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      from  a84e526   Imported Upstream version 1.5.9+ds
       new  17a2684   New upstream version 1.5.10+ds

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Summary of changes:
 .travis.yml                                        |   45 +-
 CHANGELOG                                          |   19 +-
 Makefile                                           |   15 +-
 VERSION                                            |    2 +-
 doc/RELEASE                                        |    4 -
 gtdata/modules/gtdoclib/docvisitorlatex.lua        |   27 +-
 gtdata/modules/gtdoclib/gtscript_header.lp         |    1 -
 gtdata/modules/gtdoclib/libgenometools_header.lp   |    1 -
 gtpython/README                                    |    2 +-
 scripts/SEmatch.rb                                 |  151 +
 scripts/all-vs-all.sh                              |    6 +-
 scripts/alloutputoptions.rb                        |   44 +-
 scripts/build_dists.sh                             |    8 +
 scripts/check-fstperquery.rb                       |   55 +
 scripts/cleanpp.sh                                 |    1 +
 scripts/cmp_db_query_exch.rb                       |    4 +-
 scripts/collect-mappings.rb                        |   26 -
 scripts/convert2myersformat.rb                     |   77 +-
 scripts/cutsequences.rb                            |   61 +
 scripts/enumkmers.rb                               |   26 +
 scripts/esq-in-bytes.sh                            |   25 +-
 scripts/estim-kmer-size.rb                         |   25 +
 scripts/evalue-filter.rb                           |   29 +
 scripts/extract-seed.rb                            |   18 +
 scripts/fasta.rb                                   |  112 +
 scripts/findfasta.rb                               |   28 +-
 scripts/gen-display-struct.rb                      |  226 +
 scripts/gen-intsets.rb                             |   35 +-
 scripts/gen-radixsort-ip.rb                        |  466 +-
 scripts/gen-radixsort-ip.sh                        |    1 +
 scripts/gfa2lint.rb                                |  148 +
 scripts/manyshort-somelong.rb                      |   23 +
 scripts/matches-compare.rb                         |  396 +
 scripts/matches2ani.rb                             |   52 +
 scripts/mk_ft_longest_common.rb                    |  258 +
 scripts/print_sequence.rb                          |    7 +
 scripts/reverse-complement.rb                      |   19 +
 scripts/run-se-da.sh                               |    4 +-
 scripts/se-permutation.rb                          |   45 +
 scripts/seeds2maxmatches.rb                        |   95 +
 scripts/sensitivity-test.rb                        |    4 +-
 scripts/sim-read-mapping.sh                        |   60 +-
 scripts/single-read-mapping.sh                     |   30 +
 scripts/skmake.rb                                  |   15 +-
 scripts/travis_installdeps.sh                      |   13 +
 scripts/{alloutputoptions.rb => turnwheel.rb}      |   23 +-
 src/annotationsketch/custom_track_gc_content.c     |    4 +-
 src/core/accspecialrange.gen                       |   50 +
 src/core/alphabet.c                                |   25 +-
 src/core/arraydef.h                                |   41 +-
 src/core/bitbuffer.c                               |  301 +-
 src/core/bitbuffer.h                               |   70 +-
 src/core/bitpackstringsimpleop.h                   |   11 +-
 src/core/colorspace.h                              |    6 +-
 src/core/csvline_reader.c                          |  302 +
 src/core/csvline_reader.h                          |   85 +
 src/core/encseq.c                                  |   90 +-
 src/core/encseq.h                                  |   19 +-
 src/core/fptr_api.h                                |    2 +-
 src/core/gtdatapath.c                              |   15 +-
 src/core/mail_address.h                            |    2 +-
 src/core/radix_sort.c                              |  241 +-
 src/core/radix_sort.h                              |   11 +
 src/core/radixsort-ip-flba.inc                     |  364 +
 src/core/radixsort-ip-uint64keypair.inc            |  211 +-
 src/core/radixsort-ip-ulong.inc                    |  203 +-
 src/core/radixsort-ip-ulongpair.inc                |  203 +-
 src/core/str.c                                     |    7 +
 src/core/str.h                                     |    2 +
 src/core/timer.c                                   |   45 +-
 src/core/timer_api.h                               |    3 +
 src/core/unused_api.h                              |    6 +
 src/extended/alignment.c                           |  164 +-
 src/extended/alignment.h                           |   13 +-
 src/extended/assembly_stats_calculator.c           |   95 +-
 src/extended/assembly_stats_calculator.h           |    5 +
 src/extended/blast_process_call.h                  |    8 +-
 src/extended/compressed_bitsequence.h              |    6 +-
 src/extended/condenseq.c                           |  170 +-
 src/extended/condenseq.h                           |   14 +-
 src/extended/condenseq_creator.c                   |  448 +-
 src/extended/condenseq_creator.h                   |   14 +-
 src/extended/condenseq_rep.h                       |   10 +-
 src/extended/condenseq_search_arguments.h          |    2 +
 src/extended/editscript.c                          |   54 +-
 src/extended/editscript.h                          |   92 +-
 src/extended/elias_gamma.h                         |    2 +-
 src/extended/encdesc.c                             |    1 -
 src/extended/encdesc_header_io.h                   |    2 +
 src/extended/fasta_header_iterator.h               |    6 +-
 src/extended/gff3_escaping.c                       |   14 +-
 src/extended/gff3_parser.c                         |   21 +-
 src/extended/huffcode.h                            |    2 +-
 src/extended/intset.h                              |    2 +-
 src/extended/intset_16.c                           |   37 +-
 src/extended/intset_16.h                           |    2 +-
 src/extended/intset_32.c                           |   37 +-
 src/extended/intset_32.h                           |    2 +-
 src/extended/intset_8.c                            |   37 +-
 src/extended/intset_8.h                            |    2 +-
 src/extended/io_function_pointers.h                |    6 +-
 src/extended/linspace_management.c                 |    7 +-
 src/extended/match_blast.c                         |   61 +-
 src/extended/match_blast_api.h                     |   35 +-
 src/extended/match_iterator_blast.c                |   59 +-
 src/extended/match_iterator_open.c                 |   11 +-
 src/extended/multieoplist.c                        |   16 +-
 src/extended/multieoplist.h                        |   26 +-
 src/extended/popcount_tab.h                        |    3 +-
 src/extended/ranked_list.c                         |    4 +-
 src/extended/rbtree.c                              |   51 +-
 src/extended/rbtree.h                              |   33 +-
 src/extended/rcr.h                                 |    2 +
 src/extended/safe_popen.c                          |    9 +-
 src/extended/sam_alignment.h                       |   82 +-
 src/extended/sam_query_name_iterator.h             |    4 +-
 src/extended/samfile_iterator.h                    |    2 +-
 src/extended/scorehandler.c                        |   12 +
 src/extended/scorehandler.h                        |    4 +
 src/extended/wtree.h                               |    7 +-
 src/extended/wtree_encseq.c                        |    4 +-
 src/gtt.c                                          |    4 +
 src/match/asqg_writer.c                            |    2 +-
 src/match/asqg_writer.h                            |    2 +-
 src/match/chain2dim.c                              |   19 +-
 src/match/chainofin.c                              |    9 +-
 src/match/diagband-struct.c                        |  349 +
 src/match/diagband-struct.h                        |  170 +
 src/match/diagbandseed.c                           | 4556 +++++++++---
 src/match/diagbandseed.h                           |   89 +-
 src/match/eis-bwtseq-context.c                     |    2 +-
 src/match/esa-mmsearch.c                           |   54 +-
 src/match/esa-mmsearch.h                           |    3 +
 src/match/ft-eoplist.c                             | 1349 ++++
 src/match/ft-eoplist.h                             |  222 +
 src/match/ft-front-generation.c                    |  395 +-
 src/match/ft-front-generation.h                    |   58 +-
 src/match/ft-front-prune.c                         |  981 ++-
 src/match/ft-front-prune.h                         |   57 +-
 src/match/ft-longest-common.inc                    | 1839 +++++
 src/match/ft-polish.c                              |   27 +-
 src/match/ft-polish.h                              |   25 +-
 src/match/ft-trimstat.c                            |  203 +-
 src/match/ft-trimstat.h                            |   36 +-
 src/match/gfa_writer.c                             |  227 +
 src/match/gfa_writer.h                             |   70 +
 src/match/karlin_altschul_stat.c                   |  945 +++
 src/match/karlin_altschul_stat.h                   |   90 +
 src/match/lua_tools.h                              |    3 +
 src/match/querymatch-align.c                       |  967 +--
 src/match/querymatch-align.h                       |  111 +-
 src/match/querymatch-display.c                     |  636 ++
 src/match/querymatch-display.h                     |   67 +
 src/match/querymatch.c                             | 1475 +++-
 src/match/querymatch.h                             |  156 +-
 src/match/rdj-filesuf-def.h                        |    2 +
 src/match/rdj-spmfind.c                            |    1 +
 src/match/rdj-strgraph.c                           |   67 +-
 src/match/rdj-strgraph.h                           |    4 +
 src/match/rectangle-store.c                        |  158 +
 src/match/rectangle-store.h                        |   25 +
 src/match/se-display-fwd.inc                       |   85 +
 src/match/se-display.inc                           |  426 ++
 src/match/seed-extend-iter.c                       |  231 +-
 src/match/seed-extend-iter.h                       |   99 +-
 src/match/seed-extend.c                            | 1395 ++--
 src/match/seed-extend.h                            |  254 +-
 src/match/seed_extend_parts.c                      |  325 +
 src/match/seed_extend_parts.h                      |   73 +
 src/match/seq_or_encseq.h                          |   34 +
 src/match/seqabstract.c                            |   18 +-
 src/match/seqabstract.h                            |    2 +-
 src/match/sfx-diffcov.c                            |    8 +-
 src/match/sfx-run.c                                |    2 +-
 src/match/sfx-suffixgetset.c                       |   11 +-
 src/match/shu-dfs.h                                |   10 +-
 src/match/test-maxpairs.c                          |   18 +-
 src/tools/gt_condenseq_compress.c                  |    6 +-
 src/tools/gt_kmer_database.c                       |    4 +-
 src/tools/gt_readjoiner.c                          |    2 +
 src/tools/gt_readjoiner_asqg.c                     |    2 +-
 .../{gt_readjoiner_asqg.c => gt_readjoiner_gfa.c}  |  147 +-
 .../lua_tools.h => tools/gt_readjoiner_gfa.h}      |   13 +-
 src/tools/gt_repfind.c                             |  495 +-
 src/tools/gt_seed_extend.c                         |  813 ++-
 src/tools/gt_seqorder.c                            |  247 +-
 src/tools/gt_seqstat.c                             |   41 +-
 src/tools/gt_sfxmap.c                              |    6 +-
 src/tools/gt_show_seedext.c                        |  412 +-
 src/tools/gt_sortbench.c                           |  194 +-
 testdata/at-C99887-fwd.fna                         |   14 +
 testdata/at-C99887-rev.fna                         |   14 +
 testdata/at-C99930.fna                             |   12 +
 testdata/gt_seqorder_test_sortlength.fas           |   34 +
 testdata/gt_sketch_textwidth.gff3                  |    2 +-
 testdata/matchtool_see-ext.match                   |   72 +
 testdata/query-fwd.match                           |   55 +
 testdata/query-rev.match                           |   55 +
 testdata/readjoiner/30x_800nt.gfa1                 |   64 +
 testdata/readjoiner/30x_800nt.gfa2                 |   64 +
 testdata/readjoiner/30x_long_varlen.gfa1           |   73 +
 testdata/readjoiner/30x_long_varlen.gfa2           |   73 +
 testdata/readjoiner/70x_100nt.gfa1                 |   82 +
 testdata/readjoiner/70x_100nt.gfa2                 |   82 +
 testdata/readjoiner/contained_varlen.gfa1          |   11 +
 testdata/readjoiner/contained_varlen.gfa2          |   11 +
 .../at1MB-Atinsert-greedy-20-700-75-3-39-a         | 1528 ++--
 .../at1MB-U8-greedy-r-12-30-80-2-36-a              | 1087 +--
 .../repfind-result/at1MB-U8-xdrop-20-20-80-6-a     |  359 +-
 .../repfind-result/at1MB-U8-xdrop-r-12-30-80-6-a   |  562 +-
 .../repfind-result/at1MB-greedy-70-500-90-1-39-a   | 1409 ++--
 .../repfind-result/at1MB-greedy-r-14-32-80-2-36-a  |  226 +-
 testdata/repfind-result/at1MB-xdrop-20-20-80-6     |    1 +
 .../repfind-result/at1MB-xdrop-70-500-90-1-39-a    | 1297 ++--
 testdata/repfind-result/at1MB-xdrop-r-14-32-80-6-a |  145 +-
 testdata/repfind-result/humhbb.fna-gr-ext.result   |    1 +
 testdata/repfind-result/ychrIII.fna-gr-ext.result  |    4 +
 testdata/see-ext-U8-evalue-bitscore.matches        |   11 +
 testdata/see-ext-ani-at1MB-U8.txt                  |    6 +
 testdata/see-ext-at1MB-400-al-from-dtrace.matches  | 7610 ++++++++++++++++++++
 testdata/see-ext-at1MB-400-cigar.matches           |  230 +
 testdata/see-ext-at1MB-400-cigarX.matches          |  231 +
 testdata/see-ext-at1MB-400-dtrace.matches          |  230 +
 testdata/see-ext-at1MB-400-evalue-bitscore.matches |  228 +
 testdata/see-ext-at1MB-400-seqdesc.matches         |  230 +
 testdata/see-ext-at1MB-400-seqlength.matches       |  228 +
 testdata/see-ext-at1MB-400-trace.matches           |  230 +
 testdata/see-ext-at1MB-500-al.matches              |  947 +++
 ...ee-ext-at1MB-500-alignment-seed_in_algn.matches |  321 +
 testdata/see-ext-at1MB-500-failed_seed.matches     | 1477 ++++
 ...sert100-evalue-bitscore-cigar-seqlength.matches |   11 +
 ...ert100-evalue-bitscore-cigarX-seqlength.matches |   12 +
 .../see-ext-at1MB-U8-200-al-from-dtrace.matches    |   47 +
 testdata/see-ext-at1MB-maxmat250.matches           |   94 +
 .../see-ext-at1MB-mincoverage200-tabsep.matches    |  750 ++
 .../see-ext-at1MB-u8-failed_seed-evalue.matches    |   21 +
 testdata/see-ext-at1MB-u8-maxmat30.matches         |   27 +
 testdata/see-ext-at1MB-u8.matches                  | 1397 ++++
 testdata/see-ext-at1MB.matches                     | 1865 +++++
 testdata/see-ext-fastq_long-u8.matches             |  108 +
 testdata/see-ext-fastq_long.matches                |   39 +
 ...0_queries_300.fas => see-ext-paired-u8.matches} |    0
 testdata/see-ext-paired.matches                    |    3 +
 testsuite/gt_condenseq_include.rb                  |    4 +-
 testsuite/gt_linspace_align_include.rb             |   20 +-
 testsuite/gt_readjoiner_include.rb                 |   17 +-
 testsuite/gt_repfind_include.rb                    |   89 +-
 testsuite/gt_seed_extend_include.rb                |  577 +-
 testsuite/gt_seqorder_include.rb                   |    9 +
 testsuite/gt_sortbench_include.rb                  |    3 +-
 testsuite/gt_suffixerator_include.rb               |    2 +-
 www/genometools.org/htdocs/annotationsketch.html   |    1 -
 .../htdocs/cgi-bin/annotationsketch_demo.cgi       |    1 -
 .../htdocs/cgi-bin/gff3validator.cgi               |    1 -
 www/genometools.org/htdocs/contract.html           |    1 -
 www/genometools.org/htdocs/contribute.html         |    1 -
 www/genometools.org/htdocs/customtracks.html       |    1 -
 www/genometools.org/htdocs/design.html             |    1 -
 www/genometools.org/htdocs/docs.html               |    3 +-
 www/genometools.org/htdocs/documentation.html      |    1 -
 www/genometools.org/htdocs/examples_tmpl.html      |    1 -
 www/genometools.org/htdocs/index.html              |    1 -
 www/genometools.org/htdocs/libgenometools.html     |   75 +-
 www/genometools.org/htdocs/license.html            |    1 -
 www/genometools.org/htdocs/manuals.html            |    1 -
 www/genometools.org/htdocs/style_options.html      |    1 -
 www/genometools.org/htdocs/tool.conf               |    1 -
 www/genometools.org/htdocs/tool_list.conf          |    1 -
 www/genometools.org/htdocs/tools.html              |    1 -
 www/genometools.org/htdocs/tools/gt.html           |    3 +-
 .../htdocs/tools/gt_bed_to_gff3.html               |    3 +-
 www/genometools.org/htdocs/tools/gt_cds.html       |    3 +-
 www/genometools.org/htdocs/tools/gt_chain2dim.html |    1 -
 www/genometools.org/htdocs/tools/gt_chseqids.html  |    3 +-
 www/genometools.org/htdocs/tools/gt_clean.html     |    3 +-
 www/genometools.org/htdocs/tools/gt_compreads.html |    3 +-
 .../htdocs/tools/gt_compreads_compress.html        |    3 +-
 .../htdocs/tools/gt_compreads_decompress.html      |    3 +-
 .../htdocs/tools/gt_compreads_refcompress.html     |    3 +-
 .../htdocs/tools/gt_compreads_refdecompress.html   |    3 +-
 www/genometools.org/htdocs/tools/gt_condenseq.html |    3 +-
 .../htdocs/tools/gt_congruence.html                |    3 +-
 .../htdocs/tools/gt_congruence_spacedseed.html     |    1 -
 .../htdocs/tools/gt_convertseq.html                |    3 +-
 www/genometools.org/htdocs/tools/gt_csa.html       |    3 +-
 www/genometools.org/htdocs/tools/gt_dot.html       |    3 +-
 www/genometools.org/htdocs/tools/gt_dupfeat.html   |    3 +-
 www/genometools.org/htdocs/tools/gt_encseq.html    |    3 +-
 .../htdocs/tools/gt_encseq2spm.html                |    3 +-
 .../htdocs/tools/gt_encseq_bench.html              |    3 +-
 .../htdocs/tools/gt_encseq_bitextract.html         |    3 +-
 .../htdocs/tools/gt_encseq_check.html              |    3 +-
 .../htdocs/tools/gt_encseq_decode.html             |    3 +-
 .../htdocs/tools/gt_encseq_encode.html             |    3 +-
 .../htdocs/tools/gt_encseq_info.html               |    3 +-
 .../htdocs/tools/gt_encseq_md5.html                |    3 +-
 .../htdocs/tools/gt_encseq_sample.html             |    3 +-
 www/genometools.org/htdocs/tools/gt_eval.html      |    3 +-
 .../htdocs/tools/gt_extractfeat.html               |    3 +-
 .../htdocs/tools/gt_extractseq.html                |    3 +-
 .../htdocs/tools/gt_fastq_sample.html              |    3 +-
 .../htdocs/tools/gt_featureindex.html              |    3 +-
 .../htdocs/tools/gt_fingerprint.html               |    3 +-
 .../htdocs/tools/gt_genomediff.html                |    1 -
 www/genometools.org/htdocs/tools/gt_gff3.html      |    3 +-
 .../htdocs/tools/gt_gff3_to_gtf.html               |    3 +-
 .../htdocs/tools/gt_gff3validator.html             |    3 +-
 .../htdocs/tools/gt_gtf_to_gff3.html               |    3 +-
 www/genometools.org/htdocs/tools/gt_hop.html       |    3 +-
 www/genometools.org/htdocs/tools/gt_id_to_md5.html |    3 +-
 .../htdocs/tools/gt_inlineseq_add.html             |    3 +-
 .../htdocs/tools/gt_inlineseq_split.html           |    3 +-
 www/genometools.org/htdocs/tools/gt_interfeat.html |    3 +-
 www/genometools.org/htdocs/tools/gt_loccheck.html  |    3 +-
 .../htdocs/tools/gt_ltrclustering.html             |    3 +-
 www/genometools.org/htdocs/tools/gt_ltrdigest.html |    3 +-
 .../htdocs/tools/gt_ltrharvest.html                |    3 +-
 www/genometools.org/htdocs/tools/gt_matchtool.html |    3 +-
 www/genometools.org/htdocs/tools/gt_matstat.html   |    1 -
 www/genometools.org/htdocs/tools/gt_md5_to_id.html |    3 +-
 www/genometools.org/htdocs/tools/gt_merge.html     |    3 +-
 www/genometools.org/htdocs/tools/gt_mergefeat.html |    3 +-
 .../htdocs/tools/gt_mkfeatureindex.html            |    3 +-
 .../htdocs/tools/gt_mmapandread.html               |    3 +-
 www/genometools.org/htdocs/tools/gt_orffinder.html |    3 +-
 .../htdocs/tools/gt_packedindex.html               |    3 +-
 www/genometools.org/htdocs/tools/gt_prebwt.html    |    1 -
 .../htdocs/tools/gt_readjoiner.html                |    3 +-
 .../htdocs/tools/gt_readjoiner_assembly.html       |    3 +-
 .../htdocs/tools/gt_readjoiner_overlap.html        |    3 +-
 .../htdocs/tools/gt_readjoiner_prefilter.html      |    3 +-
 www/genometools.org/htdocs/tools/gt_repfind.html   |   83 +-
 .../htdocs/tools/gt_scriptfilter.html              |    3 +-
 .../htdocs/tools/gt_seed_extend.html               |  132 +-
 www/genometools.org/htdocs/tools/gt_select.html    |    3 +-
 www/genometools.org/htdocs/tools/gt_seq.html       |    3 +-
 www/genometools.org/htdocs/tools/gt_seqfilter.html |    3 +-
 www/genometools.org/htdocs/tools/gt_seqids.html    |    3 +-
 www/genometools.org/htdocs/tools/gt_seqmutate.html |    3 +-
 www/genometools.org/htdocs/tools/gt_seqorder.html  |   11 +-
 www/genometools.org/htdocs/tools/gt_seqstat.html   |   11 +-
 .../htdocs/tools/gt_seqtransform.html              |    3 +-
 .../htdocs/tools/gt_seqtranslate.html              |    3 +-
 www/genometools.org/htdocs/tools/gt_sequniq.html   |    3 +-
 www/genometools.org/htdocs/tools/gt_shredder.html  |    3 +-
 .../htdocs/tools/gt_shulengthdist.html             |    1 -
 www/genometools.org/htdocs/tools/gt_simreads.html  |    1 -
 www/genometools.org/htdocs/tools/gt_sketch.html    |    3 +-
 .../htdocs/tools/gt_sketch_page.html               |    3 +-
 www/genometools.org/htdocs/tools/gt_snpper.html    |    3 +-
 www/genometools.org/htdocs/tools/gt_speck.html     |    3 +-
 .../htdocs/tools/gt_splicesiteinfo.html            |    3 +-
 .../htdocs/tools/gt_splitfasta.html                |    3 +-
 www/genometools.org/htdocs/tools/gt_stat.html      |    3 +-
 www/genometools.org/htdocs/tools/gt_tagerator.html |    1 -
 www/genometools.org/htdocs/tools/gt_tallymer.html  |    3 +-
 .../htdocs/tools/gt_tallymer_mkindex.html          |    1 -
 .../htdocs/tools/gt_tallymer_occratio.html         |    1 -
 .../htdocs/tools/gt_tallymer_search.html           |    1 -
 www/genometools.org/htdocs/tools/gt_tirvish.html   |    3 +-
 www/genometools.org/htdocs/tools/gt_uniq.html      |    3 +-
 www/genometools.org/htdocs/tools/gt_uniquesub.html |    1 -
 www/genometools.org/htdocs/tools/gt_wtree.html     |    3 +-
 www/genometools.org/htdocs/trackselectors.html     |    1 -
 364 files changed, 43070 insertions(+), 9498 deletions(-)
 create mode 100644 scripts/SEmatch.rb
 create mode 100755 scripts/check-fstperquery.rb
 delete mode 100755 scripts/collect-mappings.rb
 create mode 100755 scripts/cutsequences.rb
 create mode 100755 scripts/enumkmers.rb
 create mode 100755 scripts/estim-kmer-size.rb
 create mode 100755 scripts/evalue-filter.rb
 create mode 100755 scripts/extract-seed.rb
 create mode 100644 scripts/fasta.rb
 create mode 100755 scripts/gen-display-struct.rb
 create mode 100755 scripts/gfa2lint.rb
 create mode 100755 scripts/manyshort-somelong.rb
 create mode 100755 scripts/matches-compare.rb
 create mode 100755 scripts/matches2ani.rb
 create mode 100755 scripts/mk_ft_longest_common.rb
 create mode 100644 scripts/print_sequence.rb
 create mode 100755 scripts/reverse-complement.rb
 create mode 100755 scripts/se-permutation.rb
 create mode 100755 scripts/seeds2maxmatches.rb
 create mode 100755 scripts/single-read-mapping.sh
 create mode 100755 scripts/travis_installdeps.sh
 copy scripts/{alloutputoptions.rb => turnwheel.rb} (55%)
 mode change 100755 => 100644
 create mode 100644 src/core/csvline_reader.c
 create mode 100644 src/core/csvline_reader.h
 create mode 100644 src/core/radixsort-ip-flba.inc
 create mode 100644 src/match/diagband-struct.c
 create mode 100644 src/match/diagband-struct.h
 create mode 100644 src/match/ft-eoplist.c
 create mode 100644 src/match/ft-eoplist.h
 create mode 100644 src/match/ft-longest-common.inc
 create mode 100644 src/match/gfa_writer.c
 create mode 100644 src/match/gfa_writer.h
 create mode 100644 src/match/karlin_altschul_stat.c
 create mode 100644 src/match/karlin_altschul_stat.h
 create mode 100644 src/match/querymatch-display.c
 create mode 100644 src/match/querymatch-display.h
 create mode 100644 src/match/rectangle-store.c
 create mode 100644 src/match/rectangle-store.h
 create mode 100644 src/match/se-display-fwd.inc
 create mode 100644 src/match/se-display.inc
 create mode 100644 src/match/seed_extend_parts.c
 create mode 100644 src/match/seed_extend_parts.h
 copy src/tools/{gt_readjoiner_asqg.c => gt_readjoiner_gfa.c} (67%)
 copy src/{match/lua_tools.h => tools/gt_readjoiner_gfa.h} (78%)
 create mode 100644 testdata/at-C99887-fwd.fna
 create mode 100644 testdata/at-C99887-rev.fna
 create mode 100644 testdata/at-C99930.fna
 create mode 100644 testdata/gt_seqorder_test_sortlength.fas
 create mode 100644 testdata/matchtool_see-ext.match
 create mode 100644 testdata/query-fwd.match
 create mode 100644 testdata/query-rev.match
 create mode 100644 testdata/readjoiner/30x_800nt.gfa1
 create mode 100644 testdata/readjoiner/30x_800nt.gfa2
 create mode 100644 testdata/readjoiner/30x_long_varlen.gfa1
 create mode 100644 testdata/readjoiner/30x_long_varlen.gfa2
 create mode 100644 testdata/readjoiner/70x_100nt.gfa1
 create mode 100644 testdata/readjoiner/70x_100nt.gfa2
 create mode 100644 testdata/readjoiner/contained_varlen.gfa1
 create mode 100644 testdata/readjoiner/contained_varlen.gfa2
 create mode 100644 testdata/see-ext-U8-evalue-bitscore.matches
 create mode 100644 testdata/see-ext-ani-at1MB-U8.txt
 create mode 100644 testdata/see-ext-at1MB-400-al-from-dtrace.matches
 create mode 100644 testdata/see-ext-at1MB-400-cigar.matches
 create mode 100644 testdata/see-ext-at1MB-400-cigarX.matches
 create mode 100644 testdata/see-ext-at1MB-400-dtrace.matches
 create mode 100644 testdata/see-ext-at1MB-400-evalue-bitscore.matches
 create mode 100644 testdata/see-ext-at1MB-400-seqdesc.matches
 create mode 100644 testdata/see-ext-at1MB-400-seqlength.matches
 create mode 100644 testdata/see-ext-at1MB-400-trace.matches
 create mode 100644 testdata/see-ext-at1MB-500-al.matches
 create mode 100644 testdata/see-ext-at1MB-500-alignment-seed_in_algn.matches
 create mode 100644 testdata/see-ext-at1MB-500-failed_seed.matches
 create mode 100644 
testdata/see-ext-at1MB-Atinsert100-evalue-bitscore-cigar-seqlength.matches
 create mode 100644 
testdata/see-ext-at1MB-Atinsert100-evalue-bitscore-cigarX-seqlength.matches
 create mode 100644 testdata/see-ext-at1MB-U8-200-al-from-dtrace.matches
 create mode 100644 testdata/see-ext-at1MB-maxmat250.matches
 create mode 100644 testdata/see-ext-at1MB-mincoverage200-tabsep.matches
 create mode 100644 testdata/see-ext-at1MB-u8-failed_seed-evalue.matches
 create mode 100644 testdata/see-ext-at1MB-u8-maxmat30.matches
 create mode 100644 testdata/see-ext-at1MB-u8.matches
 create mode 100644 testdata/see-ext-at1MB.matches
 create mode 100644 testdata/see-ext-fastq_long-u8.matches
 create mode 100644 testdata/see-ext-fastq_long.matches
 copy testdata/{condenseq/varlen_0.01_50_queries_300.fas => 
see-ext-paired-u8.matches} (100%)
 create mode 100644 testdata/see-ext-paired.matches

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