EXAMPLES
(0 files, 0 lines)
[root]/ARBDB
EXAMPLES
(0 files, 0 lines)
| Author | Changes | Lines of Code | Lines per Change |
|---|---|---|---|
| Totals | 4062 (100.0%) | 144919 (100.0%) | 35.6 |
| westram | 3905 (96.1%) | 119863 (82.7%) | 30.6 |
| oldcode | 44 (1.1%) | 23880 (16.5%) | 542.7 |
| epruesse | 25 (0.6%) | 540 (0.4%) | 21.6 |
| meierh | 7 (0.2%) | 230 (0.2%) | 32.8 |
| boehnel | 43 (1.1%) | 181 (0.1%) | 4.2 |
| spanfeln | 9 (0.2%) | 94 (0.1%) | 10.4 |
| baderk | 15 (0.4%) | 59 (0.0%) | 3.9 |
| lai | 2 (0.0%) | 42 (0.0%) | 21.0 |
| richter | 6 (0.1%) | 12 (0.0%) | 2.0 |
| yadhu | 2 (0.0%) | 7 (0.0%) | 3.5 |
| artemov | 2 (0.0%) | 6 (0.0%) | 3.0 |
| jobb | 2 (0.0%) | 5 (0.0%) | 2.5 |
* add deadlock warning to callback loop in commit_transaction.
10 lines of code changed in 1 file:
* ignore SIGPIPE while ArbDBWriter exists
- arb does no longer terminate, but instead prints error, when pipe breaks, e.g.:
{{{
19:01.38 While writing '/home/user/data/test with space.arb~': Broken pipe
(close reports: pipe writing to
file='/home/user/data/test with space.arb~'
using cmd='xz > /home/user/data/test with space.arb~'
failed with exitcode=1 (broken pipe? corrupted archive?)
(res=256, exited=1, signaled=0, status=1))
}}}
11 lines of code changed in 2 files:
* avoid crash while saving arb database (see #840)
- mark loc where SIGPIPE occurred.
- report an error when compression is enabled and filename contains unwanted characters.
3 lines of code changed in 1 file:
* reintegrates 'help' into 'trunk'
- relocate help sources
* adds: log:branches/help@18763:18780
13 lines of code changed in 2 files:
* eliminate obsolete {{{GBT_read_name}}} from perl interface
- To fix your skript you have to replace {{{BIO::read_name}}} by
* {{{BIO::get_name}}} or
* {{{BIO::get_name_or_description}}} (=1:1 replacement).
2 lines of code changed in 2 files:
* also rename overloaded {{{GB_path_in_ARBHOME()}}} -> {{{GB_concat_path_in_ARBHOME()}}}.
- Note: before, simply removing the static modifier did break the perl interface.
11 lines of code changed in 2 files:
* fix unwanted export of overloaded functions to perl interface:
- GBT_log_to_tree_remark()
- GB_path_in_ARBLIB()
11 lines of code changed in 5 files:
* remove trailing whitespace from c source.
96 lines of code changed in 23 files:
* change many WARN_TODO triggered warnings into todo markers.
13 lines of code changed in 9 files:
* fix crash when previewing printout on OSX (thx to jan)
14 lines of code changed in 1 file:
* postscript/pdf viewers:
- use {{{open -W}}} under osx (thanks to Jan Gerken).
- add {{{xreader}}} as primary default viewer under Linux.
34 lines of code changed in 1 file:
* fail if not all possible objects were added to Makefile.
* remove object section GB_PP. add objects to GB_X.
21 lines of code changed in 1 file:
* split TEST_GB_command_interpreter...() into smaller parts.
27 lines of code changed in 1 file:
* fixes 2 failing unittest under ubuntu 20.04
- /bin and /sbin are symbolic links there -> use /usr instead
1 lines of code changed in 1 file:
* allow to 'edit bootstraps'
- document example.
- when a replacement results in an empty string => remove remark.
28 lines of code changed in 2 files:
* tweak replacement via regular expressions:
- allow replacement of whole line regexpr which matches empty source string.
- test to replace whole string by nothing.
- always fail BOL/EOL operator starting from second replace-operation. fixes some failing replacements.
* doc: describe other simpler, now working replacements.
10 lines of code changed in 1 file:
* clear error exported from {{{gbt_nonexisting_alignment}}}
- made case-only rename fail in DEBUG mode.
6 lines of code changed in 1 file:
* fix parameters of {{{GBT_rename_alignment}}} + {{{gbt_rename_alignment_of_item}}}
- rename.
- change to bool.
- callers use bool.
13 lines of code changed in 2 files:
* detect attempt to ''copy'' to alignment which differs from source only in case.
13 lines of code changed in 1 file:
* reintegrates 'top' into 'trunk'
* adds: log:branches/top@18453:18462
7 lines of code changed in 2 files:
* warn if any path used in ARB does contain spaces (too error-prone)
- added helper functions into CORE
- warn about unwanted chars
* in result from getenv_executable(), getenv_existing_directory(), getenv_autodirectory(), GB_find_executable().
* in path of sina executable and of pigz used in ARB_zfopen().
21 lines of code changed in 1 file:
* tested vectorization with misc gcc versions:
- number of reported loops differs with 7.5.0
- one vectorization succeeds for gcc 6.5.0
1 lines of code changed in 1 file:
* use prefix 'take' for descends into UNIT_TESTER.
* fix some whitespace.
7 lines of code changed in 1 file:
* full update from child 'fix' into 'trunk'
* adds: log:branches/fix@18339:18351
1 lines of code changed in 1 file:
* temporary workaround for broken SINA binary compatibility (has been broken by r18159).
9 lines of code changed in 2 files:
* fix whitespace.
12 lines of code changed in 1 file:
* rename test (test symbol defined twice).
* move testcode from ARBDB->CORE.
0 lines of code changed in 1 file:
* reintegrates 'saicalc' into 'trunk'
- implements #730
* adds: log:branches/saicalc@18141:18310
37 lines of code changed in 5 files:
* enforce destruction order of shell created via {{{GB_shell4perl}}} and {{{GB_test_shell_closed}}} by storing the former in the latter
- move code from {{{~GB_shell4perl}}} into {{{close_global_shell}}}.
- call {{{close_global_shell}}} either from {{{~GB_shell4perl}}} or from {{{~GB_test_shell_closed}}}.
- fixes #508
33 lines of code changed in 4 files:
* deny to (quick-)save while TA open
- add assertion to code that now is assumed to be "dead".
5 lines of code changed in 1 file:
* full update from child 'fix' into 'trunk'
- finish tests introduced with [18200]
* adds: log:branches/fix@18194:18207
8 lines of code changed in 2 files:
* reintegrates 'bugfix' into 'trunk'
- add unittest for "sort database"
- fix #820
* adds: log:branches/bugfix@18196:18199
1 lines of code changed in 1 file:
* reintegrates 'fts' into 'trunk'
* adds: log:branches/fts@18177:18185
16 lines of code changed in 3 files:
* full update from child 'fix' into 'trunk'
- fix item name accessors ({{{GBT_get_name}}} + {{{GBT_get_name_or_description}}})
- add {{{null2empty}}}
* adds: log:branches/fix@18140:18158
48 lines of code changed in 10 files:
* add new ACI commands {{{findspec}}}, {{{findacc}}} + {{{findgene}}}
- allow to find species and genes by name (and species by acc)
- add tests (not for findgene)
- document
125 lines of code changed in 4 files:
* publish {{{GBT_expect_item_rel_item_data}}}.
* implement {{{GEN_find_gene_rel_gene_data}}} based on {{{GBT_find_item_rel_item_data}}}.
* add {{{GEN_expect_gene}}}.
13 lines of code changed in 4 files:
* vectorization succeeds with gcc 4.9.2
- failed during build (no idea why build last friday succeeded?!)
1 lines of code changed in 1 file:
* reintegrates 'cleanup' into 'trunk'
* adds: log:branches/cleanup@18105:18112
23 lines of code changed in 2 files:
* expect LOOP_VECTORIZED for gcc 5.5.0.
* fix member initialization for gcc 443?
1 lines of code changed in 1 file:
* full update from child 'fts' into 'trunk'
- implements #562
* adds:
- [18091/branches/fts]
- log:branches/gui@17754:17924,17926:18090
66 lines of code changed in 8 files:
(1368 more)