[med-svn] [Git][med-team/blasr][master] 7 commits: Remove unused binaries from upstream source tarball
Andreas Tille
gitlab at salsa.debian.org
Mon Jan 28 15:17:03 GMT 2019
Andreas Tille pushed to branch master at Debian Med / blasr
Commits:
c4832b22 by Andreas Tille at 2019-01-28T14:55:02Z
Remove unused binaries from upstream source tarball
- - - - -
492a7e94 by Andreas Tille at 2019-01-28T14:57:13Z
DEP3
- - - - -
fed0edf9 by Andreas Tille at 2019-01-28T14:57:44Z
New upstream version 5.3.2+dfsg
- - - - -
0e378017 by Andreas Tille at 2019-01-28T14:57:44Z
Update upstream source from tag 'upstream/5.3.2+dfsg'
Update to upstream version '5.3.2+dfsg'
with Debian dir 0b31dd62aab0883e651db3160c4379f27e3a5ac3
- - - - -
1a3b1bc7 by Andreas Tille at 2019-01-28T15:06:27Z
Update manpages
- - - - -
762d4a13 by Andreas Tille at 2019-01-28T15:10:28Z
Mention tools that are not build an more in NEWS.Debian
- - - - -
f68cf4ca by Andreas Tille at 2019-01-28T15:13:54Z
Upload to unstable
- - - - -
21 changed files:
- debian/NEWS → debian/NEWS.Debian
- debian/TODO
- debian/blasr.1
- debian/changelog
- debian/copyright
- + debian/createmanpages
- debian/docs
- debian/manpages
- debian/loadPulses.1 → debian/old_manpages/loadPulses.1
- debian/pls2fasta.1 → debian/old_manpages/pls2fasta.1
- debian/samFilter.1 → debian/old_manpages/samFilter.1
- debian/samtoh5.1 → debian/old_manpages/samtoh5.1
- debian/samtom4.1 → debian/old_manpages/samtom4.1
- debian/sdpMatcher.1 → debian/old_manpages/sdpMatcher.1
- debian/toAfg.1 → debian/old_manpages/toAfg.1
- debian/patches/use_debian_packaged_pblibs.patch
- debian/sawriter.1
- debian/watch
- − tools/Darwin/clang-format
- − tools/Linux/clang-format
- − tools/win32/clang-format.exe
Changes:
=====================================
debian/NEWS → debian/NEWS.Debian
=====================================
@@ -1,3 +1,19 @@
+blasr (5.3.2+dfsg-1) unstable; urgency=medium
+
+ The following tools are not build by the default build process any more:
+
+ loadPulses
+ pls2fasta
+ samFilter
+ samtoh5
+ samtom4
+ sdpMatcher
+ toAfg
+
+ Please contact the Debian Maintainer if you really need these.
+
+ -- Andreas Tille <tille at debian.org> Mon, 28 Jan 2019 16:07:16 +0100
+
blasr (5.3-1) unstable; urgency=medium
The blasr command line interface has changed. Long options are now
=====================================
debian/TODO
=====================================
@@ -1,5 +1 @@
-* Test the get-orig-source script
-
-* Update manpages
-
* run test suite for bax2bam and bam2bax
=====================================
debian/blasr.1
=====================================
@@ -1,34 +1,27 @@
-.TH BLASR "1" "July 2015" "blasr 3ca7fe8" "User Commands"
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.8.
+.TH BLASR "1" "January 2019" "blasr 5.3.2" "User Commands"
.SH NAME
-blasr \- Map SMRT Sequences to a reference genome.
+blasr \- Map SMRT Sequences to a reference genome
.SH SYNOPSIS
-.P
.B blasr
-.I reads.bam
-.I genome.fasta \fB\-bam \-out\fI out.bam
+reads.bam genome.fasta \fB\-\-bam\fR \fB\-\-out\fR out.bam
.P
.B blasr
-.I reads.fasta
-.I genome.fasta
+reads.fasta genome.fasta
.P
.B blasr
-.I reads.fasta
-.I genome.fasta \fB\-sa\fI genome.fasta.sa
+reads.fasta genome.fasta \fB\-\-sa\fR genome.fasta.sa
.P
.B blasr
-.I reads.bax.h5
-.I genome.fasta \fR[\fB\-sa \fIgenome.fasta.sa\fR]
+reads.bax.h5 genome.fasta [\-\-sa genome.fasta.sa]
.P
.B blasr
-.I reads.bax.h5
-.I genome.fasta \fB\-sa\fI genome.fasta.sa \fB\-maxScore\fR \-100 \fB\-minMatch\fR 15 ...
+reads.bax.h5 genome.fasta \fB\-\-sa\fR genome.fasta.sa \fB\-\-maxScore\fR 100 \fB\-\-minMatch\fR 15 ...
.P
.B blasr
-.I reads.bax.h5
-.I genome.fasta \fB\-sa\fI genome.fasta.sa \fB\-nproc\fR 24 \fB\-out\fI alignment.out\fR ...
+reads.bax.h5 genome.fasta \fB\-\-sa\fR genome.fasta.sa \fB\-\-nproc\fR 24 \fB\-\-out\fR alignment.out ...
.SH DESCRIPTION
-.P
-\fBblasr\fR is a read mapping program that maps reads to positions
+blasr is a read mapping program that maps reads to positions
in a genome by clustering short exact matches between the read and
the genome, and scoring clusters using alignment. The matches are
generated by searching all suffixes of a read against the genome
@@ -42,21 +35,19 @@ precomputed suffix array index on the reference sequence is
specified.
.P
Although reads may be input in FASTA format, the recommended input is
-PacBio BAM files because these contain qualtiy value
+PacBio BAM files because these contain quality value
information that is used in the alignment and produces higher quality
variant detection.
Although alignments can be output in various formats, the recommended
output format is PacBio BAM.
-Support for bax.h5 and plx.h5 files will be \fBDEPRECATED\fR.
-Support for region tables for h5 files will be \fBDEPRECATED\fR.
+Support to bax.h5 and plx.h5 files will be DEPRECATED.
+Support to region tables for h5 files will be DEPRECATED.
.P
When suffix array index of a genome is not specified, the suffix array is
-built before producing alignment. This may be prohibitively slow
-when the genome is large (e.g. Human). It is best to precompute the
-suffix array of a genome using the program
-.BR sawriter (1),
-and then specify the suffix array on the command line using
-\fB\-sa\fR genome.fa.sa.
+built before producing alignment. This may be prohibitively slow
+when the genome is large (e.g. Human). It is best to precompute the
+suffix array of a genome using the program sawriter, and then specify
+the suffix array on the command line using \fB\-sa\fR genome.fa.sa.
.P
The optional parameters are roughly divided into three categories:
control over anchoring, alignment scoring, and output.
@@ -70,367 +61,10 @@ possibly decreasing sensitivity.
.P
Regions that are too repetitive may be ignored during mapping by
limiting the number of positions a read maps to with the
-\fB\-maxAnchorsPerPosition\fR option. Values between 500 and 1000 are effective
+\fB\-maxAnchorsPerPosition\fR option. Values between 500 and 1000 are effective
in the human genome.
.P
For small genomes such as bacterial genomes or BACs, the default parameters
are sufficient for maximal sensitivity and good speed.
-.SH OPTIONS
-.TP
-.B Input Files
-.RS
-.TP
-.B Reads
-.RS
-.TP
-.I reads.bam
-A PacBio BAM file of reads.
-This is the preferred input to \fBblasr\fR because rich quality
-value (insertion,deletion, and substitution quality values) information is
-maintained. The extra quality information improves variant detection and mapping speed.
-.TP
-.I reads.fasta
-A multi\-fasta file of reads, though any fasta file is valid input
-.TP
-.IR reads.bax.h5 | reads.plx.h5
-the old \fBDEPRECATED\fR output format of SMRT reads.
-.TP
-.I input.fofn
-File of file names
-.RE
-.TP
-\fB\-sa\fI suffixArrayFile
-Use the suffix array 'sa' for detecting matches between the reads and the
-reference.
-The suffix array has been prepared by the \fBsawriter\fR(1) program.
-.TP
-\fB\-ctab\fI tab
-A table of tuple counts used to estimate match significance.
-This is by the program 'printTupleCountTable'.
-While it is quick to generate on the fly, if there are many invocations of
-\fBblasr\fR, it is useful to precompute the ctab.
-.TP
-\fB\-regionTable\fI table\fR (\fBDEPRECATED\fR)
-Read in a read-region table in HDF format for masking portions of reads.
-This may be a single table if there is just one input file,
-or a fofn. When a region table is specified, any region table inside
-the reads.plx.h5 or reads.bax.h5 files are ignored.
-.RE
-.B (DEPRECATED) Options for modifying reads.
-.RS
-.P
-There is ancilliary information about substrings of reads
-that is stored in a 'region table' for each read file. Because
-HDF is used, the region table may be part of the .bax.h5 or .plx.h5 file,
-or a separate file. A contiguously read substring from the template
-is a subread, and any read may contain multiple subreads. The boundaries
-of the subreads may be inferred from the region table either directly or
-by definition of adapter boundaries. Typically region tables also
-contain information for the location of the high and low quality regions of
-reads. Reads produced by spurious reads from empty ZMWs have a high
-quality start coordinate equal to high quality end, making no usable read.
-.TP
-\fB\-useccs\fR
-Align the circular consensus sequence (ccs), then report alignments
-of the ccs subreads to the window that the ccs was mapped to.
-Only alignments of the subreads are reported.
-.TP
-\fB\-useccsall\fR
-Similar to \fB\-useccs\fR, except all subreads are aligned, rather than just
-the subreads used to call the ccs. This will include reads that only
-cover part of the template.
-.TP
-\fB\-useccsdenovo\fR
-Align the circular consensus, and report only the alignment of the ccs
-sequence.
-.TP
-\fB\-noSplitSubreads\fR (false)
-Do not split subreads at adapters. This is typically only
-useful when the genome in an unrolled version of a known template, and
-contains template-adapter-reverse_template sequence.
-.TP
-\fB\-ignoreRegions\fR (false)
-Ignore any information in the region table.
-.TP
-\fB\-ignoreHQRegions\fR (false)
-Ignore any hq regions in the region table.
-.RE
-.B Alignments To Report
-.RS
-.TP
-\fB\-bestn\fI n \fR(10)
-Report the top \fIn\fR alignments.
-.TP
-\fB\-hitPolicy\fR (all)
-Specify a policy to treat multiple hits from [all, allbest, random, randombest, leftmost]
-.RS
-.TP
-.I all
-report all alignments.
-.TP
-.I allbest
-report all equally top scoring alignments.
-.TP
-.I random
-report a random alignment.
-.TP
-.I randombest
-report a random alignment from multiple equally top scoring alignments.
-.TP
-.I leftmost
-report an alignment which has the best alignmentscore and has the smallest mapping coordinate in any reference.
-.RE
-.TP
-\fB\-placeRepeatsRandomly\fR (false)
-\fBDEPRECATED!\fR If true, equivalent to \fB\-hitPolicy\fI randombest\fR.
-.TP
-\fB\-randomSeed\fR (0)
-Seed for random number generator. By default (0), use current time as seed.
-.TP
-\fB\-noSortRefinedAlignments\fR (false)
-Once candidate alignments are generated and scored via sparse dynamic
-programming, they are rescored using local alignment that accounts
-for different error profiles.
-Resorting based on the local alignment may change the order the hits are returned.
-.TP
-\fB\-allowAdjacentIndels\fR
-When specified, adjacent insertion or deletions are allowed. Otherwise, adjacent
-insertion and deletions are merged into one operation. Using quality values
-to guide pairwise alignments may dictate that the higher probability alignment
-contains adjacent insertions or deletions.
-Current tools such as GATK do not permit this and so they are not reported by
-default.
-.RE
-.B Output Formats and Files
-.RS
-.TP
-\fB\-out\fI out \fR(terminal)
-Write output to \fIout\fR.
-.TP
-\fB\-sam\fR
-Write output in SAM format.
-.TP
-\fB\-m\fI t
-If not printing SAM, modify the output of the alignment.
-.TP
-When \fIt\fR is:
-.RS
-.TP
-0
-Print blast like output with |'s connecting matched nucleotides.
-.TP
-1
-Print only a summary: score and pos.
-.TP
-2
-Print in Compare.xml format.
-.TP
-3
-Print in vulgar format (\fBDEPRECATED\fR).
-.TP
-4
-Print a longer tabular version of the alignment.
-.TP
-5
-Print in a machine\-parsable format that is read by compareSequences.py.
-.RE
-.TP
-\fB\-header\fR
-Print a header as the first line of the output file describing the contents of each column.
-.TP
-\fB\-titleTable\fI tab \fR(NULL)
-Construct a table of reference sequence titles.
-The reference sequences are enumerated by row, 0,1,...
-The reference index is printed in alignment results rather than the full
-reference name.
-This makes output concise, particularly whenvery verbose titles exist in
-reference names.
-.TP
-\fB\-unaligned\fI file
-Output reads that are not aligned to \fIfile\fR
-.TP
-.IR \fB\-clipping\fI \0[ none | hard | subread | soft ] \0\fR(none)
-.IP
-Use no/hard/subread/soft clipping, ONLY for SAM/BAM output.
-.TP
-\fB\-printSAMQV\fR (false)
-Print quality values to SAM output.
-.TP
-\fB\-cigarUseSeqMatch\fR (false)
-CIGAR strings in SAM/BAM output use '=' and 'X' to represent sequence match and mismatch instead of 'M'.
-.RE
-.B Options for anchoring alignment regions.
-.RS
-.P
-This will have the greatest effect on speed and sensitivity.
-.TP
-\fB\-minMatch\fI m \fR(12)
-Minimum seed length.
-Higher minMatch will speed up alignment, but decrease sensitivity.
-.TP
-\fB\-maxMatch\fI l \fR(inf)
-Stop mapping a read to the genome when the lcp length reaches \fIl\fR.
-This is useful when the query is part of the reference, for example when
-constructing pairwise alignments for de novo assembly.
-.TP
-\fB\-maxLCPLength\fI l \fR(inf)
-The same as \fB\-maxMatch\fR.
-.TP
-\fB\-maxAnchorsPerPosition\fI m \fR(10000)
-Do not add anchors from a position if it matches to more than \fIm\fR locations in the target.
-.TP
-\fB\-advanceExactMatches\fI E \fR(0)
-Another trick for speeding up alignments with match \- E fewer anchors.
-Rather than finding anchors between the read and the genome at every position
-in the read, when an anchor is found at position i in a read of length L, the
-next position in a read to find an anchor is at i+L\-E.
-Use this when alignining already assembled contigs.
-.TP
-\fB\-nCandidates\fI n \fR(10)
-Keep up to \fIn\fR candidates for the best alignment.
-A large value of n will slow mapping because the slower dynamic programming
-steps are applied to more clusters of anchors which can be a rate limiting
-step when reads are very long.
-.TP
-\fB\-concordant\fR (false)
-Map all subreads of a zmw (hole) to where the longest full pass subread of
-the zmw aligned to. This requires to use the region table and hq regions.
-This option only works when reads are in base or pulse h5 format.
-.TP
-\fB\-concordantTemplate\fR (mediansubread)
-Select a full pass subread of a zmw as template for concordant mapping.
-longestsubread - use the longest full pass subread
-mediansubread - use the median length full pass subread
-typicalsubread - use the second longest full pass subread if length of
-the longest full pass subread is an outlier
-.TP
-\fB\-fastMaxInterval\fR (false)
-Fast search maximum increasing intervals as alignment candidates. The search
-is not as exhaustive as the default, but is much faster.
-.TP
-\fB\-aggressiveIntervalCut\fR (false)
-Agreesively filter out non-promising alignment candidates, if there
-exists at least one promising candidate. If this option is turned on,
-\fBblasr\fR is likely to ignore short alignments of ALU elements.
-.TP
-\fB\-fastSDP\fR (false)
-Use a fast heuristic algorithm to speed up sparse dynamic programming.
-.RE
-.B Options for Refining Hits
-.RS
-.TP
-\fB\-sdpTupleSize\fI K \fR(11)
-Use matches of length \fIK\fR to speed dynamic programming alignments.
-This controls
-accuracy of assigning gaps in pairwise alignments once a mapping has been found,
-rather than mapping sensitivity itself.
-.TP
-\fB\-scoreMatrix\fI score matrix string
-Specify an alternative score matrix for scoring fasta reads.
-The matrix is in the format
-.TS
-;
-L L L L L L .
- A C G T N
-A a b c d e
-C f g h i j
-G k l m n o
-T p q r s t
-N u v w x y
-.TE
-
-The values a...y should be input as a quoted space separated
-string: "a b c ... y". Lowerf scores are better, so matches should be less
-than mismatches e.g. a,g,m,s = \-5 (match), mismatch = 6.
-.TP
-\fB\-affineOpen\fI value\fR (10)
-Set the penalty for opening an affine alignment.
-.TP
-\fB\-affineExtend\fI a \fR(0)
-Change affine (extension) gap penalty. Lower value allows more gaps.
-.RE
-.B Options for overlap/dynamic programming alignments and pairwise overlap for de novo assembly.
-.RS
-.TP
-\fB\-useQuality\fR (false)
-Use substitution/insertion/deletion/merge quality values to score gap and
-mismatch penalties in pairwise alignments. Because the insertion and deletion
-rates are much higher than substitution, this will make many alignments
-favor an insertion/deletion over a substitution.nNaive consensus calling methods
-will then often miss substitution polymorphisms. This option should be
-used when calling consensus using the Quiver method. Furthermore, when
-not using quality values to score alignments, there will be a lower consensus
-accuracy in homolymer regions.
-.TP
-\fB\-affineAlign\fR (false)
-Refine alignment using affine guided align.
-.RE
-.B Options for filtering reads and alignments
-.RS
-.TP
-\fB\-minReadLength\fI l\fR (50)
-Skip reads that have a full length less than \fIl\fR. Subreads may be shorter.
-.TP
-\fB\-minSubreadLength \fIl \fR(0)
-Do not align subreads of length less than \fIl\fR.
-.TP
-\fB\-minRawSubreadScore \fIm \fR(0)
-Do not align subreads whose quality score in region table is less than \fIm\fR
-(quality scores should be in range [0, 1000]).
-.TP
-\fB\-maxScore\fI m \fR(\-200)
-Maximum score to output (high is bad, negative good).
-.TP
-\fB\-minAlnLength\fR
-(0) Report alignments only if their lengths are greater than minAlnLength.
-.HP
-\fB\-minPctSimilarity\fR
-(0) Report alignments only if their percentage similairty is greater than minPctSimilarity.
-.TP
-\fB\-minPctAccuracy\fR
-(0) Report alignments only if their percentage accuray is greater than minAccuracy.
-.RE
-.B Options for parallel alignment
-.RS
-.TP
-\fB\-nproc\fI N \fR(1)
-Align using \fIN\fR processes. All large data structures such as the suffix array and tuple count table are shared.
-.TP
-\fB\-start\fI S \fR(0)
-Index of the first read to begin aligning.
-This is useful when multiple instances are running on the same data,
-for example when on a multi-rack cluster.
-.TP
-\fB\-stride\fI S \fR(1)
-Align one read every \fIS\fR reads.
-.RE
-.B Options for subsampling reads.
-.RS
-.TP
-\fB\-subsample\fR (0)
-Proportion of reads to randomly subsample (expressed as a decimal) and align.
-.TP
-\fB\-holeNumbers\fI LIST
-When specified, only align reads whose ZMW hole numbers are in \fILIST\fR.
-\fILIST\fR is a comma-delimited string of ranges, such as '1,2,3,10\-13'.
-This option only works when reads are in bam, bax.h5 or plx.h5 format.
-.RE
-.TP
-\fB\-h\fR
-Print help information.
-.SH CITATION
-To cite BLASR, please use: Chaisson M.J., and Tesler G., Mapping
-single molecule sequencing reads using Basic Local Alignment with
-Successive Refinement (BLASR): Theory and Application, BMC
-Bioinformatics 2012, 13:238.
-.SH BUGS
-Please report any bugs to \fIhttps://github.com/PacificBiosciences/blasr/issues\fR.
-.SH SEE ALSO
-.BR loadPulses (1)
-.BR pls2fasta (1)
-.BR samFilter (1)
-.BR samtoh5 (1)
-.BR samtom4 (1)
-.BR sawriter (1)
-.BR sdpMatcher (1)
-.BR toAfg (1)
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
=====================================
debian/changelog
=====================================
@@ -1,4 +1,4 @@
-blasr (5.3.2-1) UNRELEASED; urgency=medium
+blasr (5.3.2+dfsg-1) unstable; urgency=medium
* Team upload
@@ -13,11 +13,13 @@ blasr (5.3.2-1) UNRELEASED; urgency=medium
* Build system switched from cmake to meson
* Versioned Build-Depends: libblasr-dev
* Cleanup d/rules
+ * Update manpages
+ * Mention tools that are not build an more in NEWS.Debian
[ Jelmer Vernooij ]
* Use secure copyright file specification URI.
- -- Andreas Tille <tille at debian.org> Tue, 21 Aug 2018 16:37:31 +0200
+ -- Andreas Tille <tille at debian.org> Mon, 28 Jan 2019 16:10:36 +0100
blasr (5.3+0-2) unstable; urgency=low
=====================================
debian/copyright
=====================================
@@ -2,6 +2,9 @@ Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: blasr
Upstream-Contact: Pacific Biosciences <devnet at pacificbiosciences.com>
Source: https://github.com/PacificBiosciences/blasr
+Files-Excluded: */Darwin
+ */Linux
+ */win32
Files: *
Copyright: 2011-2016 Pacific Biosciences of California, Inc.
=====================================
debian/createmanpages
=====================================
@@ -0,0 +1,33 @@
+#!/bin/sh
+MANDIR=debian
+mkdir -p $MANDIR
+
+VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'`
+NAME=`grep "^Description:" debian/control | sed 's/^Description: *//' | head -n1`
+PROGNAME=`grep "^Package:" debian/control | sed 's/^Package: *//' | head -n1`
+
+AUTHOR=".SH AUTHOR\nThis manpage was written by $DEBFULLNAME for the Debian distribution and
+can be used for any other usage of the program.
+"
+
+# If program name is different from package name or title should be
+# different from package short description change this here
+progname=${PROGNAME}
+help2man --no-info --no-discard-stderr \
+ --name="Map SMRT Sequences to a reference genome" \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=sawriter
+help2man --no-info --no-discard-stderr --help-option=" " \
+ --name="generate suffix arrays for nucleotide sequences" \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+echo "$MANDIR/*.1" > debian/manpages
+
+cat <<EOT
+Please enhance the help2man output.
+The following web page might be helpful in doing so:
+ http://liw.fi/manpages/
+EOT
=====================================
debian/docs
=====================================
@@ -1 +1,2 @@
README*
+debian/NEWS*
=====================================
debian/manpages
=====================================
@@ -1,9 +1 @@
-debian/blasr.1
-debian/loadPulses.1
-debian/pls2fasta.1
-debian/samFilter.1
-debian/samtoh5.1
-debian/samtom4.1
-debian/sawriter.1
-debian/sdpMatcher.1
-debian/toAfg.1
+debian/*.1
=====================================
debian/loadPulses.1 → debian/old_manpages/loadPulses.1
=====================================
=====================================
debian/pls2fasta.1 → debian/old_manpages/pls2fasta.1
=====================================
=====================================
debian/samFilter.1 → debian/old_manpages/samFilter.1
=====================================
=====================================
debian/samtoh5.1 → debian/old_manpages/samtoh5.1
=====================================
=====================================
debian/samtom4.1 → debian/old_manpages/samtom4.1
=====================================
=====================================
debian/sdpMatcher.1 → debian/old_manpages/sdpMatcher.1
=====================================
=====================================
debian/toAfg.1 → debian/old_manpages/toAfg.1
=====================================
=====================================
debian/patches/use_debian_packaged_pblibs.patch
=====================================
@@ -1,3 +1,7 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Mon, 28 Jan 2019 15:56:26 +0100
+Description: Add some missing libraries to linker
+
--- a/meson.build
+++ b/meson.build
@@ -51,15 +51,19 @@ blasr_thread_dep = dependency('threads',
@@ -23,13 +27,3 @@
########################
# sources + executable #
-@@ -110,7 +114,8 @@ blasr_main = executable(
- install : true,
- dependencies : blasr_deps,
- link_with : blasr_static_impl,
-- cpp_args : [blasr_warning_flags, '-DUSE_PBBAM=1', '-DCMAKE_BUILD=1'])
-+ cpp_args : [blasr_warning_flags, '-DUSE_PBBAM=1', '-DCMAKE_BUILD=1'],
-+)
-
- blasr_utils_sawriter = executable(
- 'sawriter', files([
=====================================
debian/sawriter.1
=====================================
@@ -1,60 +1,43 @@
-.TH SAWRITER "1" "July 2015" "sawriter 3ca7fe8" "User Commands"
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.8.
+.TH SAWRITER "1" "January 2019" "sawriter 5.3.2" "User Commands"
.SH NAME
sawriter \- generate suffix arrays for nucleotide sequences
.SH SYNOPSIS
.B sawriter
-.I saOut \0fastaIn
-.RI [ fastaIn2
-.IR fastaIn3 \0...]
-.RB [ \-blt
-.IR p ]
-.RB [ \-4bit ]
-.RB [ \-larsson | \-manmy | \-kar | \-mafe | \-welter ]
+saOut fastaIn [fastaIn2 fastaIn3 ...] [\-blt p] [\-larsson] [\-4bit] [\-manmy] [\-kar]
.P
.B sawriter
-.I fastaIn \fR(writes to fastaIn.sa)
+fastaIn (writes to fastIn.sa).
.SH OPTIONS
-.TP
-.BI \-blt \0p
-Build a lookup table on prefixes of length \fIp\fR. This speeds
+\fB\-blt\fR p Build a lookup table on prefixes of length 'p'. This speeds
+.IP
up lookups considerably (more than the LCP table), but misses matches
-less than \fIp\fR when searching.
+less than p when searching.
.TP
-.B \-4bit
+\fB\-4bit\fR
Read in (one) fasta file as a compressed sequence file.
.TP
-.B Methods
-.RS
-.B \-larsson
+\fB\-larsson\fR
(default) Uses the method of Larsson and Sadakane to build the array.
.TP
-.B \-mamy
+\fB\-mamy\fR
Uses the method of MAnber and MYers to build the array (slower than larsson,
+.IP
and produces the same result. This is mainly for double checking
the correctness of larsson).
.TP
-.B \-kark
-Use Karkkainen DS3 method for building the suffix array.
-This will probably be slower than larsson, but takes only an extra
-N/(sqrt 3) extra space.
+\fB\-kark\fR
+Use Karkkainen DS3 method for building the suffix array. This will probably be more
+slow than larsson, but takes only an extra N/(sqrt 3) extra space.
.TP
-.B \-mafe
+\fB\-mafe\fR
(disabled for now!) Use the lightweight construction algorithm from Manzini and Ferragina
.TP
-.B \-welter
-Use lightweight (sort of light) suffix array construction.
-This is a bit more slow than normal larsson.
-.RE
+\fB\-welter\fR
+Use lightweight (sort of light) suffix array construction. This is a bit more slow than
+normal larsson.
.TP
-.BI \-welterweight \0N
-use a difference cover of size \fIN\fR for building the suffix array.
+\fB\-welterweight\fR N use a difference cover of size N for building the suffix array.
Valid values are 7,32,64,111, and 2281.
-.SH SEE ALSO
-.BR blasr (1)
-.BR loadPulses (1)
-.BR pls2fasta (1)
-.BR samFilter (1)
-.BR samtoh5 (1)
-.BR samtom4 (1)
-.BR sdpMatcher (1)
-.BR toAfg (1)
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
=====================================
debian/watch
=====================================
@@ -1,3 +1,4 @@
version=4
-https://github.com/PacificBiosciences/blasr/releases .*/archive/@ANY_VERSION@@ARCHIVE_EXT@
+opts="repacksuffix=+dfsg,dversionmangle=auto,repack,compression=xz" \
+ https://github.com/PacificBiosciences/blasr/releases .*/archive/v?@ANY_VERSION@@ARCHIVE_EXT@
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View it on GitLab: https://salsa.debian.org/med-team/blasr/compare/8ad394ffb70fd2e90d6e923953c0eab6fb8c9277...f68cf4ca0ec8314539c2c2fe2360b91655984d7b
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View it on GitLab: https://salsa.debian.org/med-team/blasr/compare/8ad394ffb70fd2e90d6e923953c0eab6fb8c9277...f68cf4ca0ec8314539c2c2fe2360b91655984d7b
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