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Commits on Dec 4, 2018

• added new files for realignment

  vibansal

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• initial code for the automatic estimation of realignment parameters for SMS reads

  vibansal

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Commits on Dec 3, 2018

• fixed minor bug: VARIANTS-1 => VARIANTS in realignment code

  vibansal

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• minor edits

  vibansal

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Commits on Nov 28, 2018

• Merge commit '995463a'

  pjedge

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• changes to calculate_haplotype_statistics.py. N50 behaviour has been changed to be calculated with respect to the phased portion of the genome instead of the whole genome.

  pjedge

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Commits on Sep 28, 2018

• Update README.md

  pjedge

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• Update README.md

  pjedge

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• Update README.md

  pjedge

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• Update README.md

  pjedge

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• Update README.md

  pjedge

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• removed print statements from calculate_haplotype_statistics.py

  pjedge

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• added reproduce_hapcut2_paper/run_hapcut2_fosmid directory, which contains a simple bash script to test HapCUT2 with Duitama fosmid data

  pjedge

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Commits on Jul 11, 2018

• bug fix in calculate_haplotype_statistics for triallelic variants

  pjedge

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Commits on Jun 26, 2018

• resolved conflict

  pjedge

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• update to calculate_haplotype_statistics to allow phase set (PS) to be a string, as seen in GIAB datasets

  pjedge

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Commits on Jun 21, 2018

• Merge branch 'master' of https://github.com/vibansal/HapCUT2

  pjedge

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• fixed a small issue with how calculate_haplotype_statistics works at triallelic sites when the reference and test haplotypes have different genotypes

  pjedge

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Commits on Jun 20, 2018

• Update README.md

  pjedge

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• tweaked the stdout description of calculate_haplotype_statistics.py

  pjedge

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• Merge branch 'master' of https://github.com/vibansal/HapCUT2

  pjedge

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• updated calculate_haplotype_statistics.py

  pjedge

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Commits on Jun 13, 2018

• Update Snakefile

  pjedge

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Commits on May 4, 2018

• fixed issue with reading in VCFs where excluding trailing FORMAT fields causes a segfault.

  pjedge

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Commits on Mar 15, 2018

• handle cigar operations (X/=) in extracthairs

  vibansal

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• updates for output VCF

  vibansal

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Commits on Mar 13, 2018

• minor edit

  vibansal

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• updated readme for VCF output

  vibansal

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• Several updates:

  vibansal

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• updated reading of fasta file to only keep those chromosomes/contigs relevant to VCF (reduce memory footprint)

  vibansal

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Commits on Mar 12, 2018

• add option to output haplotype-assignment for each read from HapCUT2 (-rh)

  vibansal

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Commits on Mar 10, 2018

• 1. handle =/X cigar in BAM files

  vibansal

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Commits on Mar 9, 2018

• Merge branch 'master' into regions

  vibansal

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• minor edits to bam parsing

  vibansal

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• increased size of buffer for reading VCF file (should be dynamic ideally)

  vibansal

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