From 96ddb5c0bc43cd1a2c5e6effcceeaf44337eaf14 Mon Sep 17 00:00:00 2001
From: m-jahn <jahn@mpusp.mpg.de>
Date: Thu, 6 Nov 2025 13:35:16 +0100
Subject: [PATCH 1/2] fix: enable usage of point features as long as they are
 within transcript margin

---
 stringtie.cpp | 20 +++++++++++++++-----
 1 file changed, 15 insertions(+), 5 deletions(-)

diff --git a/stringtie.cpp b/stringtie.cpp
index d30b20f..1ee3808 100644
--- a/stringtie.cpp
+++ b/stringtie.cpp
@@ -146,6 +146,7 @@ uint bundledist=50;  // reads at what distance should be considered part of sepa
 uint runoffdist=200;
 float mcov=1; // fraction of bundle allowed to be covered by multi-hit reads paper uses 1
 int allowed_nodes=1000;
+int ptf_margin = 5; // define the tolerance for supplied PTFs to be used for transcript boundary refinement
 //bool adaptive=true; // adaptive read coverage -> depends on the overall gene coverage
 //GPVec<CDSparam> cds;
 
@@ -609,11 +610,20 @@ if (ballgown)
 		 if (bundle->readlist.Count()>0) { // process reads in previous bundle
 			// (readthr, junctionthr, mintranscriptlen are globals)
 			if (refptfs) { //point-features defined for this reference
-				while (ptf_idx<refptfs->Count() && (int)(refptfs->Get(ptf_idx)->coord)<currentstart)
-					ptf_idx++;
-				//TODO: what if a PtFeature is nearby, just outside the bundle?
-				while (ptf_idx<refptfs->Count() && (int)(refptfs->Get(ptf_idx)->coord)<=currentend) {
-					bundle->ptfs.Add(refptfs->Get(ptf_idx)); //keep this PtFeature
+				while (ptf_idx < refptfs->Count()) {
+					int coord = (int)(refptfs->Get(ptf_idx)->coord);
+					if (coord < currentstart - ptf_margin) {
+						if (verbose) {
+							GMessage("## Skipping PtFeature at %d not in bundle %d-%d\n", coord, currentstart, currentend);
+						}
+					} else if (coord <= currentend + ptf_margin) {
+						bundle->ptfs.Add(refptfs->Get(ptf_idx)); //keep this PtFeature
+						if (verbose) {
+							GMessage("## Adding PtFeature at %d to bundle %d-%d\n", coord, currentstart, currentend);
+						}
+					} else {
+						break; // exit the loop if coord is not between currentstart and end (+ margins)
+					}
 					ptf_idx++;
 				}
 			}

From 24662b0a2e59f6662fb8ce62a2e9362fd3d80205 Mon Sep 17 00:00:00 2001
From: m-jahn <jahn@mpusp.mpg.de>
Date: Thu, 6 Nov 2025 13:35:55 +0100
Subject: [PATCH 2/2] fix: added gitignore for typical temp files

---
 .gitignore | 5 +++++
 1 file changed, 5 insertions(+)
 create mode 100644 .gitignore

diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..1c88eaf
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,5 @@
+tests/*
+**/*.o
+htslib/*
+gclib/*
+stringtie
\ No newline at end of file