From 51f1cdfbf6e2a4da9d9bf66f2ac3f5dc7292bd5e Mon Sep 17 00:00:00 2001 From: Andrea Telatin <15690844+telatin@users.noreply.github.com> Date: Thu, 23 Dec 2021 14:45:18 +0000 Subject: [PATCH] 2.5.0 --- src/bamtocounts.nim | 15 ++++++--------- 1 file changed, 6 insertions(+), 9 deletions(-) diff --git a/src/bamtocounts.nim b/src/bamtocounts.nim index e97f3bb..7518325 100644 --- a/src/bamtocounts.nim +++ b/src/bamtocounts.nim @@ -94,8 +94,6 @@ proc alignments_count(table: var OrderedTable[string, stranded_counts], bam:Bam, if debug: stderr.writeLine("[alignments_count] Got chrom: ", chrom, " tot=", len(regions)) for aln in bam.query(chrom): - if debug: - stderr.writeLine("[alignments_count] Got aln ", aln.start) if not regions.contains(chrom) or regions[chrom].len == 0: continue @@ -120,15 +118,14 @@ proc alignments_count(table: var OrderedTable[string, stranded_counts], bam:Bam, # stderr.writeLine("[alignments_count] Warning: unknown feature: ", interval.label.l2) # table[interval.label.l2] = (fwd: 0, rev: 0) - try: - table[interval.label.l2].inc(aln.flag.reverse) - except Exception as e: - stderr.writeLine("[alignments_count] Error key table: ", e.msg) + #try: + table[interval.label.l2].inc(aln.flag.reverse) + #except Exception as e: + # stderr.writeLine("[alignments_count] Error key table: ", e.msg) - if debug: - stderr.writeLine("[alignments_count]\t\tdone ", interval.label.l2) + except Exception: - # ⛔️ ERROR TODO FIXME ALOHA [index not in ...] + # ⛔️ [index not in ...] if debug: stderr.writeLine("[alignments_count] intersections loop broken at chr=", chrom, " aln=", aln.qname, " last=", s, " c=", c)