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

-// 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

+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

debian/changelog

+blasr (5.3.3+dfsg-1) unstable; urgency=medium
+
+  * Afif removed himself from Uploaders (thanks for your work on this)
+  * Add myself to Uploaders
+  * New upstream version
+  * debhelper-compat 12
+  * Standards-Version: 4.4.0
+
+ -- Andreas Tille <tille@debian.org>  Wed, 31 Jul 2019 14:55:41 +0200
+
 blasr (5.3.2+dfsg-1.1) unstable; urgency=medium
 
   * Non-maintainer upload.

debian/compat

-12

debian/control

 Source: blasr
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+Uploaders: Andreas Tille <tille@debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 12~),
+Build-Depends: debhelper-compat (= 12),
                python,
                meson,
                pkg-config,
                libboost-dev,
                libhdf5-dev,
                zlib1g-dev,
-               libpbseq-dev (>= 0~20160912),
+               libpbseq-dev,
                libpbbam-dev (>= 0.18.0~),
                libpbdata-dev,
                libgtest-dev,
                libblasr-dev (>= 5.3.1+dfsg-2)
-Standards-Version: 4.3.0
+Standards-Version: 4.4.0
 Vcs-Browser: https://salsa.debian.org/med-team/blasr
 Vcs-Git: https://salsa.debian.org/med-team/blasr.git
 Homepage: https://github.com/PacificBiosciences/blasr
@@ -23,7 +24,7 @@ Package: blasr
 Architecture: any
 Depends: ${shlibs:Depends},
          ${misc:Depends},
-         libpbseq (>= 0~20160912)
+         libpbseq
 Description: mapping single-molecule sequencing reads
  Basic local alignment with successive refinement (BLASR) is a method
  for mapping single-molecule sequencing reads against a reference genome.

doc/EXAMPLES.md

 ## 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", &params.scoreType, "",
                           CommandLineParser::NonNegativeInteger);
     clp.RegisterFlagOption("h", &params.printVerboseHelp, "");
-    clp.RegisterFlagOption("-help", &params.printDiscussion, "");
+    clp.RegisterFlagOption("-help", &params.printVerboseHelp, "");
     clp.RegisterFloatOption("-accuracyPrior", &params.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] "
@@ -629,76 +629,9 @@ 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;
-    return helpStream.str();
-}
-
-const std::string BlasrConciseHelp(void)
-{
-    std::stringstream 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
-       << "          --help for verbose discussion of how to run blasr." << std::endl
-       << std::endl
-       << "In release v5.1 of BLASR, command-line options will use the " << std::endl
-       << "single dash/double dash convention: " << std::endl
-       << "Character options are preceded by a single dash. (Example: -v) " << std::endl
-       << "Word options are preceded by a double dash. (Example: --verbose) " << std::endl
-       << "Please modify your scripts accordingly when BLASR v5.1 is released. " << std::endl
-       << std::endl;
-    return ss.str();
-}
-
-const std::string BlasrSummaryHelp(void)
-{
-    std::stringstream ss;
-    ss << "   Basic usage: 'blasr reads.{bam|fasta|bax.h5|fofn} genome.fasta [-options] "
-       << std::endl
-       << " [option]\tDescription (default_value)." << std::endl
-       << std::endl
-       << " Input Files." << std::endl
-       << "   reads.bam is the NEW native output format for SMRT reads."
-          "This is the preferred input to blasr because rich quality"
-          "value (insertion,deletion, and substitution quality values) information is "
-          "maintained.  The extra quality information improves variant detection and mapping"
-       << "speed." << std::endl
-       << "   reads.fasta is a multi-fasta file of reads.  While any fasta file is valid input, "
-          "it is preferable to use bax.h5 or plx.h5 files because they contain "
-          "more rich quality value information."
-       << std::endl
-       << "   reads.bax.h5|reads.plx.h5 is the OLD (DEPRECATED) output format of "
-          "SMRT reads. "
-       << std::endl
-       << "   reads.fofn File of file names accepted." << std::endl
-       << 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
+        << "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
@@ -720,16 +653,9 @@ const std::string BlasrDiscussion(void)
         << "  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
+        << "  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
@@ -745,16 +671,10 @@ const std::string BlasrDiscussion(void)
         << "  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
+        << "  -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 "
@@ -762,5 +682,47 @@ const std::string BlasrDiscussion(void)
         << "  are sufficient for maximal sensitivity and good speed." << std::endl
         << std::endl
         << std::endl;
+    return helpStream.str();
+}
+
+const std::string BlasrConciseHelp(void)
+{
+    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
+       << "          --help for verbose discussion of how to run blasr." << std::endl
+       << std::endl
+       << "In release v5.1 of BLASR, command-line options will use the " << std::endl
+       << "single dash/double dash convention: " << std::endl
+       << "Character options are preceded by a single dash. (Example: -v) " << std::endl
+       << "Word options are preceded by a double dash. (Example: --verbose) " << std::endl
+       << "Please modify your scripts accordingly when BLASR v5.1 is released. " << std::endl
+       << std::endl;
+    return ss.str();
+}
+
+const std::string BlasrSummaryHelp(void)
+{
+    std::ostringstream ss;
+    ss << "   Basic usage: 'blasr reads.{bam|fasta|bax.h5|fofn} genome.fasta [-options] "
+       << std::endl
+       << " [option]\tDescription (default_value)." << std::endl
+       << std::endl
+       << " Input Files." << std::endl
+       << "   reads.bam is the NEW native output format for SMRT reads."
+          "This is the preferred input to blasr because rich quality"
+          "value (insertion,deletion, and substitution quality values) information is "
+          "maintained.  The extra quality information improves variant detection and mapping"
+       << "speed." << std::endl
+       << "   reads.fasta is a multi-fasta file of reads.  While any fasta file is valid input, "
+          "it is preferable to use bax.h5 or plx.h5 files because they contain "
+          "more rich quality value information."
+       << std::endl
+       << "   reads.bax.h5|reads.plx.h5 is the OLD (DEPRECATED) output format of "
+          "SMRT reads. "
+       << std::endl
+       << "   reads.fofn File of file names accepted." << std::endl
+       << std::endl;
     return ss.str();
 }

meson.build

 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_impl',
   blasr_sources,
-    blasr_git_commit_id],
   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,