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Updates
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@cmdcolin
cmdcolin committed Sep 7, 2023
1 parent a01fac6 commit c800782
Showing 1 changed file with 31 additions and 94 deletions.
125 changes: 31 additions & 94 deletions products/jbrowse-cli/src/commands/add-track.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -384,22 +384,17 @@ export default class AddTrack extends JBrowseCommand {
bed1: bed1!,
bed2: bed2!,
}
}
if (/\.bam$/i.test(location)) {
} else if (/\.bam$/i.test(location)) {
return {
file: location,
index: index || `${location}.bai`,
}
}

if (/\.cram$/i.test(location)) {
} else if (/\.cram$/i.test(location)) {
return {
file: location,
index: index || `${location}.crai`,
}
}

if (
} else if (
/\.gff3?\.b?gz$/i.test(location) ||
/\.vcf\.b?gz$/i.test(location) ||
/\.bed\.b?gz$/i.test(location)
Expand All @@ -408,24 +403,18 @@ export default class AddTrack extends JBrowseCommand {
file: location,
index: index || `${location}.tbi`,
}
}

if (/\.(fa|fasta|fas|fna|mfa)$/i.test(location)) {
} else if (/\.(fa|fasta|fas|fna|mfa)$/i.test(location)) {
return {
file: location,
index: index || `${location}.fai`,
}
}

if (/\.(fa|fasta|fas|fna|mfa)\.b?gz$/i.test(location)) {
} else if (/\.(fa|fasta|fas|fna|mfa)\.b?gz$/i.test(location)) {
return {
file: location,
index: `${location}.fai`,
index2: `${location}.gzi`,
}
}

if (
} else if (
/\.2bit$/i.test(location) ||
/\/trackData.jsonz?$/i.test(location) ||
/\/sparql$/i.test(location) ||
Expand Down Expand Up @@ -472,24 +461,18 @@ export default class AddTrack extends JBrowseCommand {
indexType: index?.toUpperCase().endsWith('CSI') ? 'CSI' : 'BAI',
},
}
}

if (/\.cram$/i.test(location)) {
} else if (/\.cram$/i.test(location)) {
return {
type: 'CramAdapter',
cramLocation: makeLocation(location),
craiLocation: makeLocation(`${location}.crai`),
}
}

if (/\.gff3?$/i.test(location)) {
} else if (/\.gff3?$/i.test(location)) {
return {
type: 'Gff3Adapter',
gffLocation: makeLocation(location),
}
}

if (/\.gff3?\.b?gz$/i.test(location)) {
} else if (/\.gff3?\.b?gz$/i.test(location)) {
return {
type: 'Gff3TabixAdapter',
gffGzLocation: makeLocation(location),
Expand All @@ -498,23 +481,17 @@ export default class AddTrack extends JBrowseCommand {
indexType: index?.toUpperCase().endsWith('CSI') ? 'CSI' : 'TBI',
},
}
}

if (/\.gtf?$/i.test(location)) {
} else if (/\.gtf?$/i.test(location)) {
return {
type: 'GtfAdapter',
gtfLocation: makeLocation(location),
}
}

if (/\.vcf$/i.test(location)) {
} else if (/\.vcf$/i.test(location)) {
return {
type: 'VcfAdapter',
vcfLocation: makeLocation(location),
}
}

if (/\.vcf\.b?gz$/i.test(location)) {
} else if (/\.vcf\.b?gz$/i.test(location)) {
return {
type: 'VcfTabixAdapter',
vcfGzLocation: makeLocation(location),
Expand All @@ -523,22 +500,16 @@ export default class AddTrack extends JBrowseCommand {
indexType: index?.toUpperCase().endsWith('CSI') ? 'CSI' : 'TBI',
},
}
}

if (/\.vcf\.idx$/i.test(location)) {
} else if (/\.vcf\.idx$/i.test(location)) {
return {
type: 'UNSUPPORTED',
}
}

if (/\.bed$/i.test(location)) {
} else if (/\.bed$/i.test(location)) {
return {
type: 'BedAdapter',
bedLocation: makeLocation(location),
}
}

if (/\.bed\.b?gz$/i.test(location)) {
} else if (/\.bed\.b?gz$/i.test(location)) {
return {
type: 'BedTabixAdapter',
bedGzLocation: makeLocation(location),
Expand All @@ -547,116 +518,81 @@ export default class AddTrack extends JBrowseCommand {
indexType: index?.toUpperCase().endsWith('CSI') ? 'CSI' : 'TBI',
},
}
}

if (/\.bed$/i.test(location)) {
return {
type: 'BedAdapter',
bedLocation: makeLocation(location),
}
}

if (/\.(bb|bigbed)$/i.test(location)) {
} else if (/\.(bb|bigbed)$/i.test(location)) {
return {
type: 'BigBedAdapter',
bigBedLocation: makeLocation(location),
}
}

if (/\.(bw|bigwig)$/i.test(location)) {
} else if (/\.(bw|bigwig)$/i.test(location)) {
return {
type: 'BigWigAdapter',
bigWigLocation: makeLocation(location),
}
}

if (/\.(fa|fasta|fna|mfa)$/i.test(location)) {
} else if (/\.(fa|fasta|fna|mfa)$/i.test(location)) {
return {
type: 'IndexedFastaAdapter',
fastaLocation: makeLocation(location),
faiLocation: makeLocation(index || `${location}.fai`),
}
}

if (/\.(fa|fasta|fna|mfa)\.b?gz$/i.test(location)) {
} else if (/\.(fa|fasta|fna|mfa)\.b?gz$/i.test(location)) {
return {
type: 'BgzipFastaAdapter',
fastaLocation: makeLocation(location),
faiLocation: makeLocation(`${location}.fai`),
gziLocation: makeLocation(`${location}.gzi`),
}
}

if (/\.2bit$/i.test(location)) {
} else if (/\.2bit$/i.test(location)) {
return {
type: 'TwoBitAdapter',
twoBitLocation: makeLocation(location),
}
}

if (/\.sizes$/i.test(location)) {
} else if (/\.sizes$/i.test(location)) {
return {
type: 'UNSUPPORTED',
}
}

if (/\/trackData.jsonz?$/i.test(location)) {
} else if (/\/trackData.jsonz?$/i.test(location)) {
return {
type: 'NCListAdapter',
rootUrlTemplate: makeLocation(location),
}
}

if (/\/sparql$/i.test(location)) {
} else if (/\/sparql$/i.test(location)) {
return {
type: 'SPARQLAdapter',
endpoint: location,
}
}

if (/\.hic$/i.test(location)) {
} else if (/\.hic$/i.test(location)) {
return {
type: 'HicAdapter',
hicLocation: makeLocation(location),
}
}

if (/\.paf(.gz)?$/i.test(location)) {
} else if (/\.paf(.gz)?$/i.test(location)) {
return {
type: 'PAFAdapter',
pafLocation: makeLocation(location),
}
}

if (/\.out(.gz)?$/i.test(location)) {
} else if (/\.out(.gz)?$/i.test(location)) {
return {
type: 'MashMapAdapter',
outLocation: makeLocation(location),
}
}
if (/\.chain(.gz)?$/i.test(location)) {
} else if (/\.chain(.gz)?$/i.test(location)) {
return {
type: 'ChainAdapter',
chainLocation: makeLocation(location),
}
}
if (/\.delta(.gz)?$/i.test(location)) {
} else if (/\.delta(.gz)?$/i.test(location)) {
return {
type: 'DeltaAdapter',
deltaLocation: makeLocation(location),
}
}

if (/\.anchors(.gz)?$/i.test(location)) {
} else if (/\.anchors(.gz)?$/i.test(location)) {
return {
type: 'MCScanAnchorsAdapter',
mcscanAnchorsLocation: makeLocation(location),
bed1Location: bed1 ? makeLocation(bed1) : undefined,
bed2Location: bed2 ? makeLocation(bed2) : undefined,
}
}

if (/\.anchors.simple(.gz)?$/i.test(location)) {
} else if (/\.anchors.simple(.gz)?$/i.test(location)) {
return {
type: 'MCScanSimpleAnchorsAdapter',
mcscanSimpleAnchorsLocation: makeLocation(location),
Expand All @@ -680,6 +616,7 @@ export default class AddTrack extends JBrowseCommand {
TwoBitAdapter: 'ReferenceSequenceTrack',
VcfTabixAdapter: 'VariantTrack',
VcfAdapter: 'VariantTrack',
BedAdapter: 'FeatureTrack',
HicAdapter: 'HicTrack',
PAFAdapter: 'SyntenyTrack',
DeltaAdapter: 'SyntenyTrack',
Expand Down

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