllele> > orderedVariantAlleles;
-+ //map<string, vector<vcflib::VariantAllele> > variantAlleles = currentVariant->flatAlternates();
-+ vector< vector<vcflib::VariantAllele> > orderedVariantAlleles;
- for (vector<string>::iterator a = currentVariant->alt.begin(); a != currentVariant->alt.end(); ++a) {
- orderedVariantAlleles.push_back(variantAlleles[*a]);
- }
-@@ -2259,14 +2259,14 @@ void AlleleParser::updateInputVariants(l
- vector<Allele> genotypeAlleles;
- set<long int> alternatePositions;
-
-- for (vector< vector<vcf::VariantAllele> >::iterator g = orderedVariantAlleles.begin(); g != orderedVariantAlleles.end(); ++g) {
-+ for (vector< vector<vcflib::VariantAllele> >::iterator g = orderedVariantAlleles.begin(); g != orderedVariantAlleles.end(); ++g) {
-
-- vector<vcf::VariantAllele>& altAllele = *g;
-+ vector<vcflib::VariantAllele>& altAllele = *g;
-
- vector<Allele> alleles;
-
-- for (vector<vcf::VariantAllele>::iterator v = altAllele.begin(); v != altAllele.end(); ++v) {
-- vcf::VariantAllele& variant = *v;
-+ for (vector<vcflib::VariantAllele>::iterator v = altAllele.begin(); v != altAllele.end(); ++v) {
-+ vcflib::VariantAllele& variant = *v;
- long int allelePos = variant.position - 1;
- AlleleType type;
- string alleleSequence = variant.alt;
---- a/src/AlleleParser.h
-+++ b/src/AlleleParser.h
-@@ -163,9 +163,9 @@ public:
- BedReader bedReader;
-
- // VCF
-- vcf::VariantCallFile variantCallFile;
-- vcf::VariantCallFile variantCallInputFile; // input variant alleles, to target analysis
-- vcf::VariantCallFile haplotypeVariantInputFile; // input alleles which will be used to construct haplotype alleles
-+ vcflib::VariantCallFile variantCallFile;
-+ vcflib::VariantCallFile variantCallInputFile; // input variant alleles, to target analysis
-+ vcflib::VariantCallFile haplotypeVariantInputFile; // input alleles which will be used to construct haplotype alleles
-
- // input haplotype alleles
- //
-@@ -349,7 +349,7 @@ private:
-
- int currentRefID;
- BamAlignment currentAlignment;
-- vcf::Variant* currentVariant;
-+ vcflib::Variant* currentVariant;
-
- };
-
---- a/src/ResultData.cpp
-+++ b/src/ResultData.cpp
-@@ -5,8 +5,8 @@ using namespace std;
-
-
-
--vcf::Variant& Results::vcf(
-- vcf::Variant& var, // variant to update
-+vcflib::Variant& Results::vcf(
-+ vcflib::Variant& var, // variant to update
- BigFloat pHom,
- long double bestComboOddsRatio,
- //long double alleleSamplingProb,
-@@ -630,8 +630,8 @@ vcf::Variant& Results::vcf(
- }
-
-
--vcf::Variant& Results::gvcf(
-- vcf::Variant& var,
-+vcflib::Variant& Results::gvcf(
-+ vcflib::Variant& var,
- NonCalls& nonCalls,
- AlleleParser* parser) {
-
---- a/src/ResultData.h
-+++ b/src/ResultData.h
-@@ -41,8 +41,8 @@ public:
- }
- }
-
-- vcf::Variant& vcf(
-- vcf::Variant& var, // variant to update
-+ vcflib::Variant& vcf(
-+ vcflib::Variant& var, // variant to update
- BigFloat pHom,
- long double bestComboOddsRatio,
- //long double alleleSamplingProb,
-@@ -61,8 +61,8 @@ public:
- vector<string>& sequencingTechnologies,
- AlleleParser* parser);
-
-- vcf::Variant& gvcf(
-- vcf::Variant& var,
-+ vcflib::Variant& gvcf(
-+ vcflib::Variant& var,
- NonCalls& noncalls,
- AlleleParser* parser);
- };
---- a/src/freebayes.cpp
-+++ b/src/freebayes.cpp
-@@ -144,7 +144,7 @@ int main (int argc, char *argv[]) {
- || (parameters.gVCFchunk &&
- nonCalls.lastPos().second - nonCalls.firstPos().second
- > parameters.gVCFchunk))) {
-- vcf::Variant var(parser->variantCallFile);
-+ vcflib::Variant var(parser->variantCallFile);
- out << results.gvcf(var, nonCalls, parser) << endl;
- nonCalls.clear();
- }
-@@ -658,12 +658,12 @@ int main (int argc, char *argv[]) {
-
- // write the last gVCF record(s)
- if (parameters.gVCFout && !nonCalls.empty()) {
-- vcf::Variant var(parser->variantCallFile);
-+ vcflib::Variant var(parser->variantCallFile);
- out << results.gvcf(var, nonCalls, parser) << endl;
- nonCalls.clear();
- }
-
-- vcf::Variant var(parser->variantCallFile);
-+ vcflib::Variant var(parser->variantCallFile);
-
- out << results.vcf(
- var,
-@@ -696,7 +696,7 @@ int main (int argc, char *argv[]) {
- // write the last gVCF record
- if (parameters.gVCFout && !nonCalls.empty()) {
- Results results;
-- vcf::Variant var(parser->variantCallFile);
-+ vcflib::Variant var(parser->variantCallFile);
- out << results.gvcf(var, nonCalls, parser) << endl;
- nonCalls.clear();
- }
diff --git a/debian/patches/vcffirstheader.patch b/debian/patches/vcffirstheader.patch
new file mode 100644
index 0000000..070fcd0
--- /dev/null
+++ b/debian/patches/vcffirstheader.patch
@@ -0,0 +1,29 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Fri, 10 Feb 2017 09:09:35 +0100
+Description: This script was not part of the vcflib release
+ tarball but is available in Git
+ https://github.com/vcflib/vcflib/blob/master/scripts/vcffirstheader
+ Since it is used in the test suite of freebayes 1.1 it is installed
+ here as quilt patch. Once vcflib might be release including the
+ scripts directory the patch can be dropped and replaced by an according
+ symlink inside rules or by setting PATH accordingly
+
+--- /dev/null
++++ b/vcflib/scripts/vcffirstheader
+@@ -0,0 +1,16 @@
++#!/usr/bin/env python
++
++import sys
++
++header=True
++for line in sys.stdin:
++ if line.startswith('##'):
++ if header:
++ print line.strip()
++ continue
++ elif line.startswith('#'):
++ if header:
++ print line.strip()
++ header=False
++ continue
++ print line.strip()
diff --git a/debian/rules b/debian/rules
index 8045fdf..666b949 100755
--- a/debian/rules
+++ b/debian/rules
@@ -9,5 +9,9 @@ override_dh_auto_install:
override_dh_auto_test:
mkdir -p $(CURDIR)/test/bash-tap/
for bt in $(CURDIR)/debian/bash-tap/* ; do ln -s $${bt} $(CURDIR)/test/bash-tap/`basename $${bt}` ; done
- export PATH=/usr/lib/vcflib/binaries/:$(PATH) dh_auto_test && echo "Tests were running successfully"
+ ln -s $(CURDIR)/debian/test-simple-bash/lib test/test-simple-bash
+ chmod +x vcflib/scripts/vcffirstheader
+ # export PATH=/usr/lib/vcflib/binaries/:$(PATH) dh_auto_test
+ echo "Tests should be run" && PATH=/usr/lib/vcflib/binaries/:$(PATH) dh_auto_test && echo "Tests were running successfully"
rm -rf $(CURDIR)/test/bash-tap
+ rm test/test-simple-bash/lib
diff --git a/debian/test-simple-bash/lib/test-simple.bash b/debian/test-simple-bash/lib/test-simple.bash
new file mode 100644
index 0000000..dab44e7
--- /dev/null
+++ b/debian/test-simple-bash/lib/test-simple.bash
@@ -0,0 +1,110 @@
+# test-simple.bash - Simple TAP test framework for Bash
+#
+# Copyright (c) 2013 Ingy döt Net
+
+TestSimple_VERSION='0.0.1'
+
+TestSimple.init() {
+ TestSimple_plan=0
+ TestSimple_run=0
+ TestSimple_failed=0
+ TestSimple_usage='Usage: source test-simple.bash tests <number>'
+
+ if [ $# -gt 0 ]; then
+ [[ $# -eq 2 ]] && [[ "$1" == 'tests' ]] ||
+ TestSimple.die "$TestSimple_usage"
+ [[ "$2" =~ ^-?[0-9]+$ ]] ||
+ TestSimple.die 'Plan must be a number'
+ [[ $2 -gt 0 ]] ||
+ TestSimple.die 'Plan must greater then 0'
+ TestSimple_plan=$2
+ printf "1..%d\n" $TestSimple_plan
+ fi
+
+ trap TestSimple.END EXIT
+}
+
+ok() {
+ local args=("$@")
+ local last=$((${#args[@]} - 1))
+ local label=''
+ local ending_re='^]]?$'
+ let TestSimple_run=TestSimple_run+1
+ (
+ set +e
+ local rc=
+ if [[ $last -gt 0 ]] && [[ ! "${args[$last]}" =~ $ending_re ]]; then
+ label="${args[$last]}"
+ unset args[$last]
+ fi
+ if [[ ${#args[@]} -eq 1 ]] && [[ "${args[0]}" =~ ^[0-9]+$ ]]; then
+ rc=${args[0]}
+ elif [ ${args[0]} == '[[' ]; then
+ # XXX Currently need eval to support [[. Is there another way?
+ # Is [[ overkill? So many questons!
+ eval "${args[@]}" &> /dev/null
+ rc=$?
+ else
+ "${args[@]}" &> /dev/null
+ rc=$?
+ fi
+ if [ $rc -eq 0 ]; then
+ if [ -n "$label" ]; then
+ echo "ok $TestSimple_run - $label"
+ else
+ echo "ok $TestSimple_run"
+ fi
+ else
+ let TestSimple_failed=TestSimple_failed+1
+ if [ -n "$label" ]; then
+ echo "not ok $TestSimple_run - $label"
+ TestSimple.failure "$label"
+ else
+ echo "not ok $TestSimple_run"
+ TestSimple.failure "$label"
+ fi
+ fi
+ return $rc
+ )
+}
+
+TestSimple_CALL_STACK_LEVEL=1
+TestSimple.failure() {
+ local c=( $(caller $TestSimple_CALL_STACK_LEVEL) )
+ local file=${c[2]}
+ local line=${c[0]}
+ local label="$1"
+ label=${label:+"'$label'\n# at $file line $line."}
+ label=${label:-"at $file line $line."}
+ echo -e "# Failed test $label" >&2
+}
+
+TestSimple.END() {
+ for v in plan run failed; do eval local $v=\$TestSimple_$v; done
+ if [ $plan -eq 0 ]; then
+ if [ $run -gt 0 ]; then
+ echo "# Tests were run but no plan was declared." >&2
+ fi
+ else
+ if [ $run -eq 0 ]; then
+ echo "# No tests run!" >&2
+ elif [ $run -ne $plan ]; then
+ local msg="# Looks like you planned $plan tests but ran $run."
+ [ $plan -eq 1 ] && msg=${msg/tests/test}
+ echo "$msg" >&2
+ fi
+ fi
+ local exit_code=0
+ if [ $TestSimple_failed -gt 0 ]; then
+ exit_code=$TestSimple_failed
+ [ $exit_code -gt 254 ] && exit_code=254
+ local msg="# Looks like you failed $failed tests of $run run."
+ [ $TestSimple_failed -eq 1 ] && msg=${msg/tests/test}
+ echo "$msg" >&2
+ fi
+ exit $exit_code
+}
+
+TestSimple.die() { echo "$@" >&2; trap EXIT; exit 255; }
+
+[[ "${BASH_SOURCE[0]}" != "${0}" ]] && TestSimple.init "$@"
diff --git a/debian/test-simple-bash/test/basics.t b/debian/test-simple-bash/test/basics.t
new file mode 100644
index 0000000..61949ea
--- /dev/null
+++ b/debian/test-simple-bash/test/basics.t
@@ -0,0 +1,26 @@
+#!/bin/bash
+
+PATH=lib:$PATH
+source test-simple.bash tests 14
+
+ok 0 '0 is true'
+ok $((6 * 7 -42)) 'Math result is 0'
+ok true 'true is ok'
+ok $(false || true; echo $?) 'Expression expansion'
+
+ls &> /dev/null
+ok $? '$? is success'
+ls --qqq &> /dev/null
+ok $((! $?)) 'Negate $? failure'
+
+fruit=apple
+
+ok [ $fruit = apple ] '[ … ] testing works'
+ok [ "0" == "0" -a 1 -eq 1 ] '[ … -a … ] (AND) testing works'
+ok [ ${fruit/a/A} = Apple ] 'Substitution expansion works'
+ok [ "${fruit}s" = 'app''les' ] 'Quote removal works'
+ok [[ $fruit = apple ]] '[[ … ]] works'
+ok [[ $fruit == apple ]] '== works'
+ok [[ $((6 * 7)) -eq 42 ]] '-eq works with math expression'
+ok $(ls | grep lib &> /dev/null; echo $?) \
+ 'Testing a grep command works'
diff --git a/debian/test-simple-bash/test/doc.t b/debian/test-simple-bash/test/doc.t
new file mode 100644
index 0000000..7d77db7
--- /dev/null
+++ b/debian/test-simple-bash/test/doc.t
@@ -0,0 +1,15 @@
+#!/bin/bash
+
+question() { echo yes; }
+
+PATH=lib:$PATH
+source test-simple.bash tests 5
+
+ok 0 '0 is true (other numbers are false)'
+
+answer=$(question "...?")
+ok [ $answer == yes ] 'The answer is yes!'
+ok [[ $answer =~ ^y ]] 'The answer begins with y'
+
+ok true 'true is ok'
+ok '! false' '! false is true'
diff --git a/debian/test-simple-bash/test/no-label.t b/debian/test-simple-bash/test/no-label.t
new file mode 100644
index 0000000..9b58eb4
--- /dev/null
+++ b/debian/test-simple-bash/test/no-label.t
@@ -0,0 +1,25 @@
+#!/bin/bash
+
+PATH=lib:$PATH
+source test-simple.bash tests 14
+
+ok 0
+ok $((6 * 7 -42))
+ok true
+ok $(false || true; echo $?)
+
+ls &> /dev/null
+ok $?
+ls --qqq &> /dev/null
+ok $((! $?))
+
+fruit=apple
+
+ok [ $fruit = apple ]
+ok [ "0" == "0" -a 1 -eq 1 ]
+ok [ ${fruit/a/A} = Apple ]
+ok [ "${fruit}s" = 'app''les' ]
+ok [[ $fruit = apple ]]
+ok [[ $fruit == apple ]]
+ok [[ $((6 * 7)) -eq 42 ]]
+ok $(ls | grep lib &> /dev/null; echo $?)
--
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