[med-svn] [snp-sites] branch master updated (b7f7c48 -> e9f666c)

[Jorge Soares]

This is an automated email from the git hooks/post-receive script.

jssoares-guest pushed a change to branch master
in repository snp-sites.

      from  b7f7c48   Cleaning project to prepare next upload
       new  e9f666c   Added autoreconf to the build dependencies in debian/control. This allows debian package instalation directly form upstream git project

The 1 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:
 AUTHORS                                            |   1 +
 INSTALL                                            |  15 +
 LICENSE                                            | 641 +++++++++++++++++++++
 Makefile.am                                        |   1 +
 README.md                                          |  40 ++
 VERSION                                            |   1 +
 configure.ac                                       |  14 +
 debian/changelog                                   |   5 +
 debian/compat                                      |   1 +
 debian/control                                     |  41 ++
 debian/copyright                                   |  48 ++
 debian/docs                                        |   1 +
 debian/libsnp-sites1-dev.install                   |   8 +
 debian/libsnp-sites1.install                       |   1 +
 debian/patches/series                              |   1 +
 debian/rules                                       |  13 +
 debian/snp-sites.install                           |   1 +
 debian/source/format                               |   1 +
 src/Makefile.am                                    |  22 +
 src/alignment-file.c                               | 280 +++++++++
 src/alignment-file.h                               |  41 ++
 src/fasta-of-snp-sites.c                           |  49 ++
 src/fasta-of-snp-sites.h                           |  26 +
 src/kseq.h                                         | 235 ++++++++
 src/main.c                                         |  88 +++
 src/parse-phylip.c                                 |  51 ++
 src/parse-phylip.h                                 |  33 ++
 src/phylib-of-snp-sites.c                          |  55 ++
 src/phylib-of-snp-sites.h                          |  27 +
 src/snp-sites.c                                    | 235 ++++++++
 src/snp-sites.h                                    |  33 ++
 src/string-cat.c                                   |  42 ++
 src/string-cat.h                                   |  28 +
 src/vcf.c                                          | 178 ++++++
 src/vcf.h                                          |  33 ++
 tests/check-snp-sites.c                            | 260 +++++++++
 tests/check-snp-sites.h                            |  27 +
 .../alignment_file_multiple_lines_per_sequence.aln | 226 ++++++++
 .../data/alignment_file_one_line_per_sequence.aln  | 218 +++++++
 .../alignment_file_one_line_per_sequence.aln.gz    | Bin 0 -> 3447 bytes
 ...alignment_file_one_line_per_sequence.aln.phylip | 110 ++++
 ...nt_file_one_line_per_sequence.aln.snp_sites.aln | 218 +++++++
 .../alignment_file_one_line_per_sequence.aln.vcf   |   8 +
 tests/data/alignment_file_with_n.aln               | 218 +++++++
 tests/data/alignment_file_with_n.aln.phylip        | 110 ++++
 tests/data/alignment_file_with_n.aln.snp_sites.aln | 218 +++++++
 tests/data/alignment_file_with_n.aln.vcf           |   8 +
 tests/data/small_alignment.aln                     |   6 +
 tests/data/uneven_alignment.aln                    |   6 +
 tests/helper-methods.c                             |  67 +++
 tests/helper-methods.h                             |  25 +
 tests/run-all-tests.c                              |  37 ++
 52 files changed, 4052 insertions(+)
 create mode 100644 AUTHORS
 create mode 100644 INSTALL
 create mode 100644 LICENSE
 create mode 100644 Makefile.am
 create mode 100644 README.md
 create mode 100644 VERSION
 create mode 100644 configure.ac
 create mode 100644 debian/changelog
 create mode 100644 debian/compat
 create mode 100644 debian/control
 create mode 100644 debian/copyright
 create mode 100644 debian/docs
 create mode 100644 debian/libsnp-sites1-dev.install
 create mode 100644 debian/libsnp-sites1.install
 create mode 100644 debian/patches/series
 create mode 100755 debian/rules
 create mode 100644 debian/snp-sites.install
 create mode 100644 debian/source/format
 create mode 100644 src/Makefile.am
 create mode 100644 src/alignment-file.c
 create mode 100644 src/alignment-file.h
 create mode 100644 src/fasta-of-snp-sites.c
 create mode 100644 src/fasta-of-snp-sites.h
 create mode 100644 src/kseq.h
 create mode 100644 src/main.c
 create mode 100644 src/parse-phylip.c
 create mode 100644 src/parse-phylip.h
 create mode 100644 src/phylib-of-snp-sites.c
 create mode 100644 src/phylib-of-snp-sites.h
 create mode 100644 src/snp-sites.c
 create mode 100644 src/snp-sites.h
 create mode 100644 src/string-cat.c
 create mode 100644 src/string-cat.h
 create mode 100644 src/vcf.c
 create mode 100644 src/vcf.h
 create mode 100644 tests/check-snp-sites.c
 create mode 100644 tests/check-snp-sites.h
 create mode 100644 tests/data/alignment_file_multiple_lines_per_sequence.aln
 create mode 100644 tests/data/alignment_file_one_line_per_sequence.aln
 create mode 100644 tests/data/alignment_file_one_line_per_sequence.aln.gz
 create mode 100644 tests/data/alignment_file_one_line_per_sequence.aln.phylip
 create mode 100644 tests/data/alignment_file_one_line_per_sequence.aln.snp_sites.aln
 create mode 100644 tests/data/alignment_file_one_line_per_sequence.aln.vcf
 create mode 100644 tests/data/alignment_file_with_n.aln
 create mode 100644 tests/data/alignment_file_with_n.aln.phylip
 create mode 100644 tests/data/alignment_file_with_n.aln.snp_sites.aln
 create mode 100644 tests/data/alignment_file_with_n.aln.vcf
 create mode 100644 tests/data/small_alignment.aln
 create mode 100644 tests/data/uneven_alignment.aln
 create mode 100644 tests/helper-methods.c
 create mode 100644 tests/helper-methods.h
 create mode 100644 tests/run-all-tests.c

-- 
Alioth's /git/debian-med/git-commit-notice on /srv/git.debian.org/git/debian-med/snp-sites.git