I have 50bp PE RNA-seq, and 4 of my ~200 samples end in error after running Cufflinks (v.2.2.1). Here is my pipeline prior to running Cufflinks:

 1. STAR 2-pass (GRCm38)
 2. Added read group information with Picard
 3. Marked (but did not remove) duplicates with Picard
 4. SplitNCigarReads with GATK
 5. Realigned around indels with GATK
 6. Performed base recalibration with GATK

I've been looking at one particular sample with the error and have narrowed it down to a couple reads (see below):

    PC168224:108:C90EBANXX:5:1303:19181:37569	179	6	85461128	60	43M345H	=	85461508	338	CCCTCAGATCATCATCCGAGCTTTCCGCACAGCCACCCAATTG	C46FE@3CDECDBDD>/C6FE?FD@:EA?5CDBB>33<::;<B	MC:Z:380H4I4S	BD:Z:KOOOOMMLMMLMMLLMMLNNJFLLMNNNMOPPQSSQVSSKMMM	PG:Z:MarkDuplicates	RG:Z:HL126	NH:i:1	BI:Z:JNOOSQOQNOOMNONJKKOMIBKNJNMOOPQLOPQNUSSNNMM	HI:i:1	nM:i:1	MQ:i:70	AS:i:97	XS:A:+
    
    PC168224:108:C90EBANXX:5:1303:19181:37569	179	6	85461508	70	380H4I4S	=	85461128	-338	GGTGGCTG	AC?9=5EB	MC:Z:43M345H	OC:Z:380H4M4S	BD:Z:ONNOPPMM	PG:Z:MarkDuplicates	RG:Z:HL126	NH:i:1	BI:Z:NORNPPMM	HI:i:1	nM:i:1	MQ:i:60	AS:i:97	XS:A:+

Now if I put those to reads into a separate BAM file (with original header from the sample) and running cufflinks I get the following:

    cufflinks -o test. test.bam
    You are using Cufflinks v2.2.1, which is the most recent release.
    [14:04:40] Inspecting reads and determining fragment length distribution.
    Segmentation fault

I've look at those two reads but am not sure why about them causes a segmentation fault. Any ideas?
this is a bad cigar string:

    380H4I4S

there is not "Match/M" in this cigar string: 380 hard clip, 4 insertions, 4 soft clip. Just 3 things that are not associated to a reference; 