[med-svn] [gmap] branch upstream updated (12dd632 -> eff24d5)

Alex Mestiashvili malex-guest at moszumanska.debian.org
Tue Jul 1 16:33:16 UTC 2014


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

malex-guest pushed a change to branch upstream
in repository gmap.

      from  12dd632   Imported Upstream version 2013-07-20
       new  eff24d5   Imported Upstream version 2014-06-10

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:
 ChangeLog                                          |  2272 +-
 Makefile.am                                        |     4 +-
 Makefile.in                                        |    13 +-
 NOTICE                                             |    85 +
 README                                             |   458 +-
 TODO                                               |     3 +
 VERSION                                            |     2 +-
 acinclude.m4                                       |     3 +-
 config/acx_mmap_fixed.m4                           |     4 +-
 config/acx_mmap_variable.m4                        |     4 +-
 config/ax_ext.m4                                   |   181 +-
 ...x_gcc_x86_cpuid.m4 => ax_gcc_x86_avx_xgetbv.m4} |    54 +-
 config/madvise-flags.m4                            |     9 +
 config/popcnt.m4                                   |    42 -
 config/sse2_shift_defect.m4                        |    26 +
 configure                                          |  3216 +-
 configure.ac                                       |    34 +-
 src/Makefile.am                                    |   167 +-
 src/Makefile.in                                    |  2954 +-
 src/access.c                                       |   160 +-
 src/atoiindex.c                                    |   608 +-
 src/bitpack64-access.c                             |  2135 +
 src/bitpack64-access.h                             |     9 +
 src/bitpack64-read.c                               | 14517 ++++
 src/bitpack64-read.h                               |    30 +
 src/bitpack64-readtwo.c                            | 14242 ++++
 src/bitpack64-readtwo.h                            |    15 +
 src/bitpack64-write.c                              |  5447 ++
 src/bitpack64-write.h                              |    24 +
 src/boyer-moore.c                                  |    49 +-
 src/bytecoding.c                                   |   785 +
 src/bytecoding.h                                   |    53 +
 src/{diagpool.c => cellpool.c}                     |   134 +-
 src/cellpool.h                                     |    40 +
 src/chimera.c                                      |   359 +-
 src/chimera.h                                      |    20 +-
 src/chrom.c                                        |    15 +-
 src/chrom.h                                        |     6 +-
 src/chrsubset.c                                    |   490 -
 src/chrsubset.h                                    |    43 -
 src/cmetindex.c                                    |   609 +-
 src/compress-write.c                               |   689 +
 src/{compress.h => compress-write.h}               |    28 +-
 src/compress.c                                     |  2629 +-
 src/compress.h                                     |    44 +-
 src/config.h.in                                    |    45 +-
 src/diag.c                                         |   112 +-
 src/diag.h                                         |    10 +-
 src/diagpool.c                                     |     4 +-
 src/doublelist.c                                   |   154 +
 src/doublelist.h                                   |    24 +
 src/dynprog.c                                      | 11066 +--
 src/dynprog.h                                      |   361 +-
 src/dynprog_cdna.c                                 |  1321 +
 src/dynprog_cdna.h                                 |    32 +
 src/dynprog_end.c                                  |  3202 +
 src/dynprog_end.h                                  |   117 +
 src/dynprog_genome.c                               |  3900 +
 src/dynprog_genome.h                               |    35 +
 src/dynprog_simd.c                                 |  4928 ++
 src/dynprog_simd.h                                 |   121 +
 src/dynprog_single.c                               |  1375 +
 src/dynprog_single.h                               |    57 +
 src/fastlog.h                                      |   124 +
 src/genome-write.c                                 |    40 +-
 src/genome-write.h                                 |    13 +-
 src/genome.c                                       |   726 +-
 src/genome.h                                       |    25 +-
 src/genome128_hr.c                                 | 23774 ++++++
 src/genome128_hr.h                                 |    76 +
 src/genome_hr.c                                    | 71664 -------------------
 src/genome_hr.h                                    |   146 -
 src/genome_sites.c                                 | 26262 +++++++
 src/genome_sites.h                                 |    49 +
 src/genomicpos.c                                   |    11 +-
 src/genomicpos.h                                   |    10 +-
 src/get-genome.c                                   |   248 +-
 src/gmap.c                                         |  2684 +-
 src/gmapindex.c                                    |   701 +-
 src/goby.c                                         |     8 +-
 src/goby.h                                         |     4 +-
 src/gregion.c                                      |    98 +-
 src/gsnap.c                                        |   883 +-
 src/iit-read-univ.c                                |    36 +-
 src/iit-read.c                                     |   686 +-
 src/iit-read.h                                     |    23 +-
 src/iit-write-univ.c                               |     2 +-
 src/iit-write-univ.h                               |     8 +-
 src/iit-write.c                                    |    96 +-
 src/iit-write.h                                    |     8 +-
 src/iit_get.c                                      |   522 +-
 src/iit_store.c                                    |   133 +-
 src/iitdef.h                                       |    24 +-
 src/inbuffer.c                                     |    53 +-
 src/indel.c                                        |   340 +
 src/indel.h                                        |    30 +
 src/indexdb-write.c                                |  2111 +-
 src/indexdb-write.h                                |    78 +-
 src/indexdb.c                                      |  1842 +-
 src/indexdb.h                                      |    88 +-
 src/indexdb_hr.c                                   |   412 +-
 src/indexdbdef.h                                   |    41 +-
 src/interval.c                                     |    35 +-
 src/interval.h                                     |     6 +-
 src/intlist.c                                      |    22 +-
 src/intlist.h                                      |     4 +-
 src/littleendian.c                                 |    12 +-
 src/littleendian.h                                 |     8 +-
 src/mapq.c                                         |    22 +-
 src/mapq.h                                         |     8 +-
 src/mem.c                                          |   205 +-
 src/mem.h                                          |    18 +-
 src/oligo.c                                        |   164 +-
 src/oligoindex.c                                   |  2020 -
 src/oligoindex.h                                   |   106 -
 src/oligoindex_hr.c                                |  7884 +-
 src/oligoindex_hr.h                                |    54 +-
 src/outbuffer.c                                    |  1230 +-
 src/outbuffer.h                                    |    22 +-
 src/pair.c                                         |   422 +-
 src/pair.h                                         |    28 +-
 src/pairdef.h                                      |     5 +-
 src/pairpool.c                                     |   515 +-
 src/pairpool.h                                     |    28 +-
 src/popcount.c                                     |  4116 ++
 src/popcount.h                                     |    18 +
 src/resulthr.c                                     |     3 +-
 src/saca-k.c                                       |   509 +
 src/saca-k.h                                       |    10 +
 src/samflags.h                                     |    29 +-
 src/samheader.c                                    |    52 +
 src/samheader.h                                    |    14 +
 src/samprint.c                                     |  2133 +-
 src/samprint.h                                     |    55 +-
 src/sarray-read.c                                  |  3736 +
 src/sarray-read.h                                  |    45 +
 src/sarray-write.c                                 |  1588 +
 src/sarray-write.h                                 |    54 +
 src/scores.h                                       |    10 +-
 src/segmentpos.c                                   |    19 +-
 src/segmentpos.h                                   |     4 +-
 src/sequence.c                                     |   134 +-
 src/sequence.h                                     |     8 +-
 src/shortread.c                                    |   648 +-
 src/shortread.h                                    |    20 +-
 src/smooth.c                                       |   576 +-
 src/smooth.h                                       |     6 +-
 src/snpindex.c                                     |   328 +-
 src/spanningelt.c                                  |   339 +-
 src/spanningelt.h                                  |    31 +-
 src/splice.c                                       |  1628 +
 src/splice.h                                       |    65 +
 src/splicestringpool.c                             |   223 +
 src/splicestringpool.h                             |    38 +
 src/splicetrie.c                                   |   159 +-
 src/splicetrie.h                                   |    10 +-
 src/splicetrie_build.c                             |  1593 +-
 src/splicetrie_build.h                             |    12 +-
 src/stage1.c                                       |   318 +-
 src/stage1.h                                       |     9 +-
 src/stage1hr.c                                     | 13415 ++--
 src/stage1hr.h                                     |    40 +-
 src/stage2.c                                       |  4411 +-
 src/stage2.h                                       |    68 +-
 src/stage3.c                                       |  6488 +-
 src/stage3.h                                       |    96 +-
 src/stage3hr.c                                     |  3873 +-
 src/stage3hr.h                                     |   152 +-
 src/stopwatch.c                                    |    18 +-
 src/substring.c                                    |   649 +-
 src/substring.h                                    |    47 +-
 src/table.c                                        |    21 +-
 src/table.h                                        |     4 +-
 src/translation.c                                  |    31 +-
 src/types.h                                        |    39 +-
 src/uint8list.c                                    |    20 +-
 src/uint8list.h                                    |     4 +-
 src/uintlist.c                                     |    20 +-
 src/uintlist.h                                     |     4 +-
 src/uniqscan.c                                     |   267 +-
 src/univinterval.c                                 |    63 +-
 src/univinterval.h                                 |    13 +-
 tests/Makefile.in                                  |     7 +-
 util/Makefile.am                                   |    33 +-
 util/Makefile.in                                   |    71 +-
 util/{psl_genes.pl.in => ensembl_genes.pl.in}      |    31 +-
 util/fa_coords.pl.in                               |    96 +-
 util/gmap_build.pl.in                              |   379 +-
 util/gmap_process.pl.in                            |    19 +-
 util/gmap_setup.pl.in                              |   459 -
 util/gvf_iit.pl.in                                 |    63 +
 191 files changed, 166756 insertions(+), 109157 deletions(-)
 create mode 100644 NOTICE
 create mode 100644 TODO
 copy config/{ax_gcc_x86_cpuid.m4 => ax_gcc_x86_avx_xgetbv.m4} (57%)
 delete mode 100644 config/popcnt.m4
 create mode 100644 config/sse2_shift_defect.m4
 create mode 100644 src/bitpack64-access.c
 create mode 100644 src/bitpack64-access.h
 create mode 100644 src/bitpack64-read.c
 create mode 100644 src/bitpack64-read.h
 create mode 100644 src/bitpack64-readtwo.c
 create mode 100644 src/bitpack64-readtwo.h
 create mode 100644 src/bitpack64-write.c
 create mode 100644 src/bitpack64-write.h
 create mode 100644 src/bytecoding.c
 create mode 100644 src/bytecoding.h
 copy src/{diagpool.c => cellpool.c} (51%)
 create mode 100644 src/cellpool.h
 delete mode 100644 src/chrsubset.c
 delete mode 100644 src/chrsubset.h
 create mode 100644 src/compress-write.c
 copy src/{compress.h => compress-write.h} (51%)
 create mode 100644 src/doublelist.c
 create mode 100644 src/doublelist.h
 create mode 100644 src/dynprog_cdna.c
 create mode 100644 src/dynprog_cdna.h
 create mode 100644 src/dynprog_end.c
 create mode 100644 src/dynprog_end.h
 create mode 100644 src/dynprog_genome.c
 create mode 100644 src/dynprog_genome.h
 create mode 100644 src/dynprog_simd.c
 create mode 100644 src/dynprog_simd.h
 create mode 100644 src/dynprog_single.c
 create mode 100644 src/dynprog_single.h
 create mode 100755 src/fastlog.h
 create mode 100644 src/genome128_hr.c
 create mode 100644 src/genome128_hr.h
 delete mode 100644 src/genome_hr.c
 delete mode 100644 src/genome_hr.h
 create mode 100644 src/genome_sites.c
 create mode 100644 src/genome_sites.h
 create mode 100644 src/indel.c
 create mode 100644 src/indel.h
 delete mode 100644 src/oligoindex.c
 delete mode 100644 src/oligoindex.h
 create mode 100644 src/popcount.c
 create mode 100644 src/popcount.h
 create mode 100644 src/saca-k.c
 create mode 100644 src/saca-k.h
 create mode 100644 src/samheader.c
 create mode 100644 src/samheader.h
 create mode 100644 src/sarray-read.c
 create mode 100644 src/sarray-read.h
 create mode 100644 src/sarray-write.c
 create mode 100644 src/sarray-write.h
 create mode 100644 src/splice.c
 create mode 100644 src/splice.h
 create mode 100644 src/splicestringpool.c
 create mode 100644 src/splicestringpool.h
 copy util/{psl_genes.pl.in => ensembl_genes.pl.in} (55%)
 delete mode 100755 util/gmap_setup.pl.in
 create mode 100755 util/gvf_iit.pl.in

-- 
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