use first line of filter docstring in FILTER meta, update README

README.rst

@@ -1,4 +1,4 @@
-A VCFv4.0 parser for Python.
+A VCFv4.0 and 4.1 parser for Python.
 
 Online version of PyVCF documentation is available at http://pyvcf.rtfd.org/
 
@@ -112,7 +112,6 @@ There are also a number of methods::
     >>> print call.called, call.gt_type, call.gt_bases, call.phased
     True 0 T|T True
 
-
 Metadata regarding the VCF file itself can be investigated through the
 following attributes:
 
@@ -133,6 +132,16 @@ For example::
     >>> vcf_reader.infos['AA'].desc
     'Ancestral Allele'
 
+ALT records are actually classes, so that you can interrogate them::
+
+    >>> reader = vcf.Reader(file('vcf/test/example-4.1-bnd.vcf'))
+    >>> _ = reader.next(); row = reader.next()
+    >>> print row
+    Record(CHROM=1, POS=2, REF=T, ALT=[T[2:3[])
+    >>> bnd = row.ALT[0]
+    >>> print bnd.withinMainAssembly, bnd.orientation, bnd.remoteOrientation, bnd.connectingSequence
+    True False True T
+
 Random access is supported for files with tabix indexes.  Simply call fetch for the
 region you are interested in::
 

docs/FILTERS.rst

@@ -54,7 +54,10 @@ I can create a class like this::
 
 
 This class subclasses ``vcf.filters.Base`` which provides the interface for VCF filters.
-The docstring  and ``name`` are metadata about the parser.
+The docstring  and ``name`` are metadata about the parser.  The docstring provides
+the help for the script, and the first line is included in the FILTER metadata when 
+applied to a file.
+
 The ``customize_parser`` method allows you to add arguments to the script.
 We use the ``__init__`` method to grab the argument of interest from the parser.
 Finally, the ``__call__`` method processes each record and returns a value if the 

scripts/vcf_filter.py

@@ -134,7 +134,9 @@ def addfilt(filt):
         f = filters[name](filter_args)
         chain.append(f)
         # add a filter record to the output
-        inp.filters[f.filter_name()] = _Filter(f.filter_name(), f.description)
+        short_doc = f.__doc__ or ''
+        short_doc = short_doc.split('\n')[0].lstrip()
+        inp.filters[f.filter_name()] = _Filter(f.filter_name(), short_doc)
 
     # output must be created after all the filter records have been added
     output = vcf.Writer(args.output, inp)

vcf/filters.py

@@ -51,8 +51,9 @@ def __call__(self, record):
 
 
 class VariantGenotypeQuality(Base):
-    """ Filters sites with low quality variants.  i.e. it is possible
-        to have a high site quality with many low quality calls.  This
+    """ Filters sites with only low quality variants.
+
+        It is possible to have a high site quality with many low quality calls.  This
         filter demands at least one call be above a threshold quality.
     """
 
@@ -74,7 +75,9 @@ def __call__(self, record):
 
 
 class ErrorBiasFilter(Base):
-    """ Some sequencing technologies, notably pyrosequencing, produce mutation
+    """ Filter sites that look like correlated sequencing errors.
+
+        Some sequencing technologies, notably pyrosequencing, produce mutation
         hotspots where there is a constant level of noise, producing some reference
         and some heterozygote calls.
 
@@ -98,7 +101,7 @@ def customize_parser(self, parser):
                 help='Filter sites above this error log odds ratio')
 
     def __init__(self, args):
-        self.threshold = args.errlr
+        self.threshold = args.eblr
         if robjects is None:
             raise Exception('Please install rpy2')
         self.ll_test = robjects.r('''