Commits · 4e8be8cab7610fef3437b4e2259225afc44a1a94 · ensembl-gh-mirror / ensembl

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Jul 29, 2003
- added max value to max_assembly_contig if not defined · 4e8be8ca
  Emmanuel Mongin authored 21 years ago
  
  4e8be8ca
- Ported fixes from blanch-ensembl-15-1 · 7cf23c3b
  Web Admin authored 21 years ago
  
  7cf23c3b
- converter bioperl SeqFeature as Seg result to ProteinFeature in Ensembl · db768d0f
  juguang authored 21 years ago
  
  db768d0f
Jul 28, 2003
- added do_first() to affect the order SchemaConverter does things · 806518f5
  Arne Stabenau authored 21 years ago
  
  806518f5
- added get_max_density_per_chromosome · a35f0d3c
  Patrick Meidl authored 21 years ago
  
  a35f0d3c
- saner check for store method · d0cc7085
  juguang authored 21 years ago
  
  d0cc7085
- moved to branch · d8c2d093
  Graham McVicker authored 21 years ago
  
  d8c2d093
- Forgot to enable cleanup after debugging. · 5f5d4784
  Andreas Kusalananda Kähäri authored 21 years ago
  
  5f5d4784
- Gzipped files have a higher FTP transfer survival rate if transferred · af696ab9
  Andreas Kusalananda Kähäri authored 21 years ago
```
in binary mode (oops).
```
  af696ab9
- Switched to using old-fashioned ftp with a here-document to hopefully · 48945442
  Andreas Kusalananda Kähäri authored 21 years ago
```
overcome long filename problems.
```
  48945442
- add 2600 GeneDB 1 KNOWN · ed82107b
  juguang authored 21 years ago
  
  ed82107b
Jul 25, 2003
- added seq_region_annotation table, renamed some cols of assembly table · 015c17b6
  Graham McVicker authored 21 years ago
  
  015c17b6
- Back to using tar instead of pax. Tru64 pax seems to cut off long path names. · d9625dd9
  Andreas Kusalananda Kähäri authored 21 years ago
```
Won't touch mart databases (or anything matching $avoid_re).
Will only work with revision 14 and 15 (or anything matching $require_re).
```
  d9625dd9
- Sending SIGINT (<ctrl>-C) will now make the script exit gracefully, · 0ef3f9c2
  Andreas Kusalananda Kähäri authored 21 years ago
```
after cleaning up whatever it was doing at the time.  This means
restarting the process later is easier and safer.
```
  0ef3f9c2
- Corrected cleanup bug. · c0fed0e1
  Andreas Kusalananda Kähäri authored 21 years ago
  
  c0fed0e1
- Changed from using tar to using pax. · 1afec298
  Andreas Kusalananda Kähäri authored 21 years ago
```
Reordered call tree.
Corrected redirection bug.
Removed coprocess that Tru64 KornShell88 didn't like ("memory fault").
```
  1afec298
- Addition about not verifying checksums and sizes of compressed files. · 70ca8cbd
  Andreas Kusalananda Kähäri authored 21 years ago
  
  70ca8cbd
- Don't verify the checksum or size of the new files if they are · 90b937fe
  Andreas Kusalananda Kähäri authored 21 years ago
```
compressed.  Apparantly xdelta will recompress the patched file in a
way that might result in slight differences when compared to the
original file.
```
  90b937fe
- whitespace · f56cf676
  Arne Stabenau authored 21 years ago
  
  f56cf676
- remove 4 secs on exon-peptide · 5cf199af
  Brian Gibbins authored 21 years ago
  
  5cf199af
- Display name of missing directories before dying. · cd4d6f45
  Andreas Kusalananda Kähäri authored 21 years ago
  
  cd4d6f45
- New shell script that will create deltas for all consecutive · 8f262366
  Andreas Kusalananda Kähäri authored 21 years ago
```
revisions of all databases on ftp.ensembl.org.  Uses the files
in /pub/<species>/data/mysql/<db>/*
```
  8f262366
- Retired two files. · 68bc1e02
  Andreas Kusalananda Kähäri authored 21 years ago
  
  68bc1e02
- converter now support for Bio::SearchIO::HSP::GenericHSP to Bio::EnsEMBL::ProteinFeature · 4e3dd78f
  juguang authored 21 years ago
  
  4e3dd78f
Jul 24, 2003
- rewrote a lot of haplo/PAR stuff, other minor adjustments · 49a11a35
  Graham McVicker authored 21 years ago
  
  49a11a35
- dnafrag is officially named seq_region now · bee4cf7b
  Arne Stabenau authored 21 years ago
  
  bee4cf7b
- fix off by one in length of peptide when stop residue is used in sequence · fd1888d9
  Brian Gibbins authored 21 years ago
  
  fd1888d9
Jul 23, 2003
- more haplotype ideas · 6a45446a
  Graham McVicker authored 21 years ago
  
  6a45446a
- add query_identity and target_identity tag in the argument of sub new · d83867d8
  juguang authored 21 years ago
  
  d83867d8
- add description tag in the argument of sub new · cbe02044
  juguang authored 21 years ago
  
  cbe02044
- support to convert to ProteinFeature · e46abf5d
  juguang authored 21 years ago
  
  e46abf5d
Jul 22, 2003
- uses the perc of idt (query and target) from the pmatch conf file · 987efd0a
  Emmanuel Mongin authored 21 years ago
  
  987efd0a
- translate -> transfer, move · 6d6dff8d
  Arne Stabenau authored 21 years ago
  
  6d6dff8d
- minor changes, formatting · 76b7ff0a
  Arne Stabenau authored 21 years ago
  
  76b7ff0a
- Optimized query for register region · d154c61e
  Arne Stabenau authored 21 years ago
  
  d154c61e
- should be 9 tests not 10 · 4936bb9f
  Graham McVicker authored 21 years ago
  
  4936bb9f
- added some more test data to meta table · 52bf022e
  Graham McVicker authored 21 years ago
  
  52bf022e
- added MetaContainer tests · 485ec9f3
  Graham McVicker authored 21 years ago
  
  485ec9f3
- Use cahching for all values. · 422e390a
  Arne Stabenau authored 21 years ago
```
Added get_max_assembly_contig for optimized queries on assembly table.
```
  422e390a
- ideas about haplotypes · b802ac29
  Graham McVicker authored 21 years ago
  
  b802ac29