[med-svn] [Git][med-team/tiddit][master] 3 commits: New upstream version 3.6.0+dfsg
Nilesh Patra (@nilesh)
gitlab at salsa.debian.org
Thu May 11 18:25:12 BST 2023
Nilesh Patra pushed to branch master at Debian Med / tiddit
Commits:
2a63d8ce by Nilesh Patra at 2023-05-11T22:51:38+05:30
New upstream version 3.6.0+dfsg
- - - - -
cc85cd8b by Nilesh Patra at 2023-05-11T22:51:38+05:30
Update upstream source from tag 'upstream/3.6.0+dfsg'
Update to upstream version '3.6.0+dfsg'
with Debian dir 216740c18e9ccf9c6b613d1d124ace83fa577c18
- - - - -
f5d6b073 by Nilesh Patra at 2023-05-11T22:55:11+05:30
Interim d/ch
- - - - -
5 changed files:
- debian/changelog
- setup.py
- tiddit/__main__.py
- tiddit/tiddit_cluster.pyx
- tiddit/tiddit_signal.pyx
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,10 @@
+tiddit (3.6.0+dfsg-1) UNRELEASED; urgency=medium
+
+ * Team Upload.
+ * New upstream version 3.6.0+dfsg
+
+ -- Nilesh Patra <nilesh at debian.org> Thu, 11 May 2023 22:51:54 +0530
+
tiddit (3.5.2+dfsg-1) unstable; urgency=medium
* Team upload.
=====================================
setup.py
=====================================
@@ -20,7 +20,8 @@ else:
setup(
name = 'tiddit',
- version = '3.5.2',
+ version = '3.6.0',
+
url = "https://github.com/SciLifeLab/TIDDIT",
author = "Jesper Eisfeldt",
=====================================
tiddit/__main__.py
=====================================
@@ -17,7 +17,7 @@ import tiddit.tiddit_variant as tiddit_variant
import tiddit.tiddit_contig_analysis as tiddit_contig_analysis
def main():
- version="3.5.2"
+ version="3.6.0"
parser = argparse.ArgumentParser("""tiddit-{}""".format(version),add_help=False)
parser.add_argument("--sv" , help="call structural variation", required=False, action="store_true")
parser.add_argument("--cov" , help="generate a coverage bed file", required=False, action="store_true")
@@ -155,7 +155,7 @@ def main():
args.e=int(library["avg_insert_size"]/2.0)
t=time.time()
- sv_clusters=tiddit_cluster.main(prefix,contigs,contig_length,samples,library["mp"],args.e,args.l,max_ins_len,args.min_contig,args.skip_assembly)
+ sv_clusters=tiddit_cluster.main(prefix,contigs,contig_length,samples,library["mp"],args.e,args.l,max_ins_len,args.min_contig,args.skip_assembly,args.r)
print("generated clusters in")
print(time.time()-t)
=====================================
tiddit/tiddit_cluster.pyx
=====================================
@@ -37,7 +37,7 @@ def find_discordant_pos(fragment,is_mp):
return(posA,posB)
-def main(prefix,chromosomes,contig_length,samples,is_mp,epsilon,m,max_ins_len,min_contig,skip_assembly):
+def main(prefix,chromosomes,contig_length,samples,is_mp,epsilon,m,max_ins_len,min_contig,skip_assembly,min_reads):
discordants={}
contigs=set([])
@@ -265,13 +265,18 @@ def main(prefix,chromosomes,contig_length,samples,is_mp,epsilon,m,max_ins_len,mi
candidates[chrA][chrB][candidate]["N_splits"]=len(candidates[chrA][chrB][candidate]["splits"])
candidates[chrA][chrB][candidate]["N_contigs"]=len(candidates[chrA][chrB][candidate]["contigs"])
- if candidates[chrA][chrB][candidate]["N_contigs"]:
+
+ if candidates[chrA][chrB][candidate]["N_splits"] and min_reads <= candidates[chrA][chrB][candidate]["N_splits"]:
+ candidates[chrA][chrB][candidate]["posA"]=mode(candidates[chrA][chrB][candidate]["positions_A"]["splits"])
+ candidates[chrA][chrB][candidate]["posB"]=mode(candidates[chrA][chrB][candidate]["positions_B"]["splits"])
+
+ elif candidates[chrA][chrB][candidate]["N_contigs"]:
candidates[chrA][chrB][candidate]["posA"]=mode(candidates[chrA][chrB][candidate]["positions_A"]["contigs"])
candidates[chrA][chrB][candidate]["posB"]=mode(candidates[chrA][chrB][candidate]["positions_B"]["contigs"])
+
elif candidates[chrA][chrB][candidate]["N_splits"]:
candidates[chrA][chrB][candidate]["posA"]=mode(candidates[chrA][chrB][candidate]["positions_A"]["splits"])
- candidates[chrA][chrB][candidate]["posB"]=mode(candidates[chrA][chrB][candidate]["positions_B"]["splits"])
-
+ candidates[chrA][chrB][candidate]["posB"]=mode(candidates[chrA][chrB][candidate]["positions_B"]["splits"])
else:
reverse_A = candidates[chrA][chrB][candidate]["positions_A"]["orientation_discordants"].count("True")
@@ -328,10 +333,6 @@ def main(prefix,chromosomes,contig_length,samples,is_mp,epsilon,m,max_ins_len,mi
candidates[chrA][chrB][candidate]["posB"]=mode(candidates[chrA][chrB][candidate]["positions_B"]["discordants"])
-
- candidates[chrA][chrB][candidate]["posA"]
- candidates[chrA][chrB][candidate]["posB"]
-
candidates[chrA][chrB][candidate]["startB"]=min(candidates[chrA][chrB][candidate]["positions_B"]["start"])
candidates[chrA][chrB][candidate]["endB"]=max(candidates[chrA][chrB][candidate]["positions_B"]["end"])
=====================================
tiddit/tiddit_signal.pyx
=====================================
@@ -65,7 +65,13 @@ def SA_analysis(read,min_q,tag,reference_name):
cdef long read_query_alignment_end=read.query_alignment_end
- if (read.query_alignment_start ) < (read.query_length - read_query_alignment_end):
+ clip_before=False
+
+ supplementry_alignment=find_SA_query_range(SA_data)
+ if supplementry_alignment.query_alignment_start < read.query_alignment_start:
+ clip_before=True
+
+ if not clip_before:
if read.is_reverse:
@@ -78,7 +84,6 @@ def SA_analysis(read,min_q,tag,reference_name):
else:
split_pos=read.reference_start+1
- supplementry_alignment=find_SA_query_range(SA_data)
SA_chr=SA_data[0]
startA=read.reference_start+1
@@ -87,8 +92,7 @@ def SA_analysis(read,min_q,tag,reference_name):
startB=supplementry_alignment.reference_start
endB=supplementry_alignment.reference_end
-
- if (supplementry_alignment.query_alignment_start ) < (supplementry_alignment.query_length - read_query_alignment_end):
+ if clip_before:
if SA_data[2] == "-":
SA_split_pos=supplementry_alignment.reference_start
@@ -192,6 +196,9 @@ def worker(str chromosome, str bam_file_name,str ref,str prefix,int min_q,int ma
if read.mate_is_unmapped:
continue
+ if not read.is_paired:
+ continue
+
if ( abs(read.isize) > max_ins or mate_chromosome != read_chromosome ):
read_query_name=read.query_name
View it on GitLab: https://salsa.debian.org/med-team/tiddit/-/compare/ac014976a625b86c2624215551e86875d5ae0eda...f5d6b0733ffc6bee4420cba1817b78664671dabe
--
View it on GitLab: https://salsa.debian.org/med-team/tiddit/-/compare/ac014976a625b86c2624215551e86875d5ae0eda...f5d6b0733ffc6bee4420cba1817b78664671dabe
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