Puffaligner doesn't map read pairs to different references about pufferfish

[fataltes]

Hi @apcamargo ,

Thank you for your post. However, I am not sure if I understand the request clearly.
Would you mind explaining a little bit more?

[apcamargo]

Sure, @fataltes!

Here's Puffaligner's (using --bestStrata) samtools flagstat output:

214688504 + 0 in total (QC-passed reads + QC-failed reads)
50488220 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
125913389 + 0 mapped (58.65% : N/A)
164200284 + 0 paired in sequencing
82100142 + 0 read1
82100142 + 0 read2
83360444 + 0 properly paired (50.77% : N/A)
83360444 + 0 with itself and mate mapped
6101721 + 0 singletons (3.72% : N/A)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)

Here's Bowtie2's (using -k 15):

241492571 + 0 in total (QC-passed reads + QC-failed reads)
77292287 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
159016623 + 0 mapped (65.85% : N/A)
164200284 + 0 paired in sequencing
82100142 + 0 read1
82100142 + 0 read2
74243714 + 0 properly paired (45.22% : N/A)
77436030 + 0 with itself and mate mapped
4288306 + 0 singletons (2.61% : N/A)
2489036 + 0 with mate mapped to a different chr
2027014 + 0 with mate mapped to a different chr (mapQ>=5)

Puffaligner's with mate mapped to a different chr is 0, meaning that there are no pairs with reads that mapped to different references.

Essentially, I'm interest in alignments where the 7th field is not =, for example:

HISEQ13:355:CBN0FANXX:7:1101:17319:1971	97	k147_2000503	17	38	150M	k147_584177	66	0	CGGCGGACTAAGGCTCTATAATTTCAATTTTTCACCAGACTAAGTAATCCATGAAGAAACTCATTGCAGCACTGGCTTCCAGTGTTCTGGTGATGTCCGCCGCCGTCGCCCAGACGCTGCCGGCGCCGACCATCGCCGCCAAATCGTGGC	=ABBGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGFGG>GEGGGGGGDGFGGCGDGDGGGGG<DGGGGGGGBGGGGGGGGGGGGGGGGGGGGGGGGGG@	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:150	YT:Z:UP