[med-svn] [Git][med-team/gmap][master] 14 commits: Refresh patches
Alexandre Mestiashvili
gitlab at salsa.debian.org
Tue Jul 17 17:14:31 BST 2018
Alexandre Mestiashvili pushed to branch master at Debian Med / gmap
Commits:
cdd6771e by Alexandre Mestiashvili at 2018-07-17T10:36:56+02:00
Refresh patches
- - - - -
a4cb5e96 by Alexandre Mestiashvili at 2018-07-17T10:39:54+02:00
Update Uploader's email
- - - - -
0245e499 by Alexandre Mestiashvili at 2018-07-17T10:40:42+02:00
Drop libgmap1{,-dev} package as there is no use cases so far
- - - - -
7c3f35b8 by Alexandre Mestiashvili at 2018-07-17T10:44:54+02:00
Remove --enable-shared from configure options
- - - - -
48198582 by Alexandre Mestiashvili at 2018-07-17T10:53:05+02:00
Remove install files for libgmap1*
- - - - -
58f6af00 by Alexandre Mestiashvili at 2018-07-17T11:00:48+02:00
Remove d/gmap.install
- - - - -
ada0e0cc by Alexandre Mestiashvili at 2018-07-17T11:53:21+02:00
Update d/copyright, remove section for src/saca-k*, update email
- - - - -
510a474a by Alexandre Mestiashvili at 2018-07-17T14:25:16+02:00
Update d/rules, fix directory path
- - - - -
e7dd7737 by Alexandre Mestiashvili at 2018-07-17T14:41:40+02:00
Update lintian-overrides, remove *.nosimd binaries
- - - - -
5a7493d4 by Alexandre Mestiashvili at 2018-07-17T15:22:42+02:00
Update d/filter.pl to fix gmap man page
- - - - -
357b3e41 by Alexandre Mestiashvili at 2018-07-17T16:13:24+02:00
Add autopkgtest
- - - - -
9cbfd02d by Alexandre Mestiashvili at 2018-07-17T16:53:36+02:00
Update d/rules to install tests data into examples
- - - - -
ca2e2386 by Alexandre Mestiashvili at 2018-07-17T17:07:27+02:00
Update autopkgtest to use test files from examples
- - - - -
ed55e39b by Alexandre Mestiashvili at 2018-07-17T17:09:22+02:00
Update changelog
Gbp-Dch: Ignore
- - - - -
13 changed files:
- debian/changelog
- debian/control
- debian/copyright
- debian/filter.pl
- − debian/gmap.install
- debian/gmap.lintian-overrides
- − debian/libgmap1-dev.install
- − debian/libgmap1.install
- − debian/libgmap1.symbols
- debian/patches/install-data-local
- debian/rules
- + debian/tests/control
- + debian/tests/gmap-tests
Changes:
=====================================
debian/changelog
=====================================
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,14 +1,32 @@
-gmap (2018-07-04-1) UNRELEASED; urgency=medium
+gmap (2018-07-04-1) unstable; urgency=medium
+ [ Steffen Möller ]
+ * Updated bio.tools RRID in d/u/metadata
+ * Update metadata
+
+ [ Andreas Tille ]
* Cleanup d/rules
* New upstream version
* debhelper 11
* Point Vcs fields to salsa.debian.org
* Standards-Version: 4.1.5
- * libgmap1-dev Depends: gmap, libgmap1 (instead of alternative)
- Closes: #903793
- -- Andreas Tille <tille at debian.org> Tue, 17 Jul 2018 07:24:19 +0200
+ [ Alexandre Mestiashvili ]
+ * Refresh patches
+ * d/control:
+ - update Uploader's email
+ - drop libgmap1{,-dev} as there is no use cases so far
+ Closes: #903793
+ * Update d/rules:
+ - remove --enable-shared as we dropped libgmap1
+ - add stanza to install tests files to examples
+ * Remove install files for libgmap1*
+ * Update d/copyright, remove section for src/saca-k*, update email
+ * Update lintian-overrides, remove *.nosimd binaries
+ * Update d/filter.pl to fix gmap man page
+ * Add autopkgtest
+
+ -- Alexandre Mestiashvili <mestia at debian.org> Tue, 17 Jul 2018 17:07:39 +0200
gmap (2017-11-15-1) unstable; urgency=medium
=====================================
debian/control
=====================================
--- a/debian/control
+++ b/debian/control
@@ -2,7 +2,7 @@ Source: gmap
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Uploaders: Shaun Jackman <sjackman at debian.org>,
Andreas Tille <tille at debian.org>,
- Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
+ Alexandre Mestiashvili <mestia at debian.org>
Section: non-free/science
XS-Autobuild: no
Priority: optional
@@ -32,36 +32,3 @@ Description: spliced and SNP-tolerant alignment for mRNA and short reads
* known splice sites and identify novel splice sites.
* known single-nucleotide polymorphisms (SNPs).
GSNAP can align bisulfite-treated DNA.
-
-Package: libgmap1
-Architecture: any
-Section: non-free/libs
-Depends: ${misc:Depends},
- ${shlibs:Depends}
-Description: library for gmap tool
- This package contains library for gmap tool.
- GMAP (Genomic Mapping and Alignment Program) is a tool for aligning
- EST, mRNA and cDNA sequences.
- GSNAP (Genomic Short-read Nucleotide Alignment Program) is a tool for
- aligning single-end and paired-end transcriptome reads.
- Both tools can use a database of
- * known splice sites and identify novel splice sites.
- * known single-nucleotide polymorphisms (SNPs).
- GSNAP can align bisulfite-treated DNA.
-
-Package: libgmap1-dev
-Architecture: any
-Section: non-free/libdevel
-Depends: gmap (= ${binary:Version}),
- libgmap1 (= ${binary:Version}),
- ${misc:Depends}
-Description: development files for gmap
- This package contains header files for gmap.
- GMAP (Genomic Mapping and Alignment Program) is a tool for aligning
- EST, mRNA and cDNA sequences.
- GSNAP (Genomic Short-read Nucleotide Alignment Program) is a tool for
- aligning single-end and paired-end transcriptome reads.
- Both tools can use a database of
- * known splice sites and identify novel splice sites.
- * known single-nucleotide polymorphisms (SNPs).
- GSNAP can align bisulfite-treated DNA.
=====================================
debian/copyright
=====================================
--- a/debian/copyright
+++ b/debian/copyright
@@ -2,6 +2,8 @@ Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: GMAP
Upstream-Contact: Thomas Wu <twu at gene.com>, Colin K. Watanabe <ckw at gene.com>
Source: http://research-pub.gene.com/gmap/
+Comment: gmap is in contirb/non-free due to the license,
+ see also https://lists.debian.org/debian-med/2017/09/msg00013.html
Files: *
Copyright: 2011-2014 Genentech, Inc.
@@ -105,27 +107,6 @@ License: X11
dealings in this Software without prior written authorization from the X
Consortium.
-Files: src/saca-k*
-Copyright: 2012 Ge Nong <issng at mail.sysu.edu.cn>
-License: Expat
- Permission is hereby granted, free of charge, to any person obtaining a copy
- of this software and associated documentation files (the "Software"), to deal
- in the Software without restriction, including without limitation the rights
- to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
- copies of the Software, and to permit persons to whom the Software is
- furnished to do so, subject to the following conditions:
- .
- The above copyright notice and this permission notice shall be included in
- all copies or substantial portions of the Software.
- .
- THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
- IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
- FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
- AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
- LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
- OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
- THE SOFTWARE.
-
Files: src/fastlog.h
Copyright: 2012 Paul Mineiro <paul at mineiro.com>
License: BSD-3-clause
@@ -165,7 +146,7 @@ License: BSD-3-clause
Files: debian/*
Copyright: 2011 Shaun Jackman <sjackman at debian.org>
2012-2014 Andreas Tille <tille at debian.org>
- 2016 Alex Mestiashvili <alex at biotec.tu-dresden.de>
+ 2016 Alex Mestiashvili <mestia at debian.org>
License: ISC
Permission to use, copy, modify, and/or distribute this software for any
purpose with or without fee is hereby granted, provided that the above
=====================================
debian/filter.pl
=====================================
--- a/debian/filter.pl
+++ b/debian/filter.pl
@@ -30,7 +30,15 @@ while ( <STDIN> ) {
s/(^5\s{6}see\snote\s.*)/ $1/gmxs;
s/(^Examples:\n\.TP)/\.TP\n$1/gmsx;
s/(.*be\schanged)\n\.TP\n(by\sproviding.*)/$1 $2/gmsx;
+ #gmap aligning
#fix gmap_build header
+ #s/(^Batch\smode\s\(default\s=\s2\)\n)(Mode.*)/$1\n $2/gmxs;
+ s/(^\.TP\n)(0)(\n)(mmap\s.*)/ $2 $4/gmxs;
+ s/(^\.TP\n)(1)(\n)(mmap\s.*)/ $2 $4/gmxs;
+ s/(^\.TP\n)(\(default\))(\n)(2\s{6}mmap.*)/ $2 $4/gmxs;
+ s/(^3\s{6}allocate.*)/ $1/gmxs;
+ s/(^4\s{6}allocate.*)/ $1/gmxs;
+ s/(^5\s{6}allocate.*)/ $1/gmxs;
s/(^\.SH\sDESCRIPTION\n)Unknown.*\.PP/$1/gmsx;
print;
}
=====================================
debian/gmap.install deleted
=====================================
--- a/debian/gmap.install
+++ /dev/null
@@ -1 +0,0 @@
-usr/lib/gmap/* usr/lib/gmap
=====================================
debian/gmap.lintian-overrides
=====================================
--- a/debian/gmap.lintian-overrides
+++ b/debian/gmap.lintian-overrides
@@ -1,10 +1,6 @@
gmap: binary-without-manpage usr/bin/gmap.sse41
-gmap: binary-without-manpage usr/bin/gmap.nosimd
gmap: binary-without-manpage usr/bin/gsnap.sse41
-gmap: binary-without-manpage usr/bin/gsnap.nosimd
gmap: binary-without-manpage usr/bin/gmapl
gmap: binary-without-manpage usr/bin/gmapl.sse41
-gmap: binary-without-manpage usr/bin/gmapl.nosimd
gmap: binary-without-manpage usr/bin/gsnapl
gmap: binary-without-manpage usr/bin/gsnapl.sse41
-gmap: binary-without-manpage usr/bin/gsnapl.nosimd
=====================================
debian/libgmap1-dev.install deleted
=====================================
--- a/debian/libgmap1-dev.install
+++ /dev/null
@@ -1,5 +0,0 @@
-#! /usr/bin/dh-exec
-usr/include/* usr/include/gmap
-src/.libs/libgmap.a usr/lib/${DEB_HOST_MULTIARCH}
-src/.libs/libgmap.so usr/lib/${DEB_HOST_MULTIARCH}
-
=====================================
debian/libgmap1.install deleted
=====================================
--- a/debian/libgmap1.install
+++ /dev/null
@@ -1,3 +0,0 @@
-#! /usr/bin/dh-exec
-src/.libs/libgmap.so.1 usr/lib/${DEB_HOST_MULTIARCH}
-src/.libs/libgmap.so.1.0.0 usr/lib/${DEB_HOST_MULTIARCH}
=====================================
debian/libgmap1.symbols deleted
=====================================
--- a/debian/libgmap1.symbols
+++ /dev/null
@@ -1,607 +0,0 @@
-libgmap.so.1 libgmap1 #MINVER#
- Access_allocate_private at Base 2017-10-30
- Access_allocate_shared at Base 2017-10-30
- Access_controlled_cleanup at Base 2017-10-30
- Access_deallocate at Base 2017-10-30
- Access_emergency_cleanup at Base 2017-10-30
- Access_file_copy at Base 2017-10-30
- Access_file_equal at Base 2017-10-30
- Access_file_exists_p at Base 2017-10-30
- Access_fileio at Base 2017-10-30
- Access_fileio_rw at Base 2017-10-30
- Access_filesize at Base 2017-10-30
- Access_mmap at Base 2017-10-30
- Access_mmap_and_preload at Base 2017-10-30
- Access_mmap_offset at Base 2017-10-30
- Access_mmap_offset_rw at Base 2017-10-30
- Access_mmap_rw at Base 2017-10-30
- Access_setup at Base 2017-10-30
- Assert_Failed at Base 2017-10-30
- Bigendian_convert_double at Base 2017-10-30
- Bigendian_convert_int at Base 2017-10-30
- Bigendian_convert_uint8 at Base 2017-10-30
- Bigendian_convert_uint at Base 2017-10-30
- Bigendian_fileio_read_uint8 at Base 2017-10-30
- Bigendian_fileio_read_uint at Base 2017-10-30
- Bigendian_fread_int at Base 2017-10-30
- Bigendian_fread_ints at Base 2017-10-30
- Bigendian_fread_uint8 at Base 2017-10-30
- Bigendian_fread_uint8s at Base 2017-10-30
- Bigendian_fread_uint at Base 2017-10-30
- Bigendian_fread_uints at Base 2017-10-30
- Bigendian_fwrite_double at Base 2017-10-30
- Bigendian_fwrite_int at Base 2017-10-30
- Bigendian_fwrite_ints at Base 2017-10-30
- Bigendian_fwrite_uint8 at Base 2017-10-30
- Bigendian_fwrite_uint8s at Base 2017-10-30
- Bigendian_fwrite_uint at Base 2017-10-30
- Bigendian_fwrite_uints at Base 2017-10-30
- Bigendian_write_char at Base 2017-10-30
- Bigendian_write_uint8 at Base 2017-10-30
- Bigendian_write_uint at Base 2017-10-30
- Bitpack64_block_offsets at Base 2017-10-30
- Bitpack64_differential_packsize at Base 2017-10-30
- Bitpack64_read_one at Base 2017-10-30
- Bitpack64_read_one_huge at Base 2017-10-30
- Bitpack64_read_two at Base 2017-10-30
- Bytecoding_interleave_lcpchilddc at Base 2017-10-30
- Bytecoding_lcpchilddc_child_next at Base 2017-10-30
- Bytecoding_lcpchilddc_child_up at Base 2017-10-30
- Bytecoding_lcpchilddc_dc at Base 2017-10-30
- Bytecoding_lcpchilddc_lcp at Base 2017-10-30
- Bytecoding_lcpchilddc_lcp_next at Base 2017-10-30
- Bytecoding_read at Base 2017-10-30
- Bytecoding_read_wguide at Base 2017-10-30
- Bytecoding_write at Base 2017-10-30
- Bytecoding_write_bytes at Base 2017-10-30
- Bytecoding_write_exceptions_only at Base 2017-10-30
- Bytecoding_write_lcpchilddc at Base 2017-10-30
- Bzip2_free at Base 2017-10-30
- Bzip2_new at Base 2017-10-30
- Chrnum_length at Base 2017-10-30
- Chrnum_offset at Base 2017-10-30
- Chrnum_print_position at Base 2017-10-30
- Chrnum_to_string at Base 2017-10-30
- Chrnum_to_string_signed at Base 2017-10-30
- Chrom_altlocp at Base 2017-10-30
- Chrom_circularp at Base 2017-10-30
- Chrom_cmp_alpha at Base 2017-10-30
- Chrom_cmp_chrom at Base 2017-10-30
- Chrom_cmp_numeric_alpha at Base 2017-10-30
- Chrom_cmp_order at Base 2017-10-30
- Chrom_compare_alpha at Base 2017-10-30
- Chrom_compare_chrom at Base 2017-10-30
- Chrom_compare_numeric_alpha at Base 2017-10-30
- Chrom_compare_order at Base 2017-10-30
- Chrom_compare_table at Base 2017-10-30
- Chrom_free at Base 2017-10-30
- Chrom_from_string at Base 2017-10-30
- Chrom_hash_table at Base 2017-10-30
- Chrom_string at Base 2017-10-30
- Chrpos_compare at Base 2017-10-30
- Compress_free at Base 2017-10-30
- Compress_get_16mer_left at Base 2017-10-30
- Compress_get_16mer_right at Base 2017-10-30
- Compress_nblocks at Base 2017-10-30
- Compress_new_fwd at Base 2017-10-30
- Compress_new_rev at Base 2017-10-30
- Compress_print at Base 2017-10-30
- Compress_print_blocks at Base 2017-10-30
- Compress_shift at Base 2017-10-30
- Datadir_avail_gmap_databases at Base 2017-10-30
- Datadir_avail_maps at Base 2017-10-30
- Datadir_find_genomedir at Base 2017-10-30
- Datadir_find_genomesubdir at Base 2017-10-30
- Datadir_find_mapdir at Base 2017-10-30
- Datadir_list_directory at Base 2017-10-30
- Datadir_list_directory_multicol at Base 2017-10-30
- Doublelist_fill_array at Base 2017-10-30
- Doublelist_free at Base 2017-10-30
- Doublelist_from_array at Base 2017-10-30
- Doublelist_from_string at Base 2017-10-30
- Doublelist_head at Base 2017-10-30
- Doublelist_keep_one at Base 2017-10-30
- Doublelist_length at Base 2017-10-30
- Doublelist_max at Base 2017-10-30
- Doublelist_min at Base 2017-10-30
- Doublelist_next at Base 2017-10-30
- Doublelist_pop at Base 2017-10-30
- Doublelist_print at Base 2017-10-30
- Doublelist_push at Base 2017-10-30
- Doublelist_reverse at Base 2017-10-30
- Doublelist_to_array at Base 2017-10-30
- Doublelist_to_array_out at Base 2017-10-30
- Except_advance_stack at Base 2017-10-30
- Except_inactivate at Base 2017-10-30
- Except_init_pthread at Base 2017-10-30
- Except_link_stack at Base 2017-10-30
- Except_raise at Base 2017-10-30
- Except_stack_create at Base 2017-10-30
- Except_stack_destroy at Base 2017-10-30
- Except_term_pthread at Base 2017-10-30
- Filestring_free at Base 2017-10-30
- Filestring_id at Base 2017-10-30
- Filestring_new at Base 2017-10-30
- Filestring_print at Base 2017-10-30
- Filestring_put at Base 2017-10-30
- Filestring_putc at Base 2017-10-30
- Filestring_puts at Base 2017-10-30
- Filestring_set_split_output at Base 2017-10-30
- Filestring_split_output at Base 2017-10-30
- Filestring_stringify at Base 2017-10-30
- Genome_blocks at Base 2017-10-30
- Genome_consecutive_matches_leftward at Base 2017-10-30
- Genome_consecutive_matches_pair at Base 2017-10-30
- Genome_consecutive_matches_rightward at Base 2017-10-30
- Genome_count_mismatches_fragment_left at Base 2017-10-30
- Genome_count_mismatches_fragment_right at Base 2017-10-30
- Genome_count_mismatches_limit at Base 2017-10-30
- Genome_count_mismatches_substring at Base 2017-10-30
- Genome_count_mismatches_substring_ref at Base 2017-10-30
- Genome_fill_buffer at Base 2017-10-30
- Genome_fill_buffer_blocks at Base 2017-10-30
- Genome_fill_buffer_blocks_noterm at Base 2017-10-30
- Genome_fill_buffer_convert_fwd at Base 2017-10-30
- Genome_fill_buffer_convert_rev at Base 2017-10-30
- Genome_fill_buffer_int_string at Base 2017-10-30
- Genome_fill_buffer_nucleotides at Base 2017-10-30
- Genome_fill_buffer_simple at Base 2017-10-30
- Genome_fill_buffer_simple_alt at Base 2017-10-30
- Genome_free at Base 2017-10-30
- Genome_get_char at Base 2017-10-30
- Genome_get_char_blocks at Base 2017-10-30
- Genome_get_char_lex at Base 2017-10-30
- Genome_get_segment at Base 2017-10-30
- Genome_get_segment_alt at Base 2017-10-30
- Genome_get_segment_blocks_left at Base 2017-10-30
- Genome_get_segment_blocks_right at Base 2017-10-30
- Genome_get_segment_snp at Base 2017-10-30
- Genome_hr_setup at Base 2017-10-30
- Genome_mark_mismatches at Base 2017-10-30
- Genome_mark_mismatches_ref at Base 2017-10-30
- Genome_mismatches_left at Base 2017-10-30
- Genome_mismatches_left_trim at Base 2017-10-30
- Genome_mismatches_right at Base 2017-10-30
- Genome_mismatches_right_trim at Base 2017-10-30
- Genome_new at Base 2017-10-30
- Genome_ntcounts at Base 2017-10-30
- Genome_setup at Base 2017-10-30
- Genome_totallength at Base 2017-10-30
- Genome_trim_left at Base 2017-10-30
- Genome_trim_right at Base 2017-10-30
- Genome_uncompress_memory at Base 2017-10-30
- Genome_uncompress_mmap at Base 2017-10-30
- Genome_user_setup at Base 2017-10-30
- Genomicpos_commafmt at Base 2017-10-30
- IIT_annotation at Base 2017-10-30
- IIT_annotation_firstchar at Base 2017-10-30
- IIT_annotation_strlen at Base 2017-10-30
- IIT_create at Base 2017-10-30
- IIT_debug at Base 2017-10-30
- IIT_divint at Base 2017-10-30
- IIT_divlength at Base 2017-10-30
- IIT_divstring at Base 2017-10-30
- IIT_divstring_from_index at Base 2017-10-30
- IIT_dump at Base 2017-10-30
- IIT_dump_divstrings at Base 2017-10-30
- IIT_dump_fieldstrings at Base 2017-10-30
- IIT_dump_labels at Base 2017-10-30
- IIT_dump_simple at Base 2017-10-30
- IIT_dump_typestrings at Base 2017-10-30
- IIT_exact_p at Base 2017-10-30
- IIT_exists_with_divno at Base 2017-10-30
- IIT_exists_with_divno_signed at Base 2017-10-30
- IIT_exists_with_divno_typed_signed at Base 2017-10-30
- IIT_fieldint at Base 2017-10-30
- IIT_fieldstring at Base 2017-10-30
- IIT_fieldvalue at Base 2017-10-30
- IIT_find at Base 2017-10-30
- IIT_find_linear at Base 2017-10-30
- IIT_find_one at Base 2017-10-30
- IIT_free at Base 2017-10-30
- IIT_gene_overlap at Base 2017-10-30
- IIT_gene_overlapp at Base 2017-10-30
- IIT_genestruct_chrpos at Base 2017-10-30
- IIT_get at Base 2017-10-30
- IIT_get_exact at Base 2017-10-30
- IIT_get_exact_multiple at Base 2017-10-30
- IIT_get_exact_multiple_with_divno at Base 2017-10-30
- IIT_get_flanking at Base 2017-10-30
- IIT_get_flanking_multiple_typed at Base 2017-10-30
- IIT_get_flanking_typed at Base 2017-10-30
- IIT_get_flanking_with_divno at Base 2017-10-30
- IIT_get_highs_for_low at Base 2017-10-30
- IIT_get_highs_signed at Base 2017-10-30
- IIT_get_lows_for_high at Base 2017-10-30
- IIT_get_lows_signed at Base 2017-10-30
- IIT_get_multiple_typed at Base 2017-10-30
- IIT_get_one at Base 2017-10-30
- IIT_get_signed at Base 2017-10-30
- IIT_get_signed_with_divno at Base 2017-10-30
- IIT_get_typed at Base 2017-10-30
- IIT_get_typed_signed at Base 2017-10-30
- IIT_get_typed_signed_with_divno at Base 2017-10-30
- IIT_get_typed_with_divno at Base 2017-10-30
- IIT_get_values_above at Base 2017-10-30
- IIT_get_values_below at Base 2017-10-30
- IIT_get_values_between at Base 2017-10-30
- IIT_get_with_divno at Base 2017-10-30
- IIT_high_exists_signed_p at Base 2017-10-30
- IIT_index at Base 2017-10-30
- IIT_interval at Base 2017-10-30
- IIT_interval_bounds at Base 2017-10-30
- IIT_interval_high at Base 2017-10-30
- IIT_interval_length at Base 2017-10-30
- IIT_interval_low at Base 2017-10-30
- IIT_interval_sign at Base 2017-10-30
- IIT_interval_type at Base 2017-10-30
- IIT_label at Base 2017-10-30
- IIT_length at Base 2017-10-30
- IIT_load at Base 2017-10-30
- IIT_low_exists_signed_p at Base 2017-10-30
- IIT_name at Base 2017-10-30
- IIT_ndivs at Base 2017-10-30
- IIT_nfields at Base 2017-10-30
- IIT_nintervals at Base 2017-10-30
- IIT_ntypes at Base 2017-10-30
- IIT_print_header at Base 2017-10-30
- IIT_read at Base 2017-10-30
- IIT_read_divint at Base 2017-10-30
- IIT_total_nintervals at Base 2017-10-30
- IIT_totallength at Base 2017-10-30
- IIT_typeint at Base 2017-10-30
- IIT_typelist at Base 2017-10-30
- IIT_typestring at Base 2017-10-30
- IIT_unique_positions at Base 2017-10-30
- IIT_unique_positions_given_others at Base 2017-10-30
- IIT_unique_splicep at Base 2017-10-30
- IIT_unique_splicep_given_others at Base 2017-10-30
- IIT_universalp at Base 2017-10-30
- IIT_valuep at Base 2017-10-30
- IIT_version at Base 2017-10-30
- IIT_write at Base 2017-10-30
- Interval_array_high at Base 2017-10-30
- Interval_array_low at Base 2017-10-30
- Interval_cmp at Base 2017-10-30
- Interval_cmp_high at Base 2017-10-30
- Interval_cmp_low at Base 2017-10-30
- Interval_cmp_low_struct at Base 2017-10-30
- Interval_copy at Base 2017-10-30
- Interval_copy_existing at Base 2017-10-30
- Interval_free at Base 2017-10-30
- Interval_high at Base 2017-10-30
- Interval_is_contained at Base 2017-10-30
- Interval_length at Base 2017-10-30
- Interval_low at Base 2017-10-30
- Interval_new at Base 2017-10-30
- Interval_overlap_p at Base 2017-10-30
- Interval_print at Base 2017-10-30
- Interval_qsort_by_omega at Base 2017-10-30
- Interval_qsort_by_sigma at Base 2017-10-30
- Interval_sign at Base 2017-10-30
- Interval_store_length at Base 2017-10-30
- Interval_type at Base 2017-10-30
- Interval_windex_cmp at Base 2017-10-30
- Intlist_append at Base 2017-10-30
- Intlist_array_ascending_by_key at Base 2017-10-30
- Intlist_array_dual_ascending_by_key at Base 2017-10-30
- Intlist_copy at Base 2017-10-30
- Intlist_delete at Base 2017-10-30
- Intlist_equal at Base 2017-10-30
- Intlist_exists_p at Base 2017-10-30
- Intlist_fill_array at Base 2017-10-30
- Intlist_fill_array_and_free at Base 2017-10-30
- Intlist_free at Base 2017-10-30
- Intlist_free_in at Base 2017-10-30
- Intlist_from_array at Base 2017-10-30
- Intlist_from_string at Base 2017-10-30
- Intlist_head at Base 2017-10-30
- Intlist_head_set at Base 2017-10-30
- Intlist_index at Base 2017-10-30
- Intlist_insert_second at Base 2017-10-30
- Intlist_keep_one at Base 2017-10-30
- Intlist_last_value at Base 2017-10-30
- Intlist_length at Base 2017-10-30
- Intlist_list_ascending_by_key at Base 2017-10-30
- Intlist_list_descending_by_key at Base 2017-10-30
- Intlist_max at Base 2017-10-30
- Intlist_min at Base 2017-10-30
- Intlist_next at Base 2017-10-30
- Intlist_pop at Base 2017-10-30
- Intlist_push at Base 2017-10-30
- Intlist_push_in at Base 2017-10-30
- Intlist_reverse at Base 2017-10-30
- Intlist_sort_ascending at Base 2017-10-30
- Intlist_to_array at Base 2017-10-30
- Intlist_to_array_out at Base 2017-10-30
- Intlist_to_char_array at Base 2017-10-30
- Intlist_to_char_array_in at Base 2017-10-30
- Intlist_to_string at Base 2017-10-30
- Intlist_vary at Base 2017-10-30
- List_append at Base 2017-10-30
- List_copy at Base 2017-10-30
- List_dump at Base 2017-10-30
- List_fill_array at Base 2017-10-30
- List_fill_array_and_free at Base 2017-10-30
- List_fill_array_with_handle at Base 2017-10-30
- List_free at Base 2017-10-30
- List_free_keep at Base 2017-10-30
- List_free_out at Base 2017-10-30
- List_from_string at Base 2017-10-30
- List_head at Base 2017-10-30
- List_head_set at Base 2017-10-30
- List_index at Base 2017-10-30
- List_insert at Base 2017-10-30
- List_last_item at Base 2017-10-30
- List_last_value at Base 2017-10-30
- List_length at Base 2017-10-30
- List_next at Base 2017-10-30
- List_pop at Base 2017-10-30
- List_pop_out at Base 2017-10-30
- List_push at Base 2017-10-30
- List_push_existing at Base 2017-10-30
- List_push_keep at Base 2017-10-30
- List_push_out at Base 2017-10-30
- List_reinsert at Base 2017-10-30
- List_reverse at Base 2017-10-30
- List_tail_set at Base 2017-10-30
- List_to_array at Base 2017-10-30
- List_to_array_n at Base 2017-10-30
- List_to_array_out at Base 2017-10-30
- List_to_array_out_n at Base 2017-10-30
- List_transfer_one at Base 2017-10-30
- List_truncate at Base 2017-10-30
- Littleendian_write_char at Base 2017-10-30
- Littleendian_write_uint8 at Base 2017-10-30
- Littleendian_write_uint8_as_uint at Base 2017-10-30
- Littleendian_write_uint at Base 2017-10-30
- MD5_compute at Base 2017-10-30
- MD5_print at Base 2017-10-30
- Maxent_hr_acceptor_prob at Base 2017-10-30
- Maxent_hr_antiacceptor_prob at Base 2017-10-30
- Maxent_hr_antidonor_prob at Base 2017-10-30
- Maxent_hr_donor_prob at Base 2017-10-30
- Maxent_hr_setup at Base 2017-10-30
- Mem_Failed at Base 2017-10-30
- Mem_Leak at Base 2017-10-30
- Mem_alloc at Base 2017-10-30
- Mem_alloc_in at Base 2017-10-30
- Mem_alloc_keep at Base 2017-10-30
- Mem_alloc_no_exception at Base 2017-10-30
- Mem_alloc_out at Base 2017-10-30
- Mem_calloc at Base 2017-10-30
- Mem_calloc_in at Base 2017-10-30
- Mem_calloc_keep at Base 2017-10-30
- Mem_calloc_no_exception at Base 2017-10-30
- Mem_calloc_out at Base 2017-10-30
- Mem_free at Base 2017-10-30
- Mem_free_in at Base 2017-10-30
- Mem_free_keep at Base 2017-10-30
- Mem_free_out at Base 2017-10-30
- Mem_resize at Base 2017-10-30
- Parserange_iscoordp at Base 2017-10-30
- Parserange_islengthp at Base 2017-10-30
- Parserange_israngep at Base 2017-10-30
- Parserange_query at Base 2017-10-30
- Parserange_simple at Base 2017-10-30
- Parserange_universal at Base 2017-10-30
- Parserange_universal_iit at Base 2017-10-30
- Sarray_array at Base 2017-10-30
- Sarray_free at Base 2017-10-30
- Sarray_lookup at Base 2017-10-30
- Sarray_new at Base 2017-10-30
- Sarray_position at Base 2017-10-30
- Sarray_read at Base 2017-10-30
- Sarray_size at Base 2017-10-30
- Semaphore_create at Base 2017-10-30
- Semaphore_delete at Base 2017-10-30
- Semaphore_find at Base 2017-10-30
- Semaphore_get_value at Base 2017-10-30
- Semaphore_lock at Base 2017-10-30
- Semaphore_nwaiting at Base 2017-10-30
- Semaphore_set_value at Base 2017-10-30
- Semaphore_unlock at Base 2017-10-30
- Sequence_accession at Base 2017-10-30
- Sequence_alias at Base 2017-10-30
- Sequence_firstp at Base 2017-10-30
- Sequence_free at Base 2017-10-30
- Sequence_fulllength at Base 2017-10-30
- Sequence_fulllength_given at Base 2017-10-30
- Sequence_fullpointer at Base 2017-10-30
- Sequence_genomic_new at Base 2017-10-30
- Sequence_input_init at Base 2017-10-30
- Sequence_input_init_bzip2 at Base 2017-10-30
- Sequence_input_init_gzip at Base 2017-10-30
- Sequence_ntlength at Base 2017-10-30
- Sequence_print at Base 2017-10-30
- Sequence_print_digest at Base 2017-10-30
- Sequence_print_header at Base 2017-10-30
- Sequence_quality_string at Base 2017-10-30
- Sequence_read at Base 2017-10-30
- Sequence_read_multifile at Base 2017-10-30
- Sequence_read_unlimited at Base 2017-10-30
- Sequence_revcomp at Base 2017-10-30
- Sequence_skiplength at Base 2017-10-30
- Sequence_stdout at Base 2017-10-30
- Sequence_stdout_alt at Base 2017-10-30
- Sequence_stdout_header at Base 2017-10-30
- Sequence_stdout_raw at Base 2017-10-30
- Sequence_stdout_stream_chars at Base 2017-10-30
- Sequence_stdout_stream_ints at Base 2017-10-30
- Sequence_stdout_two at Base 2017-10-30
- Sequence_subseq_length at Base 2017-10-30
- Sequence_subseq_offset at Base 2017-10-30
- Sequence_subseq_pointer at Base 2017-10-30
- Sequence_subsequence at Base 2017-10-30
- Sequence_substring at Base 2017-10-30
- Sequence_trim at Base 2017-10-30
- Sequence_trim_end at Base 2017-10-30
- Sequence_trim_start at Base 2017-10-30
- Sequence_trimlength at Base 2017-10-30
- Sequence_trimpointer at Base 2017-10-30
- Sequence_uppercase at Base 2017-10-30
- Stopwatch_free at Base 2017-10-30
- Stopwatch_new at Base 2017-10-30
- Stopwatch_start at Base 2017-10-30
- Stopwatch_stop at Base 2017-10-30
- Table_free at Base 2017-10-30
- Table_gc at Base 2017-10-30
- Table_get at Base 2017-10-30
- Table_keys at Base 2017-10-30
- Table_keys_by_timeindex at Base 2017-10-30
- Table_length at Base 2017-10-30
- Table_map at Base 2017-10-30
- Table_new at Base 2017-10-30
- Table_put at Base 2017-10-30
- Table_remove at Base 2017-10-30
- Table_remove_old_key at Base 2017-10-30
- Table_string_compare at Base 2017-10-30
- Table_string_hash at Base 2017-10-30
- Table_values at Base 2017-10-30
- Tableuint_free at Base 2017-10-30
- Tableuint_get at Base 2017-10-30
- Tableuint_keys at Base 2017-10-30
- Tableuint_keys_by_timeindex at Base 2017-10-30
- Tableuint_length at Base 2017-10-30
- Tableuint_map at Base 2017-10-30
- Tableuint_new at Base 2017-10-30
- Tableuint_put at Base 2017-10-30
- Tableuint_remove at Base 2017-10-30
- Tableuint_values at Base 2017-10-30
- UINT4_compare at Base 2017-10-30
- UINT8_compare at Base 2017-10-30
- Uint8list_append at Base 2017-10-30
- Uint8list_copy at Base 2017-10-30
- Uint8list_fill_array at Base 2017-10-30
- Uint8list_fill_array_and_free at Base 2017-10-30
- Uint8list_find at Base 2017-10-30
- Uint8list_free at Base 2017-10-30
- Uint8list_from_array at Base 2017-10-30
- Uint8list_head at Base 2017-10-30
- Uint8list_head_set at Base 2017-10-30
- Uint8list_index at Base 2017-10-30
- Uint8list_last_value at Base 2017-10-30
- Uint8list_length at Base 2017-10-30
- Uint8list_max at Base 2017-10-30
- Uint8list_min at Base 2017-10-30
- Uint8list_next at Base 2017-10-30
- Uint8list_pop at Base 2017-10-30
- Uint8list_push at Base 2017-10-30
- Uint8list_reverse at Base 2017-10-30
- Uint8list_to_array at Base 2017-10-30
- Uint8list_to_array_out at Base 2017-10-30
- Uint8list_to_string at Base 2017-10-30
- Uintlist_append at Base 2017-10-30
- Uintlist_copy at Base 2017-10-30
- Uintlist_fill_array at Base 2017-10-30
- Uintlist_fill_array_and_free at Base 2017-10-30
- Uintlist_find at Base 2017-10-30
- Uintlist_free at Base 2017-10-30
- Uintlist_from_array at Base 2017-10-30
- Uintlist_head at Base 2017-10-30
- Uintlist_head_set at Base 2017-10-30
- Uintlist_index at Base 2017-10-30
- Uintlist_keep_one at Base 2017-10-30
- Uintlist_last_value at Base 2017-10-30
- Uintlist_length at Base 2017-10-30
- Uintlist_max at Base 2017-10-30
- Uintlist_min at Base 2017-10-30
- Uintlist_next at Base 2017-10-30
- Uintlist_pop at Base 2017-10-30
- Uintlist_push at Base 2017-10-30
- Uintlist_reverse at Base 2017-10-30
- Uintlist_to_array at Base 2017-10-30
- Uintlist_to_array_out at Base 2017-10-30
- Uintlist_to_string at Base 2017-10-30
- Uinttable_fill_keys at Base 2017-10-30
- Uinttable_free at Base 2017-10-30
- Uinttable_get at Base 2017-10-30
- Uinttable_keys at Base 2017-10-30
- Uinttable_keys_by_timeindex at Base 2017-10-30
- Uinttable_length at Base 2017-10-30
- Uinttable_map at Base 2017-10-30
- Uinttable_new at Base 2017-10-30
- Uinttable_put at Base 2017-10-30
- Uinttable_remove at Base 2017-10-30
- Uinttable_values at Base 2017-10-30
- Uinttableuint_free at Base 2017-10-30
- Uinttableuint_get at Base 2017-10-30
- Uinttableuint_keys at Base 2017-10-30
- Uinttableuint_keys_by_timeindex at Base 2017-10-30
- Uinttableuint_length at Base 2017-10-30
- Uinttableuint_map at Base 2017-10-30
- Uinttableuint_new at Base 2017-10-30
- Uinttableuint_put at Base 2017-10-30
- Uinttableuint_remove at Base 2017-10-30
- Uinttableuint_values at Base 2017-10-30
- Univ_IIT_altlocp at Base 2017-10-30
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- Univ_IIT_annotation_firstchar at Base 2017-10-30
- Univ_IIT_chrlengths at Base 2017-10-30
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- Univ_IIT_coord_values_8p at Base 2017-10-30
- Univ_IIT_debug at Base 2017-10-30
- Univ_IIT_divint_crosstable at Base 2017-10-30
- Univ_IIT_dump at Base 2017-10-30
- Univ_IIT_dump_contigs at Base 2017-10-30
- Univ_IIT_dump_fai at Base 2017-10-30
- Univ_IIT_dump_labels at Base 2017-10-30
- Univ_IIT_dump_sam at Base 2017-10-30
- Univ_IIT_dump_table at Base 2017-10-30
- Univ_IIT_dump_typestrings at Base 2017-10-30
- Univ_IIT_find at Base 2017-10-30
- Univ_IIT_find_linear at Base 2017-10-30
- Univ_IIT_find_one at Base 2017-10-30
- Univ_IIT_free at Base 2017-10-30
- Univ_IIT_genomelength at Base 2017-10-30
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- Univ_IIT_interval at Base 2017-10-30
- Univ_IIT_interval_bounds at Base 2017-10-30
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- Univ_IIT_interval_length at Base 2017-10-30
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- Univ_IIT_intervals_setup at Base 2017-10-30
- Univ_IIT_label at Base 2017-10-30
- Univ_IIT_length at Base 2017-10-30
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- Univ_IIT_ntypes at Base 2017-10-30
- Univ_IIT_read at Base 2017-10-30
- Univ_IIT_string_from_position at Base 2017-10-30
- Univ_IIT_total_nintervals at Base 2017-10-30
- Univ_IIT_typeint at Base 2017-10-30
- Univ_IIT_typestring at Base 2017-10-30
- Univcoord_compare at Base 2017-10-30
- Univinterval_array_high at Base 2017-10-30
- Univinterval_array_low at Base 2017-10-30
- Univinterval_cmp at Base 2017-10-30
- Univinterval_cmp_high at Base 2017-10-30
- Univinterval_cmp_low at Base 2017-10-30
- Univinterval_copy at Base 2017-10-30
- Univinterval_equal at Base 2017-10-30
- Univinterval_free at Base 2017-10-30
- Univinterval_high at Base 2017-10-30
- Univinterval_is_contained at Base 2017-10-30
- Univinterval_length at Base 2017-10-30
- Univinterval_low at Base 2017-10-30
- Univinterval_new at Base 2017-10-30
- Univinterval_overlap_p at Base 2017-10-30
- Univinterval_print at Base 2017-10-30
- Univinterval_qsort_by_omega at Base 2017-10-30
- Univinterval_qsort_by_sigma at Base 2017-10-30
- Univinterval_sign at Base 2017-10-30
- Univinterval_store_length at Base 2017-10-30
- Univinterval_table_free at Base 2017-10-30
- Univinterval_type at Base 2017-10-30
- buffers_diff_p at Base 2017-10-30
- bzeof at Base 2017-10-30
- bzgetc at Base 2017-10-30
- bzgets at Base 2017-10-30
- clz_table at Base 2017-10-30
- count_bits at Base 2017-10-30
- global_except_stack at Base 2017-10-30
- mod_37_bit_position at Base 2017-10-30
- nt_oligo at Base 2017-10-30
- nt_oligo_truncate at Base 2017-10-30
- nt_querylength at Base 2017-10-30
=====================================
debian/patches/install-data-local
=====================================
--- a/debian/patches/install-data-local
+++ b/debian/patches/install-data-local
@@ -2,7 +2,7 @@ Description: Install data local
--- gmap.orig/Makefile.in
+++ gmap/Makefile.in
-@@ -846,7 +846,7 @@
+@@ -847,7 +847,7 @@
install-data-local:
=====================================
debian/rules
=====================================
--- a/debian/rules
+++ b/debian/rules
@@ -18,7 +18,7 @@ HELP2MAN = /usr/bin/help2man --no-info --version-string=${DEB_VERSION}
dh $@
override_dh_auto_configure:
- dh_auto_configure -- --enable-shared --with-gmapdb=/var/cache/gmap \
+ dh_auto_configure -- --with-gmapdb=/var/cache/gmap \
--bindir=/usr/lib/gmap $(EXTRA_CONFIGURE_ARGS)
override_dh_auto_install:
@@ -32,13 +32,22 @@ override_dh_auto_install:
dh_auto_install
override_dh_install:
- dh_install
mkdir -p debian/$(DEB_SOURCE)/usr/bin
+ dh_install
for bin in `echo gmap gsnap gmap_build gmapl gsnapl; \
- cd $(CURDIR)/debian/tmp/usr/lib/$(DEB_SOURCE)/; \
+ cd $(CURDIR)/debian/$(DEB_SOURCE)/usr/lib/$(DEB_SOURCE)/; \
ls -1 gmap*.* gsnap*.* `; do \
ln -s /usr/lib/gmap/$$bin debian/$(DEB_SOURCE)/usr/bin/$$bin; \
done
override_dh_auto_test:
dh_auto_test --no-parallel
+
+override_dh_installexamples:
+ mkdir $(CURDIR)/debian/$(DEB_SOURCE)/usr/share/doc/$(DEB_SOURCE)/examples
+ tar --sort=name \
+ --mtime="@${SOURCE_DATE_EPOCH}" \
+ --owner=root --group=root --numeric-owner \
+ --mode=go=rX,u+rw,a-s \
+ -cJf $(CURDIR)/debian/$(DEB_SOURCE)/usr/share/doc/$(DEB_SOURCE)/examples/tests.tar.xz tests
+ find . -print
=====================================
debian/tests/control
=====================================
--- /dev/null
+++ b/debian/tests/control
@@ -0,0 +1,2 @@
+Tests: gmap-tests
+Restrictions: allow-stderr
=====================================
debian/tests/gmap-tests
=====================================
--- /dev/null
+++ b/debian/tests/gmap-tests
@@ -0,0 +1,36 @@
+#! /bin/bash
+set -e
+
+readonly tmpdir=$(mktemp -d)
+tar -xf /usr/share/doc/gmap/examples/tests.tar.xz -C $tmpdir
+readonly srcdir=${tmpdir}/tests
+
+echo "align.test"
+gmap -A -g ${srcdir}/ss.chr17test ${srcdir}/ss.her2 > align.test.out
+diff align.test.out ${srcdir}/align.test.ok
+rm -f align.test.out
+
+
+echo "coords1.test"
+/usr/lib/gmap/fa_coords -o coords.chr17test ${srcdir}/ss.chr17test
+diff coords.chr17test ${srcdir}/coords1.test.ok
+rm -f coords.chr17test
+
+echo "iit.test"
+/usr/lib/gmap/iit_store -o iittest ${srcdir}/fa.iittest
+diff iittest.iit ${srcdir}/iittest.iit.ok
+
+/usr/lib/gmap/iit_get iittest.iit 20000 > iit_get.out
+diff iit_get.out ${srcdir}/iit_get.out.ok
+
+/usr/lib/gmap/iit_dump iittest.iit > iit_dump.out
+diff iit_dump.out ${srcdir}/fa.iittest
+rm -f iit_get.out
+rm -f iittest.iit
+rm -f iit_dump.out
+
+echo "setup1.test"
+gmap_build -k 15 -B /usr/lib/gmap -D . -d chr17test ${srcdir}/ss.chr17test
+rm -rf chr17test/
+
+rm -rf $tmpdir
View it on GitLab: https://salsa.debian.org/med-team/gmap/compare/51b72cd208f276e4c1a93e10e5532f2b562627d9...ed55e39bc3cb67f63551564df5ca6e4279caac43
--
View it on GitLab: https://salsa.debian.org/med-team/gmap/compare/51b72cd208f276e4c1a93e10e5532f2b562627d9...ed55e39bc3cb67f63551564df5ca6e4279caac43
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