diff --git a/svreader/Annotate.py b/svreader/Annotate.py index 41c734f58bf02114a45a5370cb915d7346199007..d23958ef58d5cbbfd5952f7b1ec9484c804e8fd5 100644 --- a/svreader/Annotate.py +++ b/svreader/Annotate.py @@ -40,6 +40,10 @@ class AnnotatedRecord(object): def pos(self): return self.record.pos + @property + def start(self): + return self.record.pos + @property def chrom(self): return self.record.chrom @@ -48,6 +52,10 @@ class AnnotatedRecord(object): def stop(self): return self.record.stop + @property + def end(self): + return self.record.stop + @property def svtype(self): return self._sv_type @@ -72,7 +80,7 @@ class AnnotatedRecord(object): return sum([s.isVariant for s in self.samples]) def variant_read_support(self): - return sum([s.AltSupport() for s in self.samples]) + return max([s.AltSupport() for s in self.samples]) def qual(self): return sum([s.SQ_score() for s in self.samples if s.isVariant]) @@ -84,7 +92,7 @@ class AnnotatedRecord(object): supp_reads = self.variant_read_support() num_supp_samples = self.num_variant_samples() try: - self.record.info['SUPP_READS'] = supp_reads + self.record.info['MAX_SUPP_READS'] = supp_reads self.record.info['NUM_SUPP_SAMPLES'] = num_supp_samples except KeyError: eprint("SUPP_READS or NUM_SUPP_SAMPLES absent from record info keys") @@ -130,7 +138,6 @@ class AnnotatedRecordSample(object): class VCFReader(SVReader): def __init__(self, file_name, sv_to_report=None): -<<<<<<< HEAD super(VCFReader, self).__init__(file_name) self.filename = file_name self.sv_to_report = sv_to_report @@ -165,8 +172,8 @@ class VCFReader(SVReader): def add_metadata(self): self.addInfo("SOURCEID", 1, "String", "The source sv identifier") - self.addInfo("SUPP_READS", 1, "Integer", - "Number of supporting reads") + self.addInfo("MAX_SUPP_READS", 1, "Integer", + "Max number of supporting reads") self.addInfo("NUM_SUPP_SAMPLES", 1, "Integer", "Number of supporting samples") self.addFilter("LOWSUPPORT", diff --git a/svreader/pindel.py b/svreader/pindel.py index 790e4e682a5ad4dda784b7396cf61750373c0105..93545b63e666e5628417419740cd2e72a1c6b2c4 100644 --- a/svreader/pindel.py +++ b/svreader/pindel.py @@ -284,7 +284,7 @@ class PindelRecord(SVRecord): @property def sv_len(self): - return self.__svlen + return self.__sv_len def addbatch2Id(self, batch=None): if batch: