add reverse complement comparison

[MikePone]

Bealign has a "-R" flag which also aligns the reverse complement of each query sequence, returning it if the alignment is superior. Can you add that to cawlign too? Thanks.

[spond]

Dear @MikePone,

This has been added via the -R option to v.0.1.11

No reverse complementation is considered

$cawlign -t codon -s HIV_BETWEEN_F test/cases/KX988404-rc.fa

>KX988404.1
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Reverse complementation considered, if taken it is not reported

$cawlign -t codon -s HIV_BETWEEN_F -R silent test/cases/KX988404-rc.fa

>KX988404.1
CCTCAAATCACTCTTTGGCAACGACCCCTTGTCGAAATAAGGATAGGGGGGCAATTAAAGGAAGCTCTATTAGATACAGG
AGCAGATGATACAGTATTAGAAGACATGAATTTGCCAGGAAGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTA
TCAAAGTAAGACAGTATGATCAGATACCCATAGAAATTTGTGGACACAAAGCTATAGGTACAGTATTGGTAGGACCTACA
CCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGCTTGGTTGCACTCTAAATTTTCCCATTAGTCCTATTGAAACTGT
ACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAG
TAGAAATTTGTACAGAAATGGAAAAGGAAGGAAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTT
GCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGGGAACTCAATAAAAGAACTCAAGACTTCTG
GGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTAACAGTCCTGGATGTGGGTGATGCAT
ACTTCTCAGTTCCTTTAGATAAAGACTTCAGGAAGTATACTGCATTCACCATACCTAGCACAAACAATGAGACGCCAGGG
ATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCAATGTAGCATGACAAAAATCTT
AGAGCCTTTTAGAAAACAAAATCCAGACATAGTCATCTATCAATACATGGATGATTTATATGTAGGATCTGATTTAGAAA
TAGGGCAGCATAGAATAAAAATAGAGGAACTGAGAGAACATCTGTTGAGATGGGGATTTACCACACCAGACAAAAAACAT
CAAAAAGAACCTCCATTCCTTTGGATGGGGTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAAAGCTGCCAGA
AAAAGACAGCTGGACTGTCAATGACATACAGAAATTAGTAGGGAAATTAAATTGGGCAAGTCAAATTTATTCAGGGATTA
AGATAAAGGAAGCTAATGGATGGGTTTATAGACATCATTATGACAGCAGACATCCAAAAGTAAGTTCAGAAGTACACATC
CCATTAGGAGAGGCTAGATTAGTCATAAAACAGCTAATTCATCTGTATCATTTTGATTGTTTTGCAGACTTAATTGTAGA
GGGG----------------------------------------------------------------------------
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Reverse complementation considered, if taken it is reported (|RC added to the corresponding sequence name)

$cawlign -t codon -s HIV_BETWEEN_F -R annotated test/cases/KX988404-rc.fa


>KX988404.1|RC
CCTCAAATCACTCTTTGGCAACGACCCCTTGTCGAAATAAGGATAGGGGGGCAATTAAAGGAAGCTCTATTAGATACAGG
AGCAGATGATACAGTATTAGAAGACATGAATTTGCCAGGAAGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTA
TCAAAGTAAGACAGTATGATCAGATACCCATAGAAATTTGTGGACACAAAGCTATAGGTACAGTATTGGTAGGACCTACA
CCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGCTTGGTTGCACTCTAAATTTTCCCATTAGTCCTATTGAAACTGT
ACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAG
TAGAAATTTGTACAGAAATGGAAAAGGAAGGAAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTT
GCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGGGAACTCAATAAAAGAACTCAAGACTTCTG
GGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTAACAGTCCTGGATGTGGGTGATGCAT
ACTTCTCAGTTCCTTTAGATAAAGACTTCAGGAAGTATACTGCATTCACCATACCTAGCACAAACAATGAGACGCCAGGG
ATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCAATGTAGCATGACAAAAATCTT
AGAGCCTTTTAGAAAACAAAATCCAGACATAGTCATCTATCAATACATGGATGATTTATATGTAGGATCTGATTTAGAAA
TAGGGCAGCATAGAATAAAAATAGAGGAACTGAGAGAACATCTGTTGAGATGGGGATTTACCACACCAGACAAAAAACAT
CAAAAAGAACCTCCATTCCTTTGGATGGGGTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAAAGCTGCCAGA
AAAAGACAGCTGGACTGTCAATGACATACAGAAATTAGTAGGGAAATTAAATTGGGCAAGTCAAATTTATTCAGGGATTA
AGATAAAGGAAGCTAATGGATGGGTTTATAGACATCATTATGACAGCAGACATCCAAAAGTAAGTTCAGAAGTACACATC
CCATTAGGAGAGGCTAGATTAGTCATAAAACAGCTAATTCATCTGTATCATTTTGATTGTTTTGCAGACTTAATTGTAGA
GGGG----------------------------------------------------------------------------
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Best,
Sergei