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First attempt for obiconsensus... The graph traversing algorithm is too simple

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Former-commit-id: 0456e6c7fd55d6d0fcf9856c40386b976b912cba
This commit is contained in:
Eric Coissac
2023-03-27 19:51:10 +07:00
parent d5e84ec676
commit a33e471b39
17 changed files with 868 additions and 23 deletions
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6
pkg/obitools/obiconvert/sequence_reader.go
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@ -99,9 +99,13 @@ func CLIReadBioSequences(filenames ...string) (obiiter.IBioSequence, error) {
opts = append(opts, obiformats.OptionsBatchSize(obioptions.CLIBatchSize()))
opts = append(opts, obiformats.OptionsQualityShift(CLIInputQualityShift()))
opts = append(opts, obiformats.OptionsFullFileBatch(FullFileBatch()))
if len(filenames) == 0 {
log.Printf("Reading sequences from stdin in %s\n", CLIInputFormat())
opts = append(opts, obiformats.OptionsSource("stdin"))
switch CLIInputFormat() {
case "ecopcr":
iterator = obiformats.ReadEcoPCR(os.Stdin, opts...)
@ -121,7 +125,7 @@ func CLIReadBioSequences(filenames ...string) (obiiter.IBioSequence, error) {
switch CLIInputFormat() {
case "ecopcr":
reader = obiformats.ReadEcoPCRBatchFromFile
reader = obiformats.ReadEcoPCRFromFile
case "embl":
reader = obiformats.ReadEMBLFromFile
case "genbank":