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Commits on Jul 17, 2020

• only keep self-link to package name hal around for tests

  diekhans

  committed
  5624678

Commits on Jun 25, 2020

• start hal2paf

  Show description for a29e584
  glennhickey

  committed
  a29e584

Commits on Apr 1, 2020

• added hal2mafMP very basic tests

  diekhans

  committed
  5599e29

Commits on May 19, 2019

• added reserved fields to some of the mmap objects to allow for later expansion

  diekhans

  committed
  f9b79ba

Commits on Nov 20, 2018

• dropped halChain

  diekhans

  committed
  a1c61d4

Commits on Oct 6, 2018

• try -std=c++11

  diekhans

  committed
  a3f0e0b

• change tests to run directly from makefile rather than pytest

  diekhans

  committed
  3f3c85d

Commits on Oct 5, 2018

• rework of makefiles to allow parallel builds

  diekhans

  committed
  c58d049

Commits on Oct 4, 2018

• Merge remote-tracking branch 'origin/efficient-maf-revamp' into flatbuf

  joelarmstrong

  committed
  379c083

Commits on Sep 20, 2018

• code for hal2synteny feature

  

  Ksenia Krasheninnikova

  committed
  9b639fd

Commits on Aug 23, 2018

• Efficient MAF revamp dump

  Show description for 0b490aa
  joelarmstrong

  committed
  0b490aa

Commits on Jun 26, 2015

• Call sub-makes so that flacts are passed through

  diekhans

  committed
  7a0c14e

Commits on Nov 17, 2014

• rename halAlignability to halAlignmentDepth as per Marks request

  glennhickey

  committed
  f076c71

Commits on Jan 22, 2014

• Merge branch 'modificationTools' of https://github.com/glennhickey/hal into development

  Show description for 8c70e1b
  joelarmstrong

  committed
  8c70e1b

Commits on Oct 11, 2013

• fix merge from dev

  glennhickey

  committed
  c7a44ee

Commits on Oct 2, 2013

• Modularize and move hal2assemblyHub to assemblyHub directory

  ngannguyen

  committed
  244fe86

Commits on Aug 14, 2013

• move halBlockMapper from chain to liftover to break circular dependency created by adding maf function to chain

  glennhickey

  committed
  00d0534

Commits on Aug 13, 2013

• hack in halGetMaf to the C interface in chains

  glennhickey

  committed
  109b87b

Commits on Jul 13, 2013

• Tools for adding/removing/inserting genomes

  joelarmstrong

  committed
  07bf057

Commits on Jul 1, 2013

• add hal4dExtract tool and consolidate mask and extract dirs

  glennhickey

  committed
  35cc73c

Commits on Jun 27, 2013

• revamp hal2maf to use halBedScanner

  glennhickey

  committed
  4598f96

Commits on Jun 21, 2013

• merge development

  glennhickey

  committed
  cff0c79

Commits on Jun 7, 2013

• add enable def to compiler opts

  glennhickey

  committed
  6b18d19

Commits on Jun 6, 2013

• start integrating Melissas phyloP module

  glennhickey

  committed
  a630cde

• merge development

  glennhickey

  committed
  3985e8c

Commits on May 29, 2013

• put liftover after chain in build to reflect new dependency

  glennhickey

  committed
  64b968b

Commits on Apr 16, 2013

• add Lod manager and incorporate into blockviz code

  glennhickey

  committed
  c4e81f6

Commits on Mar 21, 2013

• revise to create new node for each paralgous instance

  glennhickey

  committed
  9ef0435

Commits on Mar 5, 2013

• merge development

  glennhickey

  committed
  9ba1ed7

• merge development

  glennhickey

  committed
  de8344e

Commits on Feb 8, 2013

• add halAlignability tool to print simple alignability wiggles. next step will be gerp-like conservation scores

  glennhickey

  committed
  9f78b32

Commits on Feb 6, 2013

• fix compile

  glennhickey

  committed
  7cdcb97

Commits on Jan 31, 2013

• add hal2fasta

  glennhickey

  committed
  acc60b1

Commits on Dec 18, 2012

• start adding halTreeNI tools for neutral indel

  glennhickey

  committed
  9df4391

Commits on Dec 13, 2012

• add framewoark for mask tools

  glennhickey

  committed
  ca22797

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