V0.1 r7#61

Merged

zhengzhenxian merged 16 commits intomainfrom v0.1-r7

Oct 19, 2021

+837-196

Commits on Oct 18, 2021

compress intermediate GVCF output using lz4, and bgzip final merge_out.gvcf
zhengzhenxian
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add remove_intermediate_dir option to allow remove intermediate directory, including intermediate phased BAM, pileup and full-alignment results
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also remove intermediate files in pileup_only calling mode
zhengzhenxian
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fix splitting validation data issue, added buffers for random_validation, logic remains the same for using validation_fn option
zhengzhenxian
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multiply minimum early-stopping with mini_epochs for better robustness
zhengzhenxian
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use snp_min_af and snp_indel_af instead of min_af, to consistent with pileup AF calculation code, add full_aln_regions to allow using pileup candidates in full-alignment training
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double-check read support in subsampled BAMs and exclude miss_variant_set when creating binaries for training
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move model downloading to the last step
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set default var_pct_full from 0.3 to 0.7 for ONT platform
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full-alignment training release 1
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update model name
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update readme
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change PRO and REF_PRO to integer
zhengzhenxian
committed

Commits on Oct 19, 2021