Loading Blasr.cpp +0 −4 Original line number Diff line number Diff line Loading @@ -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. Loading LICENSE +34 −34 Original line number Diff line number Diff line // 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 +3 −11 Original line number Diff line number Diff line Loading @@ -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 ---------- Loading ctest/ecoli.t +1 −0 Original line number Diff line number Diff line Loading @@ -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 Loading ctest/long-cigar.t 0 → 100644 +14 −0 Original line number Diff line number Diff line 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 Loading
Blasr.cpp +0 −4 Original line number Diff line number Diff line Loading @@ -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. Loading
LICENSE +34 −34 Original line number Diff line number Diff line // 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 +3 −11 Original line number Diff line number Diff line Loading @@ -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 ---------- Loading
ctest/ecoli.t +1 −0 Original line number Diff line number Diff line Loading @@ -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 Loading
ctest/long-cigar.t 0 → 100644 +14 −0 Original line number Diff line number Diff line 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
