[med-svn] [Git][med-team/blasr][upstream] New upstream version 5.3.3+dfsg
Andreas Tille
gitlab at salsa.debian.org
Wed Jul 31 14:23:57 BST 2019
Andreas Tille pushed to branch upstream at Debian Med / blasr
Commits:
28dbe223 by Andreas Tille at 2019-07-31T12:55:34Z
New upstream version 5.3.3+dfsg
- - - - -
11 changed files:
- Blasr.cpp
- LICENSE
- README.md
- ctest/ecoli.t
- + ctest/long-cigar.t
- ctest/meson.build
- ctest/pgc-naive.t
- doc/EXAMPLES.md
- iblasr/MappingParameters.h
- iblasr/RegisterBlasrOptions.h
- meson.build
Changes:
=====================================
Blasr.cpp
=====================================
@@ -831,10 +831,6 @@ int main(int argc, char *argv[])
std::cout << BlasrHelp(params) << std::endl;
std::exit(EXIT_SUCCESS); // Not a failure.
}
- if (params.printDiscussion) {
- std::cout << BlasrDiscussion();
- std::exit(EXIT_SUCCESS); // Not a failure.
- }
if (argc < 3) {
std::cout << BlasrConciseHelp();
std::exit(EXIT_FAILURE); // A failure.
=====================================
LICENSE
=====================================
@@ -1,34 +1,34 @@
-// Copyright (c) 2014-2015, Pacific Biosciences of California, Inc.
-//
-// All rights reserved.
-//
-// Redistribution and use in source and binary forms, with or without
-// modification, are permitted (subject to the limitations in the
-// disclaimer below) provided that the following conditions are met:
-//
-// * Redistributions of source code must retain the above copyright
-// notice, this list of conditions and the following disclaimer.
-//
-// * 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.
-//
-// * Neither the name of Pacific Biosciences nor the names of its
-// contributors may be used to endorse or promote products derived
-// from this software without specific prior written permission.
-//
-// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
-// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
-// BIOSCIENCES AND ITS 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 PACIFIC BIOSCIENCES 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.
+Copyright (c) 2014-2018, Pacific Biosciences of California, Inc.
+
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted (subject to the limitations in the
+disclaimer below) provided that the following conditions are met:
+
+ * Redistributions of source code must retain the above copyright
+ notice, this list of conditions and the following disclaimer.
+
+ * 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.
+
+ * Neither the name of Pacific Biosciences nor the names of its
+ contributors may be used to endorse or promote products derived
+ from this software without specific prior written permission.
+
+NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+BIOSCIENCES AND ITS 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 PACIFIC BIOSCIENCES 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.
=====================================
README.md
=====================================
@@ -6,23 +6,15 @@
***
## Availability
-The latest release binary can be installed via [bioconda](https://bioconda.github.io/):
+Latest version can be installed via bioconda package `blasr`.
- conda install -c bioconda blasr
-
-Official support is only provided for official and stable
-[SMRT Analysis builds](http://www.pacb.com/products-and-services/analytical-software/)
-provided by PacBio and not for source builds.
-
-Unofficial support for binary releases is provided via github issues,
-not via mail to developers.
-**No** support for source builds; issues will be closed without comment.
+Please refer to our [official pbbioconda page](https://github.com/PacificBiosciences/pbbioconda)
+for information on Installation, Support, License, Copyright, and Disclaimer.
## Documentation
- [Wiki: all you need to know](https://github.com/PacificBiosciences/blasr/wiki)
- [Running BLASR](doc/EXAMPLES.md)
- - [Developer environment](doc/DEVELOPER.md)
DISCLAIMER
----------
=====================================
ctest/ecoli.t
=====================================
@@ -10,6 +10,7 @@ Test blasr with --bam
$ rm -rf $OUTDIR/ecoli_subset.sam
$ $BLASR_EXE $DATDIR/ecoli_subset.fasta $DATDIR/ecoli_reference.fasta --bam --out $OUTDIR/ecoli_subset.bam --nproc 15
[INFO]* (glob)
+ WARNING, BAM output without PacBio BAM or DATASET input is not supported by PacBio.
[INFO]* (glob)
$ $SAMTOOLS_EXE view -h $OUTDIR/ecoli_subset.bam > $OUTDIR/ecoli_subset.sam
=====================================
ctest/long-cigar.t
=====================================
@@ -0,0 +1,14 @@
+Test input query is not pb bam, output is sam/bam, alignment has more than 65535 cigar ops.
+
+Set up
+ $ mkdir -p $OUTDIR
+
+ $ Q=$DATDIR/long-cigar/query.fasta
+ $ T=$DATDIR/long-cigar/ref.fasta
+
+Test m4 output
+ $ O=$OUTDIR/long-cigar.sam
+ $ $BLASR_EXE $Q $T --minMatch 15 --maxMatch 25 --advanceHalf --advanceExactMatches 10 --bestn 1 --nproc 1 --noSplitSubreads --out $O 1>/dev/null 2>/dev/null && echo $?
+ 0
+ $ grep 'CG:' $O |wc -l
+ 1
=====================================
ctest/meson.build
=====================================
@@ -32,6 +32,7 @@ blasr_fast_test_list = [
['holeNumbers', 'INTERMEDIATE'],
# ['bug25328', 'SLOW'],
# ['pgc-big', 'SLOW'],
+# ['long-cigar', 'SLOW'],
]
blasr_test_remotedir = '/pbi/dept/secondary/siv/testdata/BlasrTestData/ctest'
=====================================
ctest/pgc-naive.t
=====================================
@@ -53,6 +53,7 @@ Test bam output
$ O=$OUTDIR/pgc-naive.bam
$ $BLASR_EXE $Q $T --bam --out $O --bestn 1 --placeGapConsistently && echo $?
[INFO]* (glob)
+ WARNING, BAM output without PacBio BAM or DATASET input is not supported by PacBio.
[INFO]* (glob)
0
$ $SAMTOOLS_EXE view $O
=====================================
doc/EXAMPLES.md
=====================================
@@ -1,38 +1,48 @@
## Running BLASR
Typing 'blasr -h' or 'blasr -help' on the command line will give you a
- list of options. At the least, provide a fasta, fastq, or bas.h5 file,
- and a genome.
+ list of options. At the least, provide reads and a genome, where reads file format can be
+ bam|dataset|fasta|fastq|bas.h5, and genome file format can be fasta|ReferenceSet.
### Some typical use cases
-Align reads from reads.bas.h5 to ecoli_K12 genome, and output in SAM format.
+Align subreads in movie.subreads.bam to ecoli_K12 genome, and output in BAM format.
- blasr reads.bas.h5 ecoli_K12.fasta -sam
+ blasr movie.subreads.bam ecoli_K12.fasta --bam --out alignments.bam
-Same as above, but with soft clipping
+Align subreads in movie.subreadset.xml to ecoli_K12 genome, and output in BAM format.
+
+ blasr movie.subreadset.xml ecoli_K12.fasta --bam --out alignments.bam
+
+Align subreads in movie.subreadset.xml to ecoli_K12 genome ReferenceSet, and output in BAM format.
+
+ blasr movie.subreadset.xml ecoli_K12.referenceset.xml --bam --out alignments.bam
- blasr reads.bas.h5 ecoli_K12.fasta -sam -clipping soft
+Align CCS reads in movie.consensusreadset.xml to ecoli_K12 genome, and output in BAM format.
-Use multiple threads
+ blasr movie.consensusreadset.xml ecoli_K12.fasta --bam --out alignments.bam
- blasr reads.bas.h5 ecoli_K12.fasta -sam -clipping soft -out alignments.sam -nproc 16
+Use multiple threads, e.x., 16 threads
+
+ blasr movie.subreads.bam ecoli_K12.fasta --nproc 16
Include a larger minimal match, for faster but less sensitive alignments
- blasr reads.bas.h5 ecoli_K12.fasta -sam -clipping soft -minMatch 15
+ blasr movie.subreads.bam ecoli_K12.fasta --minMatch 15
Produce alignments in a pairwise human readable format
- blasr reads.bas.h5 ecoli_K12.fasta -m 0
+ blasr movie.subreads.bam ecoli_K12.fasta -m 0
Use a precomputed suffix array for faster startup
- sawriter hg19.fasta.sa hg19.fasta #First precompute the suffix array
- blasr reads.bas.h5 hg19.fasta -sa hg19.fasta.sa
+ sawriter ecoli_K12.fasta.sa ecoli_K12.fasta #First precompute the suffix array
+ blasr movie.subreads.bam ecoli_K12.fasta --sa ecoli_K12.fasta.sa
+
+Align RSII reads from reads.bas.h5 to ecoli_K12 genome, and output in SAM format.
-Use a precomputed BWT-FM index for smaller runtime memory footprint, but slower alignments.
+ blasr reads.bas.h5 ecoli_K12.fasta --sam --out alignments.sam
- sa2bwt hg19.fasta hg19.fasta.sa hg19.fasta.bwt
- blasr reads.bas.h5 hg19.fasta -bwt hg19.fasta.bwt
+Same as above, but with soft clipping
+ blasr reads.bas.h5 ecoli_K12.fasta --sam --clipping soft --out alignments.sam
=====================================
iblasr/MappingParameters.h
=====================================
@@ -168,7 +168,6 @@ public:
bool useQVScore;
int scoreType;
bool printVerboseHelp;
- bool printDiscussion;
float sdpBypassThreshold;
bool computeAlignProbability;
float qvMatchWeight;
@@ -346,7 +345,6 @@ public:
guidedAlignBandSize = 10;
useQVScore = false;
printVerboseHelp = false;
- printDiscussion = false;
sdpBypassThreshold = 1000000.0;
scoreType = 0;
byAdapter = false;
@@ -666,7 +664,7 @@ public:
// Only support two clipping methods: soft or subread.
clipping = SAMOutput::subread;
}
- // Turn on fa fa -> bam pipe
+ // Turn on fa fa -> sam pipe
/*
if (queryFileType != FileType::PBBAM and queryFileType != FileType::PBDATASET and not enableHiddenPaths) {
// bax|fasta|fastq -> bam paths are turned off by default
@@ -674,6 +672,7 @@ public:
std::exit(EXIT_FAILURE);
}
*/
+
if (outFileName == "") {
std::cout << "ERROR, SAM output file must be specified." << std::endl;
std::exit(EXIT_FAILURE);
@@ -701,14 +700,14 @@ public:
// Only support two clipping methods: soft or subread.
clipping = SAMOutput::subread;
}
- // Turn on fa fa -> bam pipe
- /*
- if (queryFileType != FileType::PBBAM and queryFileType != FileType::PBDATASET and not enableHiddenPaths) {
- // bax|fasta|fastq -> bam paths are turned off by default
- std::cout << "ERROR, could not output alignments in BAM unless input reads are in PacBio BAM or DATASET files." << std::endl;
- std::exit(EXIT_FAILURE);
+ if (queryFileType != FileType::PBBAM and queryFileType != FileType::PBDATASET and
+ queryFileType != FileType::HDFCCS and queryFileType != FileType::HDFBase and
+ queryFileType != FileType::HDFPulse) {
+ // fasta|fastq -> bam paths are turned off by default
+ std::cout << "WARNING, BAM output without PacBio BAM or DATASET input is not "
+ "supported by PacBio."
+ << std::endl;
}
- */
if (outFileName == "") {
std::cout << "ERROR, BAM output file must be specified." << std::endl;
std::exit(EXIT_FAILURE);
=====================================
iblasr/RegisterBlasrOptions.h
=====================================
@@ -188,7 +188,7 @@ void RegisterBlasrOptions(CommandLineParser& clp, MappingParameters& params)
clp.RegisterIntOption("-scoreType", ¶ms.scoreType, "",
CommandLineParser::NonNegativeInteger);
clp.RegisterFlagOption("h", ¶ms.printVerboseHelp, "");
- clp.RegisterFlagOption("-help", ¶ms.printDiscussion, "");
+ clp.RegisterFlagOption("-help", ¶ms.printVerboseHelp, "");
clp.RegisterFloatOption("-accuracyPrior", ¶ms.readAccuracyPrior, "",
CommandLineParser::NonNegativeFloat);
// holeNumberRangesStr is a string of comma-delimited hole number ranges, such as '1,2,3,10-15'.
@@ -225,7 +225,7 @@ void RegisterBlasrOptions(CommandLineParser& clp, MappingParameters& params)
const std::string BlasrHelp(MappingParameters& params)
{
- std::stringstream helpStream;
+ std::ostringstream helpStream;
helpStream
<< " Options for blasr " << std::endl
<< " Basic usage: 'blasr reads.{bam|fasta|bax.h5|fofn} genome.fasta [-options] "
@@ -629,13 +629,65 @@ const std::string BlasrHelp(MappingParameters& params)
<< "Bioinformatics 2012, 13:238." << std::endl
<< "Please report any bugs to "
<< "'https://github.com/PacificBiosciences/blasr/issues'." << std::endl
+ << std::endl
+ << std::endl
+ << "DISCUSSION " << std::endl
+ << " blasr is a read mapping program that maps reads to positions " << std::endl
+ << " in a genome by clustering short exact matches between the read and" << std::endl
+ << " the genome, and scoring clusters using alignment. The matches are" << std::endl
+ << " generated by searching all suffixes of a read against the genome" << std::endl
+ << " using a suffix array. Global chaining methods are used to score " << std::endl
+ << " clusters of matches." << std::endl
+ << std::endl
+ << " The only required inputs to blasr are a file of reads and a" << std::endl
+ << " reference genome. It is exremely useful to have read filtering" << std::endl
+ << " information, and mapping runtime may decrease substantially when a" << std::endl
+ << " precomputed suffix array index on the reference sequence is" << std::endl
+ << " specified." << std::endl
+ << " " << std::endl
+ << " Although reads may be input in FASTA format, the recommended input is" << std::endl
+ << " PacBio BAM files because these contain quality value" << std::endl
+ << " information that is used in the alignment and produces higher quality" << std::endl
+ << " variant detection." << std::endl
+ << " Although alignments can be output in various formats, the recommended " << std::endl
+ << " output format is PacBio BAM." << std::endl
+ << " Support to bax.h5 and plx.h5 files will be DEPRECATED." << std::endl
+ << " Support to region tables for h5 files will be DEPRECATED." << std::endl
+ << " " << std::endl
+ << " When suffix array index of a genome is not specified, the suffix array is"
+ << std::endl
+ << " built before producing alignment. This may be prohibitively slow" << std::endl
+ << " when the genome is large (e.g. Human). It is best to precompute the" << std::endl
+ << " suffix array of a genome using the program sawriter, and then specify" << std::endl
+ << " the suffix array on the command line using -sa genome.fa.sa." << std::endl
+ << " " << std::endl
+ << " The optional parameters are roughly divided into three categories:" << std::endl
+ << " control over anchoring, alignment scoring, and output. " << std::endl
+ << " " << std::endl
+ << " The default anchoring parameters are optimal for small genomes and" << std::endl
+ << " samples with up to 5% divergence from the reference genome. The main" << std::endl
+ << " parameter governing speed and sensitivity is the -minMatch parameter." << std::endl
+ << " For human genome alignments, a value of 11 or higher is recommended. " << std::endl
+ << " Several methods may be used to speed up alignments, at the expense of" << std::endl
+ << " possibly decreasing sensitivity. " << std::endl
+ << " " << std::endl
+ << " Regions that are too repetitive may be ignored during mapping by" << std::endl
+ << " limiting the number of positions a read maps to with the" << std::endl
+ << " -maxAnchorsPerPosition option. Values between 500 and 1000 are effective"
+ << std::endl
+ << " in the human genome." << std::endl
+ << " " << std::endl
+ << " For small genomes such as bacterial genomes or BACs, the default parameters "
+ << std::endl
+ << " are sufficient for maximal sensitivity and good speed." << std::endl
+ << std::endl
<< std::endl;
return helpStream.str();
}
const std::string BlasrConciseHelp(void)
{
- std::stringstream ss;
+ std::ostringstream ss;
ss << "blasr - a program to map reads to a genome" << std::endl
<< " usage: blasr reads genome " << std::endl
<< " Run with -h for a list of commands " << std::endl
@@ -652,7 +704,7 @@ const std::string BlasrConciseHelp(void)
const std::string BlasrSummaryHelp(void)
{
- std::stringstream ss;
+ std::ostringstream ss;
ss << " Basic usage: 'blasr reads.{bam|fasta|bax.h5|fofn} genome.fasta [-options] "
<< std::endl
<< " [option]\tDescription (default_value)." << std::endl
@@ -674,93 +726,3 @@ const std::string BlasrSummaryHelp(void)
<< std::endl;
return ss.str();
}
-
-const std::string BlasrDiscussion(void)
-{
- std::stringstream ss;
- ss << "NAME" << std::endl
- << " blasr - Map SMRT Sequences to a reference genome." << std::endl
- << std::endl
- << "SYNOPSIS" << std::endl
- << " blasr reads.bam genome.fasta --bam --out out.bam" << std::endl
- << std::endl
- << " blasr reads.fasta genome.fasta " << std::endl
- << std::endl
- << " blasr reads.fasta genome.fasta --sa genome.fasta.sa" << std::endl
- << std::endl
- << " blasr reads.bax.h5 genome.fasta [--sa genome.fasta.sa] " << std::endl
- << std::endl
- << " blasr reads.bax.h5 genome.fasta --sa genome.fasta.sa --maxScore 100 --minMatch "
- "15 ... "
- << std::endl
- << std::endl
- << " blasr reads.bax.h5 genome.fasta --sa genome.fasta.sa --nproc 24 --out "
- "alignment.out ... "
- << std::endl
- << std::endl
- << "DESCRIPTION " << std::endl
- << " blasr is a read mapping program that maps reads to positions " << std::endl
- << " in a genome by clustering short exact matches between the read and" << std::endl
- << " the genome, and scoring clusters using alignment. The matches are" << std::endl
- << " generated by searching all suffixes of a read against the genome" << std::endl
- << " using a suffix array. Global chaining methods are used to score " << std::endl
- << " clusters of matches." << std::endl
- << std::endl
- << " The only required inputs to blasr are a file of reads and a" << std::endl
- << " reference genome. It is exremely useful to have read filtering" << std::endl
- << " information, and mapping runtime may decrease substantially when a" << std::endl
- << " precomputed suffix array index on the reference sequence is" << std::endl
- << " specified." << std::endl
- << " " << std::endl
- << " Although reads may be input in FASTA format, the recommended input is" << std::endl
- << " PacBio BAM files because these contain quality value" << std::endl
- << " information that is used in the alignment and produces higher quality" << std::endl
- << " variant detection." << std::endl
- << " Although alignments can be output in various formats, the recommended " << std::endl
- << " output format is PacBio BAM." << std::endl
- << " Support to bax.h5 and plx.h5 files will be DEPRECATED." << std::endl
- << " Support to region tables for h5 files will be DEPRECATED." << std::endl
- //<< " Read filtering information is contained in the .bax.h5 input files as" << std::endl
- //<< " well as generated by other post-processing programs with analysis of" << std::endl
- //<< " pulse files and read in from a separate .region.h5 file. The current" << std::endl
- //<< " set of filters that are applied to reads are high quality region" << std::endl
- //<< " filtering, and adapter filtering. Regions outside high-quality" << std::endl
- //<< " regions are ignored in mapping. Reads that contain regions annotated" << std::endl
- //<< " as adapter are split into non-adapter (template) regions, and mapped" << std::endl
- //<< " separately." << std::endl
- << " " << std::endl
- << " When suffix array index of a genome is not specified, the suffix array is" << std::endl
- << " built before producing alignment. This may be prohibitively slow" << std::endl
- << " when the genome is large (e.g. Human). It is best to precompute the" << std::endl
- << " suffix array of a genome using the program sawriter, and then specify" << std::endl
- << " the suffix array on the command line using -sa genome.fa.sa." << std::endl
- << " " << std::endl
- << " The optional parameters are roughly divided into three categories:" << std::endl
- << " control over anchoring, alignment scoring, and output. " << std::endl
- << " " << std::endl
- << " The default anchoring parameters are optimal for small genomes and" << std::endl
- << " samples with up to 5% divergence from the reference genome. The main" << std::endl
- << " parameter governing speed and sensitivity is the -minMatch parameter." << std::endl
- << " For human genome alignments, a value of 11 or higher is recommended. " << std::endl
- << " Several methods may be used to speed up alignments, at the expense of" << std::endl
- << " possibly decreasing sensitivity. " << std::endl
- << " " << std::endl
- // << " If the genome is highly repetitive or divergent from the read" << std::endl
- // << " sequences, the value of -maxExpand should be increased. This option" << std::endl
- // << " controls how much the search for anchors is expanded past a simple" << std::endl
- // << " greedy search. A value for -maxExpand of 1 is sufficent for" << std::endl
- // << " non-repetitive genomes, and values of -maxExpand greater than 5 are" << std::endl
- // << " not recommended." << std::endl
- // << " " << std::endl
- << " Regions that are too repetitive may be ignored during mapping by" << std::endl
- << " limiting the number of positions a read maps to with the" << std::endl
- << " -maxAnchorsPerPosition option. Values between 500 and 1000 are effective" << std::endl
- << " in the human genome." << std::endl
- << " " << std::endl
- << " For small genomes such as bacterial genomes or BACs, the default parameters "
- << std::endl
- << " are sufficient for maximal sensitivity and good speed." << std::endl
- << std::endl
- << std::endl;
- return ss.str();
-}
=====================================
meson.build
=====================================
@@ -1,7 +1,7 @@
project(
'blasr',
'cpp',
- version : '5.3.2',
+ version : '5.3.3',
default_options : [
'buildtype=release',
'warning_level=3',
@@ -77,13 +77,13 @@ blasr_config.set('BLASR_VERSION_MAJOR', blasr_major_version)
blasr_config.set('BLASR_VERSION_MINOR', blasr_minor_version)
blasr_config.set('BLASR_VERSION_PATCH', blasr_patch_version)
-configure_file(
+blasr_BlasrVersion_h = configure_file(
input : 'BlasrVersion.h.in',
output : 'BlasrVersion.h',
configuration : blasr_config)
# replace git commit id
-blasr_git_commit_id = vcs_tag(
+blasr_BlasrGitHash_h = vcs_tag(
input : 'BlasrGitHash.h.in',
output : 'BlasrGitHash.h',
command : ['git', 'describe', '--always', '--dirty=*'],
@@ -97,16 +97,17 @@ subdir('extrautils')
subdir('utils')
blasr_static_impl = static_library(
- 'blasr_impl', [
- blasr_sources,
- blasr_git_commit_id],
+ 'blasr_impl',
+ blasr_sources,
install : false,
dependencies : blasr_deps,
cpp_args : [blasr_warning_flags, '-DUSE_PBBAM=1'])
blasr_main = executable(
- 'blasr', files([
- 'Blasr.cpp']),
+ 'blasr', [
+ blasr_BlasrGitHash_h,
+ blasr_BlasrVersion_h,
+ files('Blasr.cpp')],
install : true,
dependencies : blasr_deps,
link_with : blasr_static_impl,
View it on GitLab: https://salsa.debian.org/med-team/blasr/commit/28dbe2237a2275a474cd2bf0300c0559cf4ce4d3
--
View it on GitLab: https://salsa.debian.org/med-team/blasr/commit/28dbe2237a2275a474cd2bf0300c0559cf4ce4d3
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