From bb57c2352f82ce9fac29a2a1a471f61f2ae7d5cd Mon Sep 17 00:00:00 2001 From: Xian Chang Date: Mon, 24 Aug 2020 18:55:46 -0400 Subject: [PATCH 1/2] Fixed paired end mapq calc --- pairedCapper.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pairedCapper.py b/pairedCapper.py index ebac10c..e1fc1e2 100644 --- a/pairedCapper.py +++ b/pairedCapper.py @@ -75,7 +75,7 @@ def __init__(self, line, correct): equivalent_or_better_clusters, equivalent_clusters, equivalent_clusters_kept, cluster_score, alignment_score)) - self.alignment_scores = sorted(alignment_scores) + self.alignment_scores = sorted(alignment_scores, key=lambda x : x.alignment_score) #print("Alignment scores", self.alignment_scores) From 34f889af1b76d6e789fb03cb3e24437c00398c80 Mon Sep 17 00:00:00 2001 From: Xian Chang Date: Mon, 24 Aug 2020 19:06:16 -0400 Subject: [PATCH 2/2] Don't sort alignment scores at all since they're already sorted --- pairedCapper.py | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/pairedCapper.py b/pairedCapper.py index e1fc1e2..3fa99dc 100644 --- a/pairedCapper.py +++ b/pairedCapper.py @@ -67,15 +67,14 @@ def __init__(self, line, correct): 'equivalent_clusters', 'equivalent_clusters_kept', 'cluster_score', 'alignment_score']) - alignment_scores = [] + self.alignment_scores = [] #print(all_aln_scores) for score1, score2, log_likelihood, multiplicity, equivalent_or_better_clusters, equivalent_clusters, \ equivalent_clusters_kept, cluster_score, alignment_score in all_aln_scores: - alignment_scores.append(AlignmentScore(score1, score2, log_likelihood, multiplicity, + self.alignment_scores.append(AlignmentScore(score1, score2, log_likelihood, multiplicity, equivalent_or_better_clusters, equivalent_clusters, equivalent_clusters_kept, cluster_score, alignment_score)) - self.alignment_scores = sorted(alignment_scores, key=lambda x : x.alignment_score) #print("Alignment scores", self.alignment_scores)