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Feat: BAI support for random accessing BAM file #449

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merged 10 commits into from Mar 11, 2021
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@taoliu taoliu commented Mar 11, 2021

BAI (BAM index) file is now supported in MACS3/IO/BAM.pyx. The reader in BAM.pyx is named as BAMaccessor. Now, the BAM file as input for callvar doesn't have to be a subset of the original BAM file. callvar will use BAMaccessor to retrieve the reads from indexed BAM (with BAI) file located in given peak regions. Corresponding unit tests and cmdlinetest have been implemented.

@taoliu taoliu self-assigned this Mar 11, 2021
@taoliu taoliu added the v3 label Mar 11, 2021
@taoliu taoliu added this to In progress in MACS3 via automation Mar 11, 2021
@taoliu taoliu added this to the MACS3 milestone Mar 11, 2021
@taoliu taoliu merged commit bce60cf into master Mar 11, 2021
MACS3 automation moved this from In progress to Done Mar 11, 2021
@taoliu taoliu deleted the feat/macs3/BAIsupport branch August 14, 2023 15:57
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