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Allow space in IntervalList species header value #2356

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merged 1 commit into from
Mar 8, 2022
Merged

Allow space in IntervalList species header value #2356

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2 changes: 1 addition & 1 deletion adam-core/src/main/scala/org/bdgenomics/adam/ds/feature/FeatureParser.scala
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Original file line number Diff line number Diff line change
Expand Up @@ -245,7 +245,7 @@ private[ds] class IntervalListParser extends FeatureParser {
def parseHeader(line: String,
stringency: ValidationStringency): Option[SequenceRecord] = {

val fields = line.split("[ \t]+")
val fields = line.split("[\t]+")

if (fields(0).startsWith("@SQ")) {
val (name, length, url, md5) = {
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31 changes: 31 additions & 0 deletions adam-core/src/test/resources/wgs_calling_regions.hg38.interval_list
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Original file line number Diff line number Diff line change
@@ -0,0 +1,31 @@
@HD VN:1.5 SO:coordinate
@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens
@SQ SN:chr2 LN:242193529 M5:f98db672eb0993dcfdabafe2a882905c AS:38 UR:/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.fasta SP:Homo sapiens
@PG ID:1 CL:picard.util.IntervalListTools INPUT=[HG38excludeNs.interval_list, genome.interval_list] OUTPUT=wgs_calling_regions.v3.interval_list SORT=true ACTION=INTERSECT PADDING=0 UNIQUE=false SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION INVERT=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json PN:IntervalListTools
chr1 10001 207666 + . intersection ACGTmer
chr1 257667 297968 + . intersection ACGTmer
chr1 347969 535988 + . intersection ACGTmer
chr1 585989 2702781 + . intersection ACGTmer
chr1 2746291 12954384 + . intersection ACGTmer
chr1 13004385 16799163 + . intersection ACGTmer
chr1 16849164 29552233 + . intersection ACGTmer
chr1 29553836 121976459 + . intersection ACGTmer
chr1 122026460 124977944 + . intersection ACGTmer
chr1 124978327 125130246 + . intersection ACGTmer
chr1 125131848 125171347 + . intersection ACGTmer
chr1 125173584 125184587 + . intersection ACGTmer
chr1 143184588 223558935 + . intersection ACGTmer
chr1 223608936 228558364 + . intersection ACGTmer
chr1 228608365 248946422 + . intersection ACGTmer
chr2 10001 16145119 + . intersection ACGTmer
chr2 16146120 32867130 + . intersection ACGTmer
chr2 32868131 32916625 + . intersection ACGTmer
chr2 32917626 89330679 + . intersection ACGTmer
chr2 89530680 89685992 + . intersection ACGTmer
chr2 89753993 90402511 + . intersection ACGTmer
chr2 91402512 92138145 + . intersection ACGTmer
chr2 92188146 94090557 + . intersection ACGTmer
chr2 94140558 94293015 + . intersection ACGTmer
chr2 94496016 97439618 + . intersection ACGTmer
chr2 97489619 238903659 + . intersection ACGTmer
chr2 238904048 242183529 + . intersection ACGTmer
6 changes: 6 additions & 0 deletions adam-core/src/test/scala/org/bdgenomics/adam/ds/feature/FeatureDatasetSuite.scala
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Original file line number Diff line number Diff line change
Expand Up @@ -471,6 +471,12 @@ class FeatureDatasetSuite extends ADAMFunSuite {
})
}

sparkTest("allow space in IntervalList SP header value") {
val inputPath = testFile("wgs_calling_regions.hg38.interval_list")
val features = sc.loadIntervalList(inputPath)
assert(features.rdd.count() == 27)
}

sparkTest("save NarrowPeak as GTF format") {
val inputPath = testFile("wgEncodeOpenChromDnaseGm19238Pk.trunc10.narrowPeak")
val features = sc.loadNarrowPeak(inputPath)
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