Commits on Oct 17, 2020

  1. add Ash1_2 and T2T indexes to sidebar

    @BenLangmead
    BenLangmead committed Oct 17, 2020
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Commits on Dec 2, 2020

  1. Add Zstandard I/O

    @vejnar
    vejnar committed Dec 2, 2020
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  2. Replace "samtools mpileup" with "bcftools mpileup" #325

    @ch4rr0
    ch4rr0 committed Dec 2, 2020
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Commits on Dec 3, 2020

  1. Fix an issue causing compilation errors when building with CMake #323

    @ch4rr0
    ch4rr0 committed Dec 3, 2020
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Commits on Dec 6, 2020

  1. Extend build wait times by 5 mins to prevent timeouts

    @ch4rr0
    ch4rr0 committed Dec 6, 2020
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  2. Increase timeout to 25 mins

    @ch4rr0
    ch4rr0 committed Dec 6, 2020
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Commits on Dec 20, 2020

  1. Replace TBB with C++11 features

    @ch4rr0
    ch4rr0 committed Dec 20, 2020
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Commits on Dec 21, 2020

  1. Fix compiler warning

    @ch4rr0
    ch4rr0 committed Dec 21, 2020
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  2. Add missing files and require C++11 for compilation

    @ch4rr0
    ch4rr0 committed Dec 21, 2020
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  3. Remove C++11 guards

    @ch4rr0
    ch4rr0 committed Dec 21, 2020
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  4. Add experimental native support for processing ZSTD compressed read f… 

    …iles
    @ch4rr0
    ch4rr0 committed Dec 21, 2020
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  5. Remove non-portable header

    @ch4rr0
    ch4rr0 committed Dec 21, 2020
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  6. Merge pull request #326 from vejnar/zstd 

    Adds Zstandard compression input/output
    @ch4rr0
    ch4rr0 authored Dec 21, 2020
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  7. Fix resource leaks and change the way zstd.h gets included

    @ch4rr0
    ch4rr0 committed Dec 21, 2020
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Commits on Dec 22, 2020

  1. Fix compiler warnings

    @ch4rr0
    ch4rr0 committed Dec 22, 2020
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  2. Fix semantic errors

    @ch4rr0
    ch4rr0 committed Dec 22, 2020
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Commits on Dec 31, 2020

  1. upgrade to SIMDe 0.7.0

    @mr-c
    mr-c committed Dec 31, 2020
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  2. Fix memory leaks during index build

    @ch4rr0
    ch4rr0 committed Dec 31, 2020
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  3. Fix an issue preventing bowtie2-build from placing suffixes in bucket… 

    …s when running single threaded
    @ch4rr0
    ch4rr0 committed Dec 31, 2020
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Commits on Jan 3, 2021

  1. Merge pull request #330 from mr-c/simde_v0.7.0 

    upgrade to SIMDe 0.7.0
    @ch4rr0
    ch4rr0 authored Jan 3, 2021
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Commits on Jan 22, 2021

  1. Potential fix for issue #321

    @ch4rr0
    ch4rr0 committed Jan 22, 2021
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Commits on Feb 22, 2021

  1. Potential solution to issue #114

    @ch4rr0
    ch4rr0 committed Feb 22, 2021
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Commits on Mar 9, 2021

  1. Make index files built on little-endian machines work on big-endian m… 

    …achines and vice-versa
    @ch4rr0
    ch4rr0 committed Mar 9, 2021
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Commits on Mar 10, 2021

  1. Add type to XT flag and enable s390x testing

    @ch4rr0
    ch4rr0 committed Mar 10, 2021
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  2. Temporarily disable SAM flag used to identify unique reads

    @ch4rr0
    ch4rr0 committed Mar 10, 2021
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  3. Refactor platform checks and fix issue causing CXXFLAGS to get overri… 

    …dden for aarch64, and POWER cpus
    @ch4rr0
    ch4rr0 committed Mar 10, 2021
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Commits on Mar 11, 2021

  1. Track master branch of simde submodule

    @ch4rr0
    ch4rr0 committed Mar 11, 2021
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  2. Track master branch of simde submodule

    @ch4rr0
    ch4rr0 committed Mar 11, 2021
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Commits on Mar 12, 2021

  1. Update commit ID for simde submodule

    @ch4rr0
    ch4rr0 committed Mar 12, 2021
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  2. Merge branch 'master' into bug_fixes

    @ch4rr0
    ch4rr0 committed Mar 12, 2021
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  3. Fix compilation errors caused by changes to simde submodule

    @ch4rr0
    ch4rr0 committed Mar 12, 2021
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  4. Update commit ID for simde submodule

    @ch4rr0
    ch4rr0 committed Mar 12, 2021
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  5. Fix overflow on MacOS

    @ch4rr0
    ch4rr0 committed Mar 12, 2021
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  6. Limit make to 4 threads when running travis tests

    @ch4rr0
    ch4rr0 committed Mar 12, 2021
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Commits on Mar 13, 2021

  1. Update dist to xenial and temporarily disable all but s390x and ppc t… 

    …ests
    @ch4rr0
    ch4rr0 committed Mar 13, 2021
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Commits on Mar 16, 2021

  1. Fix issue causing simple tests to fail on big-engian machines

    @ch4rr0
    ch4rr0 committed Mar 16, 2021
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Commits on Mar 17, 2021

  1. Second attempt at fixing simple test failures

    @ch4rr0
    ch4rr0 committed Mar 17, 2021
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  2. Remove unnecessary resetting of AlnScore member variables

    @ch4rr0
    ch4rr0 committed Mar 17, 2021
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  3. Reinstate previous change but in a way that does not trip ASAN

    @ch4rr0
    ch4rr0 committed Mar 17, 2021
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  4. Third attempt at fixing ASAN failure

    @ch4rr0
    ch4rr0 committed Mar 17, 2021
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  5. Use clang instead of GCC for ppc64le due to compiler bug -- simd-ever… 

    …ywhere/simde#535
    @ch4rr0
    ch4rr0 committed Mar 17, 2021
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Commits on Mar 19, 2021

  1. Fix overflow issue

    @ch4rr0
    ch4rr0 committed Mar 19, 2021
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  2. Use clang for compiling on s390x

    @ch4rr0
    ch4rr0 committed Mar 19, 2021
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Commits on Mar 24, 2021

  1. Fix an issue causing Bowtie2 to set an incorrect MAPQ when AS and XS … 

    …are the maximum for read length #337
    @ch4rr0
    ch4rr0 committed Mar 24, 2021
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  2. Re-enable tests across all platforms

    @ch4rr0
    ch4rr0 committed Mar 24, 2021
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Commits on Apr 5, 2021

  1. Add support for BAM pattern source on big-endian machines

    @ch4rr0
    ch4rr0 committed Apr 5, 2021
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  2. Use clang when running ARM tests

    @ch4rr0
    ch4rr0 committed Apr 5, 2021
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  3. Use system-installed python for running tests

    @ch4rr0
    ch4rr0 committed Apr 5, 2021
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Commits on Apr 6, 2021

  1. Add native support for reading zstd compressed files to bowtie2-build

    @ch4rr0
    ch4rr0 committed Apr 6, 2021
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  2. Add ifdef guards around zstd code

    @ch4rr0
    ch4rr0 committed Apr 6, 2021
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