Contents

## version 0.1.7

1. A couple of scripts and subroutines were hashing peptides but not on the file
basename.  This would result in slightly incorrect results (any time there
were overlapping scan numbers in multiple datasets, only the top one would be
chosen).  The results would be correct for single runs.

Output files that could be affected:
*.top_per_scan.txt
*.all_peps_per_scan.txt

Scripts that could be affected:
script/top_hit_per_scan.rb
bin/filter_spec_id.rb
script/filter-peps.rb
bin/id_precision.rb

Subroutines that were affected:
spec_id.rb (pep_probs_by_* )
spec_id.rb (top_peps_prefilter!)
proph.rb uniq_by_seqcharge
align.rb called uniq_by_seqcharge


2. false_positive_rate.rb and protein_summary.rb (by extension) were using
number of true positives on the x axis while in reality I was plotting the
number of hits.  I've updated x axis labels to reflect this change.  In
addition, since the term 'false positive rate' has such a distinct definition
in classical ROC plots and binary statistics, I've decided to work primarily
in terms of precision (TP/(TP+FP)).  I've purged the terms 'False Positive
Rate' and 'FPR' from the package. It's been suggested that FP/(TP+FP) be
called the False Positive Predictive Rate (FPPR).  I will probably implement
this in a future release.

## version 0.2.0

Revamped the way SpecID works (it is now mixed-in).
Added support for modifications to bioworks_to_pepxml.rb
Can read .srf files (nearly interchangeable with bioworks files)
Redid filter.rb

## version 0.2.1

minor bugfix

## version 0.2.2

made compatible with Bioworks fasta file reverser and updated tutorial.
Killed classify_by_prefix routine in favor of classify_by_false_flag which has
a prefix option

Version data entries

1 entries across 1 versions & 1 rubygems

Version	Path
mspire-0.2.2	changelog.txt