dbolser

[dbolser@nanna bioperl-live]$ git branch -a
* master
  origin/HEAD
  origin/anydbm-branch
  origin/branch-1-6
  origin/master
  origin/my_root_branch
  origin/topic/adsj-seqobj-return
  origin/topic/davemessina-multiphylip
  origin/topic/lstein-seqfeature-store-summaries

dbolser

[dbolser@nanna bioperl-live]$ git remote -v
dbolser git@github.com:dbolser/bioperl-live.git
origin  git://github.com/bioperl/bioperl-live.git

[dbolser@nanna bioperl-live]$ git push dbolser
To git@github.com:dbolser/bioperl-live.git
 ! [rejected]        master -> master (non-fast forward)
error: failed to push some refs to 'git@github.com:dbolser/bioperl-live.git'

dbolser

[dbolser@nanna bioperl-live]$ git pull origin
remote: Counting objects: 49, done.
remote: Compressing objects: 100% (25/25), done.
remote: Total 25 (delta 19), reused 0 (delta 0)
Unpacking objects: 100% (25/25), done.
From git://github.com/bioperl/bioperl-live
   0fe0648..cc09af2  master     -> origin/master
Bio/DB/SeqFeature/Store/DBI/mysql.pm: needs update
error: Entry 'Bio/DB/SeqFeature/Store/DBI/mysql.pm' not uptodate. Cannot merge.
fatal: merging of trees 7d7a541ce7666e14b0b374b935295f9e45b1b46c and ad242f654a85bd850e6d508319c1adc15e88c27b failed

dbolser

git add Bio/DB/SeqFeature/Store/DBI/mysql.pm

git commit
Created commit ec01fac: Adding my updated version of the DBI/mysql.pm which fixes problems when using -namespace. I thought this had been comitted elsewhere and pulled by me, but I guess I'm git'ing confused. You see what I did there?
 1 files changed, 68 insertions(+), 64 deletions(-)

git status
# On branch master
# Untracked files:
#   (use "git add <file>..." to include in what will be committed)

dbolser

git push dbolser
Counting objects: 33, done.
Compressing objects: 100% (20/20), done.
Writing objects: 100% (20/20), 4.89 KiB, done.
Total 20 (delta 15), reused 0 (delta 0)
To git@github.com:dbolser/bioperl-live.git
   825d572..99421f7  master -> master

dbolser

cd build/src/bioperl-live
[dbolser@nanna bioperl-live]$ git diff origin/master master --stat
 Bio/FeatureIO.pm                                   |   44 ++--
 Bio/FeatureIO/agp.pm                               |  320 ++++++++++++++++++++
 Bio/FeatureIO/gff.pm                               |    2 +-
 .../Bio-SeqFeature-Store/bp_seqfeature_load.PLS    |   11 +-
 scripts/bioperl_netinstall.pl                      |    4 +-
 scripts/utilities/repeat_mask_sequence.PLS         |  206 +++++++++++++
 6 files changed, 561 insertions(+), 26 deletions(-)

dbolser

[dbolser@cricket Compare_To_OPA_SNPs]$ 
[dbolser@cricket Compare_To_OPA_SNPs]$ cpan

cpan shell -- CPAN exploration and modules installation (v1.9402)
Enter 'h' for help.

                                                                                                                        cpan[1]> install Bio::DB::Sam
CPAN: Storable loaded ok (v2.21)
Going to read '/homes/dbolser/.cpan/Metadata'
  Database was generated on Mon, 01 Nov 2010 02:46:56 GMT

dbolser

[dbolser@cricket Compare_To_OPA_SNPs]$ cpan

cpan shell -- CPAN exploration and modules installation (v1.9402)
Enter 'h' for help.

                                                                                                                        cpan[1]> install Bio::DB::Sam                        
CPAN: Storable loaded ok (v2.21)
Going to read '/homes/dbolser/.cpan/Metadata'
  Database was generated on Mon, 01 Nov 2010 02:46:56 GMT
Running install for module 'Bio::DB::Sam'

dbolser

my @fwd_intensity = $intensities->
    features( -seqid => $scaff, -type => 'fwd link intensity',
	      -start => $end,
	      -end   => $end,
	    );

dbolser

  
  my @fwd_intensity = $intensities->
    features( -seqid => $scaff, -type => 'fwd link intensity',
	      -start => $end,
	      -end   => $end,
	    );
  warn Dumper @fwd_intensity if $verbose > 1;
  exit;