Commits · 21329512b160c77839913a398df8083bf5a8484a · ensembl-gh-mirror / ensembl

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Feb 11, 2004
- updated tests for new toplevel implementation · 21329512
  Graham McVicker authored 21 years ago
  
  21329512
- changed test data for coord_system table by adding rank column · 6fbe1d5a
  Graham McVicker authored 21 years ago
  
  6fbe1d5a
- · 58b3621e
  Laura Clarke authored 21 years ago
```
changes to make elegans xrefs work
```
  58b3621e
Feb 10, 2004
- fixed bug in which undef was being returned from rearrange when zero should... · f5ab681a
  Graham McVicker authored 21 years ago
```
fixed bug in which undef was being returned from rearrange when zero should have been returned instead
```
  f5ab681a
- added additional test for rearrange. Was returning undef instead of 0 or "" · ab8d701a
  Graham McVicker authored 21 years ago
  
  ab8d701a
Feb 09, 2004
- map_density table deleted. · f10bda44
  Arne Stabenau authored 21 years ago
```
Superseeded by density_feature and density_type
```
  f10bda44
- prepare to use dna_db · 3dad467e
  Arne Stabenau authored 21 years ago
  
  3dad467e
- changed sliceadaptor to hang on db · c3ffc0eb
  Arne Stabenau authored 21 years ago
  
  c3ffc0eb
Feb 06, 2004
- more stats collection · 82251f6a
  Graham McVicker authored 21 years ago
  
  82251f6a
- name changes to follow naming conventions · 4492f88f
  Ian Longden authored 21 years ago
  
  4492f88f
- changed overlaps tests · 6d9450df
  Graham McVicker authored 21 years ago
  
  6d9450df
- Changed Feature::overlaps so that all it does is a simple integer range... · 10523a09
  Graham McVicker authored 21 years ago
```
Changed Feature::overlaps so that all it does is a simple integer range comparison, ignoring the possibility that the features could be on different seq_regions.
```
  10523a09
- Intron class added with test · 243c7bbf
  Ian Longden authored 21 years ago
  
  243c7bbf
Feb 05, 2004
- add more classes of mapping failure · cd9ab8bc
  Graham McVicker authored 21 years ago
  
  cd9ab8bc
- keep track of some more stats · a2a4f6ae
  Graham McVicker authored 21 years ago
  
  a2a4f6ae
- script for running other script so i don't have to type all the command line args · 1323e26b
  Graham McVicker authored 21 years ago
  
  1323e26b
- slice method was incorrectly named contig · 31eaa6f5
  Graham McVicker authored 21 years ago
```
this could have caused sequence caching problems
```
  31eaa6f5
Feb 04, 2004
- keep track of types of mapping problems now · 6d276ea9
  Graham McVicker authored 21 years ago
  
  6d276ea9
- helper module to keep track of types of mapping failures · be886aaa
  Graham McVicker authored 21 years ago
  
  be886aaa
- made rearrange method a lot faster (but uglier) · 6ec062e1
  Graham McVicker authored 21 years ago
  
  6ec062e1
- *** empty log message *** · b4ab841b
  Graham McVicker authored 21 years ago
  
  b4ab841b
Feb 03, 2004
- names of coords systems and ids in mapper no longer counter-intuitive · faa79c74
  Graham McVicker authored 21 years ago
  
  faa79c74
- added tests for IdentityXref mapping · 7a6af8fd
  Graham McVicker authored 21 years ago
  
  7a6af8fd
Feb 01, 2004
- renamed human2chimp2.pl back to human2chimp.pl · ee137a51
  Graham McVicker authored 21 years ago
  
  ee137a51
- added transcript construction code, fixed some more bugs · d8e3e35a
  Graham McVicker authored 21 years ago
  
  d8e3e35a
Jan 31, 2004
- lots of debugging and bug fixes; script does something now · 656f58fd
  Graham McVicker authored 21 years ago
  
  656f58fd
Jan 30, 2004
- *** empty log message *** · f88aac19
  Graham McVicker authored 21 years ago
  
  f88aac19
Jan 29, 2004
- temporary file for some reworking of script · 83e245a7
  Graham McVicker authored 21 years ago
  
  83e245a7
- *** empty log message *** · c9f32319
  Graham McVicker authored 21 years ago
  
  c9f32319
- handle features that only have seqnames (and no slices!) · f6753cbf
  Arne Stabenau authored 21 years ago
  
  f6753cbf
- test overlaps with just seqname features · 93cb056d
  Arne Stabenau authored 21 years ago
  
  93cb056d
Jan 28, 2004
- fixed Danio converter I hope. Need to test still. · 6d5d994d
  Graham McVicker authored 21 years ago
  
  6d5d994d
- · d2fbb187
  Laura Clarke authored 21 years ago
```
some changes for new schema and api
```
  d2fbb187
Jan 27, 2004
- skeleton of script to perform (experimental) human -> chimp gene transfer · cac42482
  Graham McVicker authored 21 years ago
  
  cac42482
- genomic2cds now correctly gives back gaps for pseudogenes · 450692c3
  Graham McVicker authored 21 years ago
  
  450692c3
- meta_coord info is now stored both in dnadb and feature db when storing features · 975c2c87
  Graham McVicker authored 21 years ago
  
  975c2c87
- made dnadb unsettable once set · c686f3a1
  Graham McVicker authored 21 years ago
  
  c686f3a1
- overlaps function added. · b0ec954c
  Arne Stabenau authored 21 years ago
  
  b0ec954c
- 3 tests for overlaps function. Should have some more... · 92a52abb
  Arne Stabenau authored 21 years ago
  
  92a52abb
Jan 26, 2004
- removed unneeded load_genomic_mapper method · 6121a6cf
  Graham McVicker authored 21 years ago
  
  6121a6cf