1. 01 Apr, 2014 12 commits
  2. 27 Mar, 2014 8 commits
  3. 26 Mar, 2014 2 commits
    • Mikaël Salson's avatar
      .gitignore: conf.js · bea5d4bd
      Mikaël Salson authored
      This is a file specific to each people. No reason for versioning
      bea5d4bd
    • Mikaël Salson's avatar
      Tests: Representative has become larger. · 039218c5
      Mikaël Salson authored
      Because of the value for min_cover_representative that has changed (commit
      4ee616a) the value computed in that case is now 4 instead of 5. So the
      representative is slightly longer which shifted the positions.
      039218c5
  4. 25 Mar, 2014 1 commit
    • Mikaël Salson's avatar
      Makefile: Improve management of dependencies · 082b6b4f
      Mikaël Salson authored
      The library is now built in core, where we have the list of dependencies
      (dep.mk). Before dep.mk was in algo/ but the files it was refering to were in
      core/. Thus the dep.mk file was useless.
      082b6b4f
  5. 26 Mar, 2014 11 commits
  6. 25 Mar, 2014 6 commits
    • Mathieu Giraud's avatar
      vidjil: prepare CHANGELOG for release · a9dd3ea5
      Mathieu Giraud authored
      a9dd3ea5
    • Mathieu Giraud's avatar
    • Mathieu Giraud's avatar
      vidjil.cpp: update help examples · 6ba3b43f
      Mathieu Giraud authored
      Now that a representative is almost always found, it is better to limit short
      examples to a small number of clones.
      6ba3b43f
    • Mathieu Giraud's avatar
      vidjil.cpp: min_cover_representative is now a ratio of min_reads_clone (-R) · 0bfd51db
      Mathieu Giraud authored
      This enables to have representatives even when setting -R to very small values.
      As a side effect, option -A should return representatives for every clone (-R is 1).
      0bfd51db
    • Mikaël Salson's avatar
      Tests: Changes in germline dataset · 9c2b6a90
      Mikaël Salson authored
      Changes in some sequences (in particular IGHV7-40*03) are responsible for
      those number changes. There is no such changes when using the previous
      germline dataset.
      
      For information IGHV7-40*03 changed from:
      >Z12320|IGHV7-40*03|Homo sapiens|P|V-REGION|1..291|289 nt|1| | | | |289+0=289|partial in 5'| |
      ctgcagctggtgcagtctgggcctgaggtgaagaagcctggggcctcagtgaaggtctcc
      tataagtcttctggttacaccttcaccatctatggtatgaattgggtatgatagacccct
      ggacagggctttgagtggatgtgatggatcatcacctacactgggaacccaacgtatacc
      cacggcttcacaggatggtttgtcttctccatggacacgtctgtcagcacggcgtgtctt
      cagatcagcagcctaaaggctgaggacacggccgagtattactgtgcga
      to:
      >AC241995|IGHV7-40*03|Homo sapiens|P|V-REGION|10101..10396|296 nt|1| | | | |296+0=296| | |
      ttttcaatagaaaagtcaaataatctaagtgtcaatcagtggatgattagataaaatatg
      atatatgtaaatcatggaatactatgcagccagtatggtatgaattcagtgtgaccagcc
      cctggacaagggcttgagtggatgggatggatcatcacctacactgggaacccaacatat
      accaacggcttcacaggacggtttctattctccatggacacctctgtcagcatggcgtat
      ctgcagatcagcagcctaaaggctgaggacacggccgtgtatgactgtatgagaga
      9c2b6a90
    • Mikaël Salson's avatar
      Tests: Default behaviour changed in Vidjil · 80d0e0d6
      Mikaël Salson authored
      Maybe we don't need to monitor default behaviour changes in every test.
      So I set the seed as a parameter to avoid test failures.
      80d0e0d6