Adds optional arguments to report k-best alignments with a NH tag

[milkschen]

Design

This PR describes two new input, optional arguments for bowtie2-align:

1. --kbest. This argument is expected to be used along with the -k alignment mode to report up to k alignments, with a constraint that all reported alignments share the same alignment score with the primary alignment.
2. --show-nh-tag. When this is set, shows the NH:i tag to report the number of alignments of a query. This is particularly useful in the -k/-a modes.

The changes should not change the default bowtie2-align behaviors, at least in my test runs.

Test case

FASTQ (two tRNA sequences):

>TRL-CAA6-1 Homo sapiens (human) tRNA-Leu (anticodon CAA) 6-1 (TRL-CAA6-1) URS00006DCB39_9606
GTCAGGATGGCCGAGCAGTCTTAAGGCGCTGCGTTCAAATCGCACCCTCCGCTGGAGGCGTGGGTTCGAATCCCACTTTTGACA
>TRS-AGA1-1 Homo sapiens (human) tRNA-Ser (anticodon AGA) 1-1 (TRS-AGA1-1) URS00006C14B2_9606
GTAGTCGTGGCCGAGTGGTTAAGGCGATGGACTAGAAATCCATTGGGGTTTCCCCGCGCAGGTTCGAATCCTGCCGACTACG

Resulting SAM mapped to chm13v2 with -k 3 (changes in this PR would not affect this run):

TRL-CAA6-1	16	chr1	160874498	1	84M	*	0	0	TGTCAAAAGTGGGATTCGAACCCACGCCTCCAGCGGAGGGTGCGATTTGAACGCAGCGCCTTAAGACTGCTCGGCCATCCTGAC	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:84	YT:Z:UU
TRL-CAA6-1	272	chr1	160956287	255	84M	*	0	0	TGTCAAAAGTGGGATTCGAACCCACGCCTCCAGCGGAGGGTGCGATTTGAACGCAGCGCCTTAAGACTGCTCGGCCATCCTGAC	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:84	YT:Z:UU
TRL-CAA6-1	272	chr16	63096452	255	62M1I21M	*	0	0	TGTCAAAAGTGGGATTCGAACCCACGCCTCCAGCGGAGGGTGCGATTTGAACGCAGCGCCTTAAGACTGCTCGGCCATCCTGAC	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:-50	XS:i:0	XN:i:0	XM:i:7	XO:i:1	XG:i:1	NM:i:8	MD:Z:5G27G4A0C5C0C19C16	YT:Z:UU
TRS-AGA1-1	16	chr6	27411350	30	82M	*	0	0	CGTAGTCGGCAGGATTCGAACCTGCGCGGGGAAACCCCAATGGATTTCTAGTCCATCGCCTTAACCACTCGGCCACGACTAC	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:-6	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:82	YT:Z:UU
TRS-AGA1-1	272	chr8	96394913	255	82M	*	0	0	CGTAGTCGGCAGGATTCGAACCTGCGCGGGGAAACCCCAATGGATTTCTAGTCCATCGCCTTAACCACTCGGCCACGACTAC	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:-6	XS:i:-6	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:32G49	YT:Z:UU
TRS-AGA1-1	272	chr17	8132840	255	82M	*	0	0	CGTAGTCGGCAGGATTCGAACCTGCGCGGGGAAACCCCAATGGATTTCTAGTCCATCGCCTTAACCACTCGGCCACGACTAC	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:-6	XS:i:-6	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:32G49	YT:Z:UU

Resulting SAM mapped to chm13v2 with -k 3 --kbest:

TRL-CAA6-1	16	chr1	160874498	1	84M	*	0	0	TGTCAAAAGTGGGATTCGAACCCACGCCTCCAGCGGAGGGTGCGATTTGAACGCAGCGCCTTAAGACTGCTCGGCCATCCTGAC	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:84	YT:Z:UU
TRL-CAA6-1	272	chr1	160956287	255	84M	*	0	0	TGTCAAAAGTGGGATTCGAACCCACGCCTCCAGCGGAGGGTGCGATTTGAACGCAGCGCCTTAAGACTGCTCGGCCATCCTGAC	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:84	YT:Z:UU
TRS-AGA1-1	16	chr6	27411350	30	82M	*	0	0	CGTAGTCGGCAGGATTCGAACCTGCGCGGGGAAACCCCAATGGATTTCTAGTCCATCGCCTTAACCACTCGGCCACGACTAC	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:-6	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:82	YT:Z:UU

Resulting SAM mapped to chm13v2 with -k 3 --kbest --show-nh-tag:

TRL-CAA6-1	16	chr1	160874498	1	84M	*	0	0	TGTCAAAAGTGGGATTCGAACCCACGCCTCCAGCGGAGGGTGCGATTTGAACGCAGCGCCTTAAGACTGCTCGGCCATCCTGAC	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NH:i:2	NM:i:0	MD:Z:84	YT:Z:UU
TRL-CAA6-1	272	chr1	160956287	255	84M	*	0	0	TGTCAAAAGTGGGATTCGAACCCACGCCTCCAGCGGAGGGTGCGATTTGAACGCAGCGCCTTAAGACTGCTCGGCCATCCTGAC	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NH:i:2	NM:i:0	MD:Z:84	YT:Z:UU
TRS-AGA1-1	16	chr6	27411350	30	82M	*	0	0	CGTAGTCGGCAGGATTCGAACCTGCGCGGGGAAACCCCAATGGATTTCTAGTCCATCGCCTTAACCACTCGGCCACGACTAC	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:-6	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NH:i:1	NM:i:0	MD:Z:82	YT:Z:UU