Commit 798f296b authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Improved logging

parent a161a802
...@@ -52,15 +52,16 @@ object GvcfToBed extends ToolCommand { ...@@ -52,15 +52,16 @@ object GvcfToBed extends ToolCommand {
logger.info("Start") logger.info("Start")
for (r <- reader) { for (r <- reader) {
if (counter % 100000 == 0) {
logger.info(s"Processed $counter records")
}
counter += 1
if (!hasMinGenomeQuality(r, cmdArgs.sample, cmdArgs.minGenomeQuality) && cmdArgs.inverse) { if (!hasMinGenomeQuality(r, cmdArgs.sample, cmdArgs.minGenomeQuality) && cmdArgs.inverse) {
writer.println(createBedRecord(r).toString) writer.println(createBedRecord(r).toString)
} else if (hasMinGenomeQuality(r, cmdArgs.sample, cmdArgs.minGenomeQuality) && !cmdArgs.inverse) { } else if (hasMinGenomeQuality(r, cmdArgs.sample, cmdArgs.minGenomeQuality) && !cmdArgs.inverse) {
writer.println(createBedRecord(r).toString) writer.println(createBedRecord(r).toString)
} }
counter += 1
if (counter % 100000 == 0) {
logger.info(s"Processed $counter records")
}
} }
logger.debug("Closing writer") logger.debug("Closing writer")
......
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