Commits · f4036606f8428a96319da736392cee7bdfe27826 · ensembl-gh-mirror / ensembl

This project is mirrored from https://:*****@github.com/Ensembl/ensembl.git. Pull mirroring updated Feb 04, 2023.

11 Feb, 2004 4 commits
- modifications so that toplevel is now a pseudo coordinate system representing... · f4036606
  Graham McVicker authored Feb 11, 2004
```
modifications so that toplevel is now a pseudo coordinate system representing the highest real coordinate system in a given region
```
  f4036606
- updated tests for new toplevel implementation · 21329512
  Graham McVicker authored Feb 11, 2004
  
  21329512
- changed test data for coord_system table by adding rank column · 6fbe1d5a
  Graham McVicker authored Feb 11, 2004
  
  6fbe1d5a
- · 58b3621e
  Laura Clarke authored Feb 11, 2004
```
changes to make elegans xrefs work
```
  58b3621e
10 Feb, 2004 2 commits
- fixed bug in which undef was being returned from rearrange when zero should... · f5ab681a
  Graham McVicker authored Feb 10, 2004
```
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 Feb 10, 2004
  
  ab8d701a
09 Feb, 2004 3 commits
- map_density table deleted. · f10bda44
  Arne Stabenau authored Feb 09, 2004
```
Superseeded by density_feature and density_type
```
  f10bda44
- prepare to use dna_db · 3dad467e
  Arne Stabenau authored Feb 09, 2004
  
  3dad467e
- changed sliceadaptor to hang on db · c3ffc0eb
  Arne Stabenau authored Feb 09, 2004
  
  c3ffc0eb
06 Feb, 2004 5 commits
- more stats collection · 82251f6a
  Graham McVicker authored Feb 06, 2004
  
  82251f6a
- name changes to follow naming conventions · 4492f88f
  Ian Longden authored Feb 06, 2004
  
  4492f88f
- changed overlaps tests · 6d9450df
  Graham McVicker authored Feb 06, 2004
  
  6d9450df
- Changed Feature::overlaps so that all it does is a simple integer range... · 10523a09
  Graham McVicker authored Feb 06, 2004
```
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 Feb 06, 2004
  
  243c7bbf
05 Feb, 2004 4 commits
- add more classes of mapping failure · cd9ab8bc
  Graham McVicker authored Feb 05, 2004
  
  cd9ab8bc
- keep track of some more stats · a2a4f6ae
  Graham McVicker authored Feb 05, 2004
  
  a2a4f6ae
- script for running other script so i don't have to type all the command line args · 1323e26b
  Graham McVicker authored Feb 05, 2004
  
  1323e26b
- slice method was incorrectly named contig · 31eaa6f5
  Graham McVicker authored Feb 05, 2004
```
this could have caused sequence caching problems
```
  31eaa6f5
04 Feb, 2004 4 commits
- keep track of types of mapping problems now · 6d276ea9
  Graham McVicker authored Feb 04, 2004
  
  6d276ea9
- helper module to keep track of types of mapping failures · be886aaa
  Graham McVicker authored Feb 04, 2004
  
  be886aaa
- made rearrange method a lot faster (but uglier) · 6ec062e1
  Graham McVicker authored Feb 04, 2004
  
  6ec062e1
- *** empty log message *** · b4ab841b
  Graham McVicker authored Feb 04, 2004
  
  b4ab841b
03 Feb, 2004 2 commits
- names of coords systems and ids in mapper no longer counter-intuitive · faa79c74
  Graham McVicker authored Feb 03, 2004
  
  faa79c74
- added tests for IdentityXref mapping · 7a6af8fd
  Graham McVicker authored Feb 03, 2004
  
  7a6af8fd
01 Feb, 2004 2 commits
- renamed human2chimp2.pl back to human2chimp.pl · ee137a51
  Graham McVicker authored Feb 01, 2004
  
  ee137a51
- added transcript construction code, fixed some more bugs · d8e3e35a
  Graham McVicker authored Feb 01, 2004
  
  d8e3e35a
31 Jan, 2004 1 commit
- lots of debugging and bug fixes; script does something now · 656f58fd
  Graham McVicker authored Jan 31, 2004
  
  656f58fd
30 Jan, 2004 1 commit
- *** empty log message *** · f88aac19
  Graham McVicker authored Jan 30, 2004
  
  f88aac19
29 Jan, 2004 4 commits
- temporary file for some reworking of script · 83e245a7
  Graham McVicker authored Jan 29, 2004
  
  83e245a7
- *** empty log message *** · c9f32319
  Graham McVicker authored Jan 29, 2004
  
  c9f32319
- handle features that only have seqnames (and no slices!) · f6753cbf
  Arne Stabenau authored Jan 29, 2004
  
  f6753cbf
- test overlaps with just seqname features · 93cb056d
  Arne Stabenau authored Jan 29, 2004
  
  93cb056d
28 Jan, 2004 2 commits
- fixed Danio converter I hope. Need to test still. · 6d5d994d
  Graham McVicker authored Jan 28, 2004
  
  6d5d994d
- · d2fbb187
  Laura Clarke authored Jan 28, 2004
```
some changes for new schema and api
```
  d2fbb187
27 Jan, 2004 6 commits
- skeleton of script to perform (experimental) human -> chimp gene transfer · cac42482
  Graham McVicker authored Jan 27, 2004
  
  cac42482
- genomic2cds now correctly gives back gaps for pseudogenes · 450692c3
  Graham McVicker authored Jan 27, 2004
  
  450692c3
- meta_coord info is now stored both in dnadb and feature db when storing features · 975c2c87
  Graham McVicker authored Jan 27, 2004
  
  975c2c87
- made dnadb unsettable once set · c686f3a1
  Graham McVicker authored Jan 27, 2004
  
  c686f3a1
- overlaps function added. · b0ec954c
  Arne Stabenau authored Jan 27, 2004
  
  b0ec954c
- 3 tests for overlaps function. Should have some more... · 92a52abb
  Arne Stabenau authored Jan 27, 2004
  
  92a52abb