TranscriptClean v1.0.5

• Fixed bugs affecting transcripts that were mapped using the GMAP aligner, including a problem with mitochondrial genome coordinates and some noncanonical edge cases

TranscriptClean v1.0.4

• Fixed small syntax error in function check_CIGAR_validity

TranscriptClean v1.0.3

• Fixed a bug observed when running TranscriptClean on Oxford Nanopore data (probably a function of the higher error rate). In rare cases, corrected NCSJ exons ended up with an uncorrected deletion adjoining the intron, resulting in an invalid CIGAR string.
• Minor changes to generate_report.R

TranscriptClean v1.0.2

• Bug fix: Certain noncanonical splice junction correction events were being counted improperly in the Transcript Error log file.

TranscriptClean v1.0.1

• Bug fix: Noncanonical splice junctions bordering a micro-exon (exon of length smaller than the correction distance) are now skipped. Previously, attempts to correct these led to empty exons and inconsistencies in the SAM output. This patch includes an update to generate_report.R to track such cases.
• Bug fix: MD/NM fields of noncanonical splice junctions were being updated incorrectly after correction
• Added option to skip output for unmapped/multimapping transcripts

TranscriptClean v1.0

TranscriptClean: A variant-aware tool for correcting indels, mismatches, and splice junctions in long-read transcripts