bowtie2 with local alignment soft-clips nt difference at end of genome

[ArtPoon]

See #7
Raw data suggests the genome sequence is polymorphic or unreliable at first position of genome (either A or T).
Either we use bowtie2 with global alignment (will probably reduce mapping efficiency) or make some special exception for soft-clips at 5' or 3' end of genome when calculating the consensus.

[ArtPoon]

Global alignment isn't that bad:

Elzar:data artpoon$ bowtie2 -x NC_045512 -S SRR11241254.global.sam -U SRR11241254.fastq
Warning: skipping read 'SRR11241254.131951 131951 length=1' because length (1) <= # seed mismatches (0)
Warning: skipping read 'SRR11241254.131951 131951 length=1' because it was < 2 characters long
Warning: skipping read 'SRR11241254.131952 131952 length=1' because length (1) <= # seed mismatches (0)
Warning: skipping read 'SRR11241254.131952 131952 length=1' because it was < 2 characters long
131952 reads; of these:
  131952 (100.00%) were unpaired; of these:
    1970 (1.49%) aligned 0 times
    129978 (98.50%) aligned exactly 1 time
    4 (0.00%) aligned >1 times
98.51% overall alignment rate

[ArtPoon]

Elzar:data artpoon$ grep TTTAAAGGTTTATA SRR11241254.global.sam 
SRR11241254.9	0	NC_045512.2	1	40	40M	*	0	0	TTTAAAGGTTTATACCTTCCCAGGTAACAAACCAACCAAC	GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCCCCC	AS:i:-5	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:0A39	YT:Z:UU
SRR11241254.10	0	NC_045512.2	1	40	40M	*	0	0	TTTAAAGGTTTATACCTTCCCAGGTAACAAACCAACCAAC	GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCCCCC	AS:i:-5	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:0A39	YT:Z:UU
SRR11241254.11	0	NC_045512.2	1	40	40M	*	0	0	TTTAAAGGTTTATACCTTCCCAGGTAACAAACCAACCAAC	GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCCCCC	AS:i:-5	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:0A39	YT:Z:UU
SRR11241254.12	0	NC_045512.2	1	42	70M	*	0	0	TTTAAAGGTTTATACCTTCCCAGGTAACAAACCAACCAACTTTCGATCTCTTGTAGATCTGTTCTCTAAA	FEEDGFGFGGGGGGGGGGFDFGGGGGGGGFBGF@GGGGF@CDCEGFEFGGGGGGGGFGGGGGFFFCCCCC	AS:i:-5	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:0A69	YT:Z:UU
SRR11241254.13	0	NC_045512.2	1	42	70M	*	0	0	TTTAAAGGTTTATACCTTCCCAGGTAACAAACCAACCAACTTTCGATCTCTTGTAGATCTGTTCTCTAAA	GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCCCCC	AS:i:-5	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:0A69	YT:Z:UU
SRR11241254.14	0	NC_045512.2	1	42	70M	*	0	0	TTTAAAGGTTTATACCTTCCCAGGTAACAAACCAACCAACTTTCGATCTCTTGTAGATCTGTTCTCTAAA	GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGFCGGGGGGGGGFAGGGGGGGGCCCCC	AS:i:-5	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:0A69	YT:Z:UU
SRR11241254.15	0	NC_045512.2	1	42	70M	*	0	0	TTTAAAGGTTTATACCTTCCCAGGTAACAAACCAACCAACTTTCGATCTCTTGTAGATCTGTTCTCTAAA	GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCCCCC	AS:i:-5	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:0A69	YT:Z:UU
SRR11241254.16	0	NC_045512.2	1	42	70M	*	0	0	TTTAAAGGTTTATACCTTCCCAGGTAACAAACCAACCAACTTTCGATCTCTTGTAGATCTGTTCTCTAAA	GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCCCCC	AS:i:-5	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:0A69	YT:Z:UU
Elzar:data artpoon$ grep ATTAAAGGTTTATA SRR11241254.global.sam 
SRR11241254.17	0	NC_045512.2	1	40	80M	*	0	0	ATTAAAGGTTTATACCTTCCCAGGTAACAAACCAACCAACTTTCGATCTCTTGTAGATCTGTTCTCTAAACGAACATGAA	GGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGFFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGFG	AS:i:-1XN:i:0	XM:i:2	XO:i:0	XG:i:0	NM:i:2	MD:Z:75T1T2	YT:Z:UU
SRR11241254.22	0	NC_045512.2	1	42	162M	*	0	0	ATTAAAGGTTTATACCTTCCCAGGTAACAAACCAACCAACTTTCGATCTCTTGTAGATCTGTTCTCTAAACGAACTTTAAAATCTGTGTGGCTGTCACTCGGCTGCATGCTTAGTGCACTCACGCAGTATAATTAATAACTAATTACTGTCGTTGACAGGAC	GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGFGGGGGGGGGGGGGGGGGGGGGGGGGF	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:162	YT:Z:UU
SRR11241254.23	0	NC_045512.2	1	42	162M	*	0	0	ATTAAAGGTTTATACCTTCCCAGGTAACAAACCAACCAACTTTCGATCTCTTGTAGATCTGTTCTCTAAACGAACTTTAAAATCTGTGTGGCTGTCACTCGGCTGCATGCTTAGTGCACTCACGCAGTATAATTAATAACTAATTACTGTCGTTGACAGGAC	GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGF	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:162	YT:Z:UU
SRR11241254.24	0	NC_045512.2	1	42	162M	*	0	0	ATTAAAGGTTTATACCTTCCCAGGTAACAAACCAACCAACTTTCGATCTCTTGTAGATCTGTTCTCTAAACGAACTTTAAAATCTGTGTGGCTGTCACTCGGCTGCATGCTTAGTGCACTCACGCAGTATAATTAATAACTAATTACTGTCGTTGACAGGAC	GGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGFCFGGCFGGGGGGGGGCFFGFFGGGGGGGGGGGGGGGGGFGGGGGGFGGGGGGGGGGGGGGGGGGFFCCFGGFGGGGGGGGGGG9FGFCGC<F?FGGGGGGGGGGGGGGCBFFGF;EDGGGGGGGGGGGGC	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:162	YT:Z:UU

Note this is very low coverage - best approach would probably be to report this first base as a mixture W.