From ecdbdde9a3882970d1cbc68063c52ed3f46b9f79 Mon Sep 17 00:00:00 2001
From: Thomas Faraut <Thomas.Faraut@inra.fr>
Date: Thu, 28 Nov 2019 11:56:16 +0100
Subject: [PATCH] supp_reads becomes max support reads
---
svreader/Annotate.py | 16 ++++++++++++----
svreader/pindel.py | 2 +-
2 files changed, 13 insertions(+), 5 deletions(-)
diff --git a/svreader/Annotate.py b/svreader/Annotate.py
index 66d6813..bb9b9cd 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")
@@ -165,8 +173,8 @@ 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 30d3357..29c3593 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:
--
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