diff --git a/src/sam.ts b/src/sam.ts index 09c660c4..fe9b7702 100644 --- a/src/sam.ts +++ b/src/sam.ts @@ -1,20 +1,36 @@ -export type HeaderDataItem = { - tag: string - data: Array<{ tag: string; value: string }> -} - -export function parseHeaderText(text: string): HeaderDataItem[] { +export function parseHeaderText(text: string) { const lines = text.split(/\r?\n/) - const data: HeaderDataItem[] = [] - lines.forEach(line => { + const data: { + tag: string + data: { + tag: string + value: string | undefined + }[] + }[] = [] + for (const line of lines) { const [tag, ...fields] = line.split(/\t/) - const parsedFields = fields.map(f => { - const [fieldTag, value] = f.split(':', 2) - return { tag: fieldTag, value } - }) if (tag) { - data.push({ tag: tag.substr(1), data: parsedFields }) + data.push({ + tag: tag.slice(1), + data: fields.map(f => { + const r = f.indexOf(':') + if (r !== -1) { + return { + tag: f.slice(0, r), + value: f.slice(r + 1), + } + } else { + // @CO lines are not comma separated. + // See "samtools view -H c2\#pad.3.0.cram" + // so, just store value tag itself + return { + tag: f, + value: undefined, + } + } + }), + }) } - }) + } return data } diff --git a/test/__snapshots__/dump2.test.ts.snap b/test/__snapshots__/dump2.test.ts.snap index 8f4fd051..c4c169ed 100644 --- a/test/__snapshots__/dump2.test.ts.snap +++ b/test/__snapshots__/dump2.test.ts.snap @@ -2966723,7 +2966723,7 @@ exports[`dumping cram files can dump the whole grc37-1#HG03297.mapped.ILLUMINA.b }, { "tag": "UR", - "value": "ftp", + "value": "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", }, { "tag": "AS", @@ -2966752,7 +2966752,7 @@ exports[`dumping cram files can dump the whole grc37-1#HG03297.mapped.ILLUMINA.b }, { "tag": "UR", - "value": "ftp", + "value": "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", }, { "tag": "AS", @@ -2966781,7 +2966781,7 @@ exports[`dumping cram files can dump the whole grc37-1#HG03297.mapped.ILLUMINA.b }, { "tag": "UR", - "value": "ftp", + "value": "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", }, { "tag": "AS", @@ -2966810,7 +2966810,7 @@ exports[`dumping cram files can dump the whole grc37-1#HG03297.mapped.ILLUMINA.b }, { "tag": "UR", - "value": "ftp", + "value": "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", }, { "tag": "AS", @@ -2966839,7 +2966839,7 @@ exports[`dumping cram files can dump the whole grc37-1#HG03297.mapped.ILLUMINA.b }, { "tag": "UR", - "value": "ftp", + "value": "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", }, { "tag": "AS", @@ -2966868,7 +2966868,7 @@ exports[`dumping cram files can dump the whole grc37-1#HG03297.mapped.ILLUMINA.b }, { "tag": "UR", - "value": "ftp", + "value": "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", }, { "tag": "AS", @@ -2966897,7 +2966897,7 @@ exports[`dumping cram files can dump the whole grc37-1#HG03297.mapped.ILLUMINA.b }, { "tag": "UR", - "value": "ftp", + "value": "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", }, { "tag": "AS", @@ -2966926,7 +2966926,7 @@ exports[`dumping cram files can dump the whole grc37-1#HG03297.mapped.ILLUMINA.b }, { "tag": "UR", - "value": "ftp", + "value": "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", }, { "tag": "AS", @@ -2966955,7 +2966955,7 @@ exports[`dumping cram files can dump the whole grc37-1#HG03297.mapped.ILLUMINA.b }, { "tag": "UR", - "value": "ftp", + "value": "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", }, { "tag": "AS", @@ -2966984,7 +2966984,7 @@ exports[`dumping cram files can dump the whole grc37-1#HG03297.mapped.ILLUMINA.b }, { "tag": "UR", - "value": "ftp", + "value": "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", }, { "tag": "AS", @@ -2967013,7 +2967013,7 @@ exports[`dumping cram files can dump the whole grc37-1#HG03297.mapped.ILLUMINA.b }, { "tag": "UR", - "value": "ftp", + "value": "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", }, { "tag": "AS", @@ -2967042,7 +2967042,7 @@ exports[`dumping cram files can dump the whole grc37-1#HG03297.mapped.ILLUMINA.b }, { "tag": "UR", - "value": "ftp", + "value": "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", }, { "tag": "AS", @@ -2967071,7 +2967071,7 @@ exports[`dumping cram files can dump the whole grc37-1#HG03297.mapped.ILLUMINA.b }, { "tag": "UR", - "value": "ftp", + "value": "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", }, { "tag": "AS", @@ -2967100,7 +2967100,7 @@ exports[`dumping cram files can dump the whole grc37-1#HG03297.mapped.ILLUMINA.b }, { "tag": "UR", - "value": "ftp", + "value": "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", }, { "tag": "AS", @@ -2967129,7 +2967129,7 @@ exports[`dumping cram files can dump the whole grc37-1#HG03297.mapped.ILLUMINA.b }, { "tag": "UR", - "value": "ftp", + "value": "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", }, { "tag": "AS", @@ -2967158,7 +2967158,7 @@ exports[`dumping cram files can dump the whole grc37-1#HG03297.mapped.ILLUMINA.b }, { "tag": "UR", - "value": "ftp", + "value": "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", }, { "tag": "AS", @@ -2967187,7 +2967187,7 @@ exports[`dumping cram files can dump the whole grc37-1#HG03297.mapped.ILLUMINA.b }, { "tag": "UR", - "value": "ftp", + "value": "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", }, { "tag": "AS", @@ -2967216,7 +2967216,7 @@ exports[`dumping cram files can dump the whole grc37-1#HG03297.mapped.ILLUMINA.b }, { "tag": "UR", - "value": "ftp", + "value": "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", }, { "tag": "AS", @@ -2967245,7 +2967245,7 @@ exports[`dumping cram files can dump the whole grc37-1#HG03297.mapped.ILLUMINA.b }, { "tag": "UR", - "value": "ftp", + "value": "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", }, { "tag": "AS", @@ -2967274,7 +2967274,7 @@ exports[`dumping cram files can dump the whole grc37-1#HG03297.mapped.ILLUMINA.b }, { "tag": "UR", - "value": "ftp", + "value": "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", }, { "tag": "AS", @@ -2967303,7 +2967303,7 @@ exports[`dumping cram files can dump the whole grc37-1#HG03297.mapped.ILLUMINA.b }, { "tag": "UR", - "value": "ftp", + "value": "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", }, { "tag": "AS", @@ -2967332,7 +2967332,7 @@ exports[`dumping cram files can dump the whole grc37-1#HG03297.mapped.ILLUMINA.b }, { "tag": "UR", - "value": "ftp", + "value": "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", }, { "tag": "AS", @@ -2967361,7 +2967361,7 @@ exports[`dumping cram files can dump the whole grc37-1#HG03297.mapped.ILLUMINA.b }, { "tag": "UR", - "value": "ftp", + "value": "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", }, { "tag": "AS", @@ -2967390,7 +2967390,7 @@ exports[`dumping cram files can dump the whole grc37-1#HG03297.mapped.ILLUMINA.b }, { "tag": "UR", - "value": "ftp", + "value": "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", }, { "tag": "AS", @@ -2967419,7 +2967419,7 @@ exports[`dumping cram files can dump the whole grc37-1#HG03297.mapped.ILLUMINA.b }, { "tag": "UR", - "value": "ftp", + "value": "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", }, { "tag": "AS", @@ -2967448,7 +2967448,7 @@ exports[`dumping cram files can dump the whole grc37-1#HG03297.mapped.ILLUMINA.b }, { "tag": "UR", - "value": "ftp", + "value": "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", }, { "tag": "AS", @@ -2967477,7 +2967477,7 @@ exports[`dumping cram files can dump the whole grc37-1#HG03297.mapped.ILLUMINA.b }, { "tag": "UR", - "value": "ftp", + "value": "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", }, { "tag": "AS", @@ -2967506,7 +2967506,7 @@ exports[`dumping cram files can dump the whole grc37-1#HG03297.mapped.ILLUMINA.b }, { "tag": "UR", - "value": "ftp", + "value": "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", }, { "tag": "AS", @@ -2967535,7 +2967535,7 @@ exports[`dumping cram files can dump the whole grc37-1#HG03297.mapped.ILLUMINA.b }, { "tag": "UR", - "value": "ftp", + "value": "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", }, { "tag": "AS", @@ -2967564,7 +2967564,7 @@ exports[`dumping cram files can dump the whole grc37-1#HG03297.mapped.ILLUMINA.b }, { "tag": "UR", - "value": "ftp", + "value": "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", }, { "tag": "AS", @@ -2967593,7 +2967593,7 @@ exports[`dumping cram files can dump the whole grc37-1#HG03297.mapped.ILLUMINA.b }, { "tag": "UR", - "value": "ftp", + "value": "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", }, { "tag": "AS", @@ -2967622,7 +2967622,7 @@ exports[`dumping cram files can dump the whole grc37-1#HG03297.mapped.ILLUMINA.b }, { "tag": "UR", - "value": "ftp", + "value": "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", }, { "tag": "AS", @@ -2967651,7 +2967651,7 @@ exports[`dumping cram files can dump the whole grc37-1#HG03297.mapped.ILLUMINA.b }, { "tag": "UR", - "value": "ftp", + "value": "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", }, { "tag": "AS", @@ -2967680,7 +2967680,7 @@ exports[`dumping cram files can dump the whole grc37-1#HG03297.mapped.ILLUMINA.b }, { "tag": "UR", - "value": "ftp", + "value": "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", }, { "tag": "AS", @@ -2967709,7 +2967709,7 @@ exports[`dumping cram files can dump the whole grc37-1#HG03297.mapped.ILLUMINA.b }, { "tag": "UR", - "value": "ftp", + "value": "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", }, { "tag": "AS", @@ -2967738,7 +2967738,7 @@ exports[`dumping cram files can dump the whole grc37-1#HG03297.mapped.ILLUMINA.b }, { "tag": "UR", - "value": "ftp", + "value": "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", }, { "tag": "AS", @@ -2967767,7 +2967767,7 @@ exports[`dumping cram files can dump the whole grc37-1#HG03297.mapped.ILLUMINA.b }, { "tag": "UR", - "value": "ftp", + "value": "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", }, { "tag": "AS", @@ -2967796,7 +2967796,7 @@ exports[`dumping cram files can dump the whole grc37-1#HG03297.mapped.ILLUMINA.b }, { "tag": "UR", - "value": "ftp", + "value": "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", }, { "tag": "AS", @@ -2967825,7 +2967825,7 @@ exports[`dumping cram files can dump the whole grc37-1#HG03297.mapped.ILLUMINA.b }, { "tag": "UR", - "value": "ftp", + "value": "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", }, { "tag": "AS", @@ -2967854,7 +2967854,7 @@ exports[`dumping cram files can dump the whole grc37-1#HG03297.mapped.ILLUMINA.b }, { "tag": "UR", - "value": "ftp", + "value": "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", }, { "tag": "AS", @@ -2967883,7 +2967883,7 @@ exports[`dumping cram files can dump the whole grc37-1#HG03297.mapped.ILLUMINA.b }, { "tag": "UR", - "value": "ftp", + "value": "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", }, { "tag": "AS", @@ -2967912,7 +2967912,7 @@ exports[`dumping cram files can dump the whole grc37-1#HG03297.mapped.ILLUMINA.b }, { "tag": "UR", - "value": "ftp", + "value": "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", }, { "tag": "AS", @@ -2967941,7 +2967941,7 @@ exports[`dumping cram files can dump the whole grc37-1#HG03297.mapped.ILLUMINA.b }, { "tag": "UR", - "value": "ftp", + "value": "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", }, { "tag": "AS", @@ -2967970,7 +2967970,7 @@ exports[`dumping cram files can dump the whole grc37-1#HG03297.mapped.ILLUMINA.b }, { "tag": "UR", - "value": "ftp", + "value": "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", }, { "tag": "AS", @@ -2967999,7 +2967999,7 @@ exports[`dumping cram files can dump the whole grc37-1#HG03297.mapped.ILLUMINA.b }, { "tag": "UR", - "value": "ftp", + "value": "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", }, { "tag": "AS", @@ -2968028,7 +2968028,7 @@ exports[`dumping cram files can dump the whole grc37-1#HG03297.mapped.ILLUMINA.b }, { "tag": "UR", - "value": "ftp", + "value": "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", }, { "tag": "AS", @@ -2968057,7 +2968057,7 @@ exports[`dumping cram files can dump the whole grc37-1#HG03297.mapped.ILLUMINA.b }, { "tag": "UR", - "value": "ftp", + "value": "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", }, { "tag": "AS", @@ -2968086,7 +2968086,7 @@ exports[`dumping cram files can dump the whole grc37-1#HG03297.mapped.ILLUMINA.b }, { "tag": "UR", - "value": "ftp", + "value": "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", }, { "tag": "AS", @@ -2968115,7 +2968115,7 @@ exports[`dumping cram files can dump the whole grc37-1#HG03297.mapped.ILLUMINA.b }, { "tag": "UR", - "value": "ftp", + "value": "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", }, { "tag": "AS", @@ -2968144,7 +2968144,7 @@ exports[`dumping cram files can dump the whole grc37-1#HG03297.mapped.ILLUMINA.b }, { "tag": "UR", - "value": "ftp", + "value": "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", }, { "tag": "AS", @@ -2968173,7 +2968173,7 @@ exports[`dumping cram files can dump the whole grc37-1#HG03297.mapped.ILLUMINA.b }, { "tag": "UR", - "value": "ftp", + "value": "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", }, { "tag": "AS", @@ -2968202,7 +2968202,7 @@ exports[`dumping cram files can dump the whole grc37-1#HG03297.mapped.ILLUMINA.b }, { "tag": "UR", - "value": "ftp", + "value": "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", }, { "tag": "AS", @@ -2968231,7 +2968231,7 @@ exports[`dumping cram files can dump the whole grc37-1#HG03297.mapped.ILLUMINA.b }, { "tag": "UR", - "value": "ftp", + "value": "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", }, { "tag": "AS", @@ -2968260,7 +2968260,7 @@ exports[`dumping cram files can dump the whole grc37-1#HG03297.mapped.ILLUMINA.b }, { "tag": "UR", - "value": "ftp", + "value": "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", }, { "tag": "AS", @@ -2968289,7 +2968289,7 @@ exports[`dumping cram files can dump the whole grc37-1#HG03297.mapped.ILLUMINA.b }, { "tag": "UR", - "value": "ftp", + "value": "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", }, { "tag": "AS", @@ -2968318,7 +2968318,7 @@ exports[`dumping cram files can dump the whole grc37-1#HG03297.mapped.ILLUMINA.b }, { "tag": "UR", - "value": "ftp", + "value": "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", }, { "tag": "AS", @@ -2968347,7 +2968347,7 @@ exports[`dumping cram files can dump the whole grc37-1#HG03297.mapped.ILLUMINA.b }, { "tag": "UR", - "value": "ftp", + "value": "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", }, { "tag": "AS", @@ -2968376,7 +2968376,7 @@ exports[`dumping cram files can dump the whole grc37-1#HG03297.mapped.ILLUMINA.b }, { "tag": "UR", - "value": "ftp", + "value": "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", }, { "tag": "AS", @@ -2968405,7 +2968405,7 @@ exports[`dumping cram files can dump the whole grc37-1#HG03297.mapped.ILLUMINA.b }, { "tag": "UR", - "value": "ftp", + "value": "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", }, { "tag": "AS", @@ -2968434,7 +2968434,7 @@ exports[`dumping cram files can dump the whole grc37-1#HG03297.mapped.ILLUMINA.b }, { "tag": "UR", - "value": "ftp", + "value": "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", }, { "tag": "AS", @@ -2968463,7 +2968463,7 @@ exports[`dumping cram files can dump the whole grc37-1#HG03297.mapped.ILLUMINA.b }, { "tag": "UR", - "value": "ftp", + "value": "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", }, { "tag": "AS", @@ -2968492,7 +2968492,7 @@ exports[`dumping cram files can dump the whole grc37-1#HG03297.mapped.ILLUMINA.b }, { "tag": "UR", - "value": "ftp", + "value": "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", }, { "tag": "AS", @@ -2968521,7 +2968521,7 @@ exports[`dumping cram files can dump the whole grc37-1#HG03297.mapped.ILLUMINA.b }, { "tag": "UR", - "value": "ftp", + "value": "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", }, { "tag": "AS", @@ -2968550,7 +2968550,7 @@ exports[`dumping cram files can dump the whole grc37-1#HG03297.mapped.ILLUMINA.b }, { "tag": "UR", - "value": "ftp", + "value": "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", }, { "tag": "AS", @@ -2968579,7 +2968579,7 @@ exports[`dumping cram files can dump the whole grc37-1#HG03297.mapped.ILLUMINA.b }, { "tag": "UR", - "value": "ftp", + "value": "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", }, { "tag": "AS", @@ -2968608,7 +2968608,7 @@ exports[`dumping cram files can dump the whole grc37-1#HG03297.mapped.ILLUMINA.b }, { "tag": "UR", - "value": "ftp", + "value": "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", }, { "tag": "AS", @@ -2968637,7 +2968637,7 @@ exports[`dumping cram files can dump the whole grc37-1#HG03297.mapped.ILLUMINA.b }, { "tag": "UR", - "value": "ftp", + "value": "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", }, { "tag": "AS", @@ -2968666,7 +2968666,7 @@ exports[`dumping cram files can dump the whole grc37-1#HG03297.mapped.ILLUMINA.b }, { "tag": "UR", - "value": "ftp", + "value": "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", }, { "tag": "AS", @@ -2968695,7 +2968695,7 @@ exports[`dumping cram files can dump the whole grc37-1#HG03297.mapped.ILLUMINA.b }, { "tag": "UR", - "value": "ftp", + "value": "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", }, { "tag": "AS", @@ -2968724,7 +2968724,7 @@ exports[`dumping cram files can dump the whole grc37-1#HG03297.mapped.ILLUMINA.b }, { "tag": "UR", - "value": "ftp", + "value": "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", }, { "tag": "AS", @@ -2968753,7 +2968753,7 @@ exports[`dumping cram files can dump the whole grc37-1#HG03297.mapped.ILLUMINA.b }, { "tag": "UR", - "value": "ftp", + "value": "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", }, { "tag": "AS", @@ -2968782,7 +2968782,7 @@ exports[`dumping cram files can dump the whole grc37-1#HG03297.mapped.ILLUMINA.b }, { "tag": "UR", - "value": "ftp", + "value": "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", }, { "tag": "AS", @@ -2968811,7 +2968811,7 @@ exports[`dumping cram files can dump the whole grc37-1#HG03297.mapped.ILLUMINA.b }, { "tag": "UR", - "value": "ftp", + "value": "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", }, { "tag": "AS", @@ -2968840,7 +2968840,7 @@ exports[`dumping cram files can dump the whole grc37-1#HG03297.mapped.ILLUMINA.b }, { "tag": "UR", - "value": "ftp", + "value": "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", }, { "tag": "AS", @@ -2968869,7 +2968869,7 @@ exports[`dumping cram files can dump the whole grc37-1#HG03297.mapped.ILLUMINA.b }, { "tag": "UR", - "value": "ftp", + "value": "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", }, { "tag": "AS", @@ -2968898,7 +2968898,7 @@ exports[`dumping cram files can dump the whole grc37-1#HG03297.mapped.ILLUMINA.b }, { "tag": "UR", - "value": "ftp", + "value": "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", }, { "tag": "AS", @@ -2968927,7 +2968927,7 @@ exports[`dumping cram files can dump the whole grc37-1#HG03297.mapped.ILLUMINA.b }, { "tag": "UR", - "value": "ftp", + "value": "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", }, { "tag": "AS", @@ -2968956,7 +2968956,7 @@ exports[`dumping cram files can dump the whole grc37-1#HG03297.mapped.ILLUMINA.b }, { "tag": "UR", - "value": "ftp", + "value": "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", }, { "tag": "AS", @@ -2968985,7 +2968985,7 @@ exports[`dumping cram files can dump the whole grc37-1#HG03297.mapped.ILLUMINA.b }, { "tag": "UR", - "value": "ftp", + "value": "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", }, { "tag": "AS", @@ -2969014,7 +2969014,7 @@ exports[`dumping cram files can dump the whole grc37-1#HG03297.mapped.ILLUMINA.b }, { "tag": "UR", - "value": "ftp", + "value": "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", }, { "tag": "AS", @@ -2969043,7 +2969043,7 @@ exports[`dumping cram files can dump the whole grc37-1#HG03297.mapped.ILLUMINA.b }, { "tag": "UR", - "value": "ftp", + "value": "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", }, { "tag": "AS", @@ -2969072,7 +2969072,7 @@ exports[`dumping cram files can dump the whole grc37-1#HG03297.mapped.ILLUMINA.b }, { "tag": "UR", - "value": "ftp", + "value": "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", }, { "tag": "AS", @@ -2969101,7 +2969101,7 @@ exports[`dumping cram files can dump the whole grc37-1#HG03297.mapped.ILLUMINA.b }, { "tag": "UR", - "value": "ftp", + "value": "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", }, { "tag": "AS", @@ -2969130,7 +2969130,7 @@ exports[`dumping cram files can dump the whole grc37-1#HG03297.mapped.ILLUMINA.b }, { "tag": "UR", - "value": "ftp", + "value": "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", }, { "tag": "AS", @@ -2969159,7 +2969159,7 @@ exports[`dumping cram files can dump the whole grc37-1#HG03297.mapped.ILLUMINA.b }, { "tag": "UR", - "value": "ftp", + "value": "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", }, { "tag": "AS", @@ -2969188,7 +2969188,7 @@ exports[`dumping cram files can dump the whole grc37-1#HG03297.mapped.ILLUMINA.b }, { "tag": "UR", - "value": "ftp", + "value": "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz", }, { "tag": "AS", @@ -2969383,7 +2969383,7 @@ exports[`dumping cram files can dump the whole grc37-1#HG03297.mapped.ILLUMINA.b }, { "tag": "VN", - "value": "0.1.17 (r973", + "value": "0.1.17 (r973:277)", }, { "tag": "CL", @@ -2969408,7 +2969408,7 @@ exports[`dumping cram files can dump the whole grc37-1#HG03297.mapped.ILLUMINA.b }, { "tag": "VN", - "value": "0.1.17 (r973", + "value": "0.1.17 (r973:277)", }, { "tag": "CL", @@ -2969633,7 +2969633,7 @@ exports[`dumping cram files can dump the whole grc37-1#HG03297.mapped.ILLUMINA.b }, { "tag": "VN", - "value": "0.1.17 (r973", + "value": "0.1.17 (r973:277)", }, { "tag": "CL", @@ -2969658,7 +2969658,7 @@ exports[`dumping cram files can dump the whole grc37-1#HG03297.mapped.ILLUMINA.b }, { "tag": "VN", - "value": "0.1.17 (r973", + "value": "0.1.17 (r973:277)", }, { "tag": "CL", @@ -4372322,7 +4372322,7 @@ exports[`dumping cram files can dump the whole hg19mini#cramQueryTest.cram witho }, { "tag": "VN", - "value": "Version", + "value": "Version:4.alpha-382-gd7b2d9f-SNAPSHOT", }, { "tag": "CL", @@ -4380726,7 +4380726,7 @@ exports[`dumping cram files can dump the whole hg19mini#cramQueryTestEmpty.cram }, { "tag": "VN", - "value": "Version", + "value": "Version:4.alpha-382-gd7b2d9f-SNAPSHOT", }, { "tag": "CL", @@ -4380747,7 +4380747,7 @@ exports[`dumping cram files can dump the whole hg19mini#cramQueryTestEmpty.cram }, { "tag": "VN", - "value": "Version", + "value": "Version:4.alpha-419-ga8d5c11-SNAPSHOT", }, { "tag": "CL", @@ -4539737,7 +4539737,7 @@ exports[`dumping cram files can dump the whole xx#rg.2.1.cram without error 1`] }, { "tag": "PG", - "value": "foo", + "value": "foo:bar", }, { "tag": "PI", @@ -4540470,7 +4540470,7 @@ exports[`dumping cram files can dump the whole xx#rg.3.0.cram without error 1`] }, { "tag": "PG", - "value": "foo", + "value": "foo:bar", }, { "tag": "PI", @@ -4540593,7 +4540593,7 @@ exports[`dumping cram files can dump the whole xx#rg.3.0.cram without error 1`] }, { "tag": "PG", - "value": "foo", + "value": "foo:bar", }, { "tag": "PI", @@ -4541281,7 +4541281,7 @@ exports[`dumping cram files can dump the whole xx#rg.tmp.cram without error 1`] }, { "tag": "PG", - "value": "foo", + "value": "foo:bar", }, { "tag": "PI", @@ -4541404,7 +4541404,7 @@ exports[`dumping cram files can dump the whole xx#rg.tmp.cram without error 1`] }, { "tag": "PG", - "value": "foo", + "value": "foo:bar", }, { "tag": "PI",