[med-svn] [hisat2] 01/05: Updated version 2.1.0 from 'upstream/2.1.0'

[Andreas Tille]

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tille pushed a commit to tag debian/2.1.0-1
in repository hisat2.

commit f2507fbc66b1f50e33f12bc91881f383f9922bf5
Merge: 4ea99af 81f4522
Author: Andreas Tille <tille at debian.org>
Date:   Mon Sep 4 14:37:20 2017 +0200

    Updated version 2.1.0 from 'upstream/2.1.0'
    
    with Debian dir 0ccdbdb0fb254230ed4ea3ad90a0fbc721fbccad

 MANUAL                                             |   17 +-
 MANUAL.markdown                                    |   54 +-
 Makefile                                           |    2 +
 VERSION                                            |    2 +-
 aligner_swsse.h                                    |    2 +-
 aligner_swsse_ee_i16.cpp                           |    2 +-
 aligner_swsse_ee_u8.cpp                            |    2 +-
 aligner_swsse_loc_i16.cpp                          |    2 +-
 aligner_swsse_loc_u8.cpp                           |    2 +-
 aln_sink.h                                         |  535 ++--
 alt.h                                              |  109 +-
 diff_sample.h                                      |    4 +-
 doc/manual.inc.html                                |   28 +-
 ds.cpp                                             |    2 +-
 fast_mutex.h                                       |  542 ++--
 gbwt_graph.h                                       |   34 +-
 gfm.h                                              |   77 +-
 gp.h                                               |   24 +-
 hgfm.h                                             |   15 +-
 hi_aligner.h                                       |  629 ++++-
 hisat2                                             |  124 +-
 hisat2.cpp                                         |  107 +-
 hisat2_build.cpp                                   |   11 +-
 hisat2_genotype.py                                 | 1099 --------
 hisat2_inspect.cpp                                 |   23 +-
 hisat2_test_BRCA_genotyping.py                     |  827 ------
 hisat2_test_HLA_genotyping.py                      | 2699 --------------------
 hisatgenotype.py                                   |  489 ++++
 ...type_genome.py => hisatgenotype_build_genome.py |  382 ++-
 hisatgenotype_extract_reads.py                     |  430 ++++
 hisatgenotype_extract_vars.py                      | 1264 +++++----
 ...tgenotype_typing.py => hisatgenotype_hla_cyp.py |  223 +-
 hisatgenotype_locus.py                             | 2335 +++++++++++++++++
 hisatgenotype_modules/__init__.py                  |    0
 .../hisatgenotype_assembly_graph.py                | 1771 +++++++++++++
 .../hisatgenotype_convert_codis.py                 |  627 +++++
 .../hisatgenotype_extract_codis_data.py            |  166 ++
 .../hisatgenotype_extract_cyp_data.py              | 1061 ++++++++
 hisatgenotype_modules/hisatgenotype_gene_typing.py |   18 +
 .../hisatgenotype_typing_common.py                 | 1549 +++++++++++
 hisatgenotype_scripts/compare_HLA_Omixon.py        |  129 +
 hisatgenotype_scripts/extract_Omixon_HLA.py        |  115 +
 .../get_haplotype_ILMN_StrandSeq.py                |   97 +
 .../hisatgenotype_HLA_genotyping_PGs.py            |  199 ++
 .../hisatgenotype_locus_samples.py                 |  275 ++
 old_hisat2_test_HLA_genotyping.py                  | 1341 ----------
 opts.h                                             |    6 +
 pe.cpp                                             |    1 +
 processor_support.h                                |    9 +-
 qual.h                                             |    1 +
 spliced_aligner.h                                  |  149 +-
 tp.h                                               |   12 +-
 util.h                                             |    2 +-
 53 files changed, 11897 insertions(+), 7728 deletions(-)

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