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Parallel bgzip with cram support #21

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Parallel bgzip with cram support #21

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Commits on Sep 26, 2018

  1. WIP of updating to samtools/htslib 1.9 and enabling parallal bgzf.

    @daheise
    daheise committed Sep 26, 2018
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  2. Insulate bgzf_open from the specialized mode for specifying threads.

    @daheise
    daheise committed Sep 26, 2018
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Commits on Sep 27, 2018

  1. Remove dependency on a samtools subdirectory

    @daheise
    daheise committed Sep 27, 2018
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  2. Use system paths for samtools and htslib.

    @daheise
    daheise committed Sep 27, 2018
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  3. Remove dependency on local samtools and rely on system locations.

    @daheise
    daheise committed Sep 27, 2018
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  4. Note dependency on samtools and htslib 1.9

    @daheise
    daheise committed Sep 27, 2018
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Commits on Oct 1, 2018

  1. Fix a segfault on gzip files.

    @daheise
    daheise committed Oct 1, 2018
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Commits on Oct 4, 2018

  1. Add a write buffer to speed up small writes.

    @daheise
    daheise committed Oct 4, 2018
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  2. Fix misused variable.

    @daheise
    daheise committed Oct 4, 2018
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Commits on Oct 10, 2018

  1. Merge branch 'cram-support' of github.com:statgen/libStatGen into par… 

    …allel-bgzip-cram

Conflicts:
	Makefile
	bam/Makefile.depends
	bam/SamRecord.cpp
	general/BgzfFileType.h
	general/PhoneHome.cpp
    @daheise
    daheise committed Oct 10, 2018
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  2. Change dependencies based on the new cram code.

    @daheise
    daheise committed Oct 10, 2018
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  3. add dependency on htslib

    @daheise
    daheise committed Oct 10, 2018
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Commits on Oct 11, 2018

  1. Remove debugging statement.

    @daheise
    daheise committed Oct 11, 2018
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  2. Fix a memort leak.

    @daheise
    daheise committed Oct 11, 2018
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Commits on Nov 30, 2020

  1. Merge branch 'master' of github.com:statgen/libStatGen into parallel-… 

    …bgzip-cram
    @daheise
    daheise committed Nov 30, 2020
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  2. Fix pointer issue

    @daheise
    daheise committed Nov 30, 2020
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Commits on Dec 1, 2020

  1. Merge branch 'cram-support' of github.com:statgen/libStatGen into par… 

    …allel-bgzip-cram
    @daheise
    daheise committed Dec 1, 2020
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Commits on Sep 22, 2021

  1. Revert default constructor.

    @daheise
    daheise committed Sep 22, 2021
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