[med-svn] [Git][med-team/lumpy-sv][upstream] New upstream version 0.3.1+dfsg

[Nilesh Patra]

Nilesh Patra pushed to branch upstream at Debian Med / lumpy-sv


Commits:
8c3bee8a by Nilesh Patra at 2020-09-18T19:02:33+00:00
New upstream version 0.3.1+dfsg
- - - - -


5 changed files:

- − data/pe.pos_sorted.bam
- − data/sr.pos_sorted.bam
- src/filter/filter.c
- src/lumpy/SV_Pair.cpp
- src/lumpy/SV_Pair.h


Changes:

=====================================
data/pe.pos_sorted.bam deleted
=====================================
Binary files a/data/pe.pos_sorted.bam and /dev/null differ


=====================================
data/sr.pos_sorted.bam deleted
=====================================
Binary files a/data/sr.pos_sorted.bam and /dev/null differ


=====================================
src/filter/filter.c
=====================================
@@ -375,4 +375,5 @@ int main(int argc, char **argv)
     if(ret < -1) {
         errx(1, "lumpy_filter: error reading bam: %s\n", bam_file_name);
     }
+    return 0;
 }


=====================================
src/lumpy/SV_Pair.cpp
=====================================
@@ -52,6 +52,8 @@ SV_Pair(const BamAlignment &bam_a,
     else
         min_mapping_quality = bam_b.MapQuality;
 
+    read_id = bam_a.Name;
+
     struct interval tmp_a, tmp_b;
     tmp_a.start = bam_a.Position;
     tmp_a.end = bam_a.GetEndPosition(false, false) - 1;
@@ -341,6 +343,7 @@ void
 SV_Pair::
 print_evidence()
 {
+    cout << read_id << "\t";
     print_bedpe(0);
 }
 //}}}


=====================================
src/lumpy/SV_Pair.h
=====================================
@@ -61,6 +61,7 @@ class SV_Pair: public SV_Evidence
 		struct interval read_r;
 		bool read_l_is_split, read_r_is_split;
 		SV_PairReader *reader;
+		std::string read_id;
 
 
 		SV_Pair(const BamAlignment &bam_a,



View it on GitLab: https://salsa.debian.org/med-team/lumpy-sv/-/commit/8c3bee8abe76155dbbed1ededd0cc945bdaa44bf

-- 
View it on GitLab: https://salsa.debian.org/med-team/lumpy-sv/-/commit/8c3bee8abe76155dbbed1ededd0cc945bdaa44bf
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