[med-svn] [plink1.9] branch master updated (54a8a21 -> ee54642)

[Dylan Aïssi]

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bob.dybian-guest pushed a change to branch master
in repository plink1.9.

      from  54a8a21   Updated d/changelog
       new  71a56b4   Imported Upstream version 1.90~b3l-150418
       new  ee54642   Merge tag 'upstream/1.90_b3l-150418'

The 2 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 Makefile         |    2 +-
 bgzf.c           | 1123 +++++++++++++++++++++++++++++++++++++++++++++++++
 bgzf.h           |  313 ++++++++++++++
 hfile.c          |  578 ++++++++++++++++++++++++++
 hfile.h          |  212 ++++++++++
 hfile_internal.h |   76 ++++
 hts.h            |  456 ++++++++++++++++++++
 hts_defs.h       |   55 +++
 khash.h          |  619 +++++++++++++++++++++++++++
 pigz.c           |  463 +++++++++++++++++----
 pigz.h           |  148 ++++++-
 plink.c          |  525 +++++++++++++++--------
 plink_assoc.c    |    8 +-
 plink_calc.c     |  993 +++++++++++++++++++++++---------------------
 plink_calc.h     |    4 +-
 plink_cluster.c  |    7 +-
 plink_common.c   |  153 +++----
 plink_common.h   |  149 ++++---
 plink_data.c     |  376 ++++++++++++-----
 plink_dosage.c   |  330 +++++----------
 plink_family.c   | 1216 +++++++++++++++++++++++++++++++++++++++++++++++++-----
 plink_family.h   |   26 +-
 plink_filter.c   |  233 +++++++----
 plink_filter.h   |    8 +-
 plink_glm.c      |   45 +-
 plink_help.c     |   78 ++--
 plink_ld.c       |   43 +-
 plink_misc.c     |  326 +++++++--------
 plink_misc.h     |   10 +-
 plink_set.c      |    1 +
 yarn.h           |    5 +
 31 files changed, 6969 insertions(+), 1612 deletions(-)
 create mode 100644 bgzf.c
 create mode 100644 bgzf.h
 create mode 100644 hfile.c
 create mode 100644 hfile.h
 create mode 100644 hfile_internal.h
 create mode 100644 hts.h
 create mode 100644 hts_defs.h
 create mode 100644 khash.h

-- 
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