clintval

/** Creates a fixed size thread pool executor that will rethrow exceptions from submitted jobs. */
class ThreadPoolExecutorWithExceptions(val threads: Int)
  extends ThreadPoolExecutor(threads, threads, 0, TimeUnit.SECONDS, new LinkedBlockingDeque[Runnable]) {

  /** A place to hold an exception that may have been raised by any of the executed futures. */
  protected var exception: Option[Throwable] = None

  override protected def afterExecute(runnable: Runnable, throwable: Throwable): Unit = {
    if (throwable == null && runnable.isInstanceOf[Future[_]]) try {
      val future = runnable.asInstanceOf[Future[_]]

clintval

package io.cvbio.sam

import com.fulcrumgenomics.FgBioDef.View
import com.fulcrumgenomics.bam._
import com.fulcrumgenomics.bam.api.{SamRecord, SamSource}
import htsjdk.samtools.SAMRecord
import htsjdk.samtools.filter.{DuplicateReadFilter, FailsVendorReadQualityFilter, SamRecordFilter, SecondaryAlignmentFilter}
import htsjdk.samtools.util.AbstractRecordAndOffset.AlignmentType.{Deletion, Insertion, Match}
import htsjdk.samtools.util.SamLocusIterator.LocusInfo
import htsjdk.samtools.util.{Interval, SamLocusIterator => HtsJdkSamLocusIterator}

clintval

# syntax=docker/dockerfile:1.3
FROM openjdk:8-slim-buster AS builder

RUN apt-get update && apt-get install -y git

# Not actually needed by any subsequent commands, but shows how you can bake
# things into the builder layer if they are commonly needed by other layers.
RUN mkdir -p -m 0600 ~/.ssh \
    && ssh-keyscan github.com >> ~/.ssh/known_hosts

clintval

package io.cvbio.coord

import com.fulcrumgenomics.fasta.SequenceDictionary
import htsjdk.samtools.util.{Interval => HtsJdkInterval, Locatable => HtsJdkLocatable}

/** Any interface that can be stranded. */
trait Stranded { def positiveStrand: Boolean }

/** An intermediate mixin that will provide access to HTSJDK's interval API. */
private[coord] trait IntervalIntermediate extends HtsJdkInterval

clintval

import com.fulcrumgenomics.bam.api.SamSource
import com.fulcrumgenomics.commons.CommonsDef._

/** Namespace for SAM/BAM source utilities. */
object SamSourceUtil {

  /** Return the only sample in this SAM/BAM source otherwise raise an exception. */
  def onlySample(source: SamSource): String = {
    validateHasSingleSample(source)
    source.header.getReadGroups.map(_.getSample).toSeq.head

clintval

package io.cvbio.collection

import io.cvbio.io.Io
import com.fulcrumgenomics.commons.collection.SelfClosingIterator

import java.util.concurrent.atomic.AtomicReference
import java.util.concurrent._
import scala.concurrent.duration.{Duration, DurationInt}
import scala.concurrent.{Await, ExecutionContext, Future}

clintval

/*
 * The MIT License
 *
 * Copyright © 2022 Clint Valentine
 *
 * Permission is hereby granted, free of charge, to any person obtaining a copy
 * of this software and associated documentation files (the "Software"), to deal
 * in the Software without restriction, including without limitation the rights
 * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
 * copies of the Software, and to permit persons to whom the Software is

clintval

export TOKEN=???

curl -s -X GET \
  -H "Content-Type: application/octet-stream" \
  -H "Authorization: Bearer ${TOKEN}" "https://my.qiagendigitalinsights.com/bbp/data/files/cosmic" \
  -o files.txt
  
parallel -k \
  'curl -X GET \
     -H "Content-Type: application/octet-stream" \

clintval

package com.twinstrandbio.collection

import scala.collection.compat._
import scala.collection.{StrictOptimizedIterableOps, mutable}

/** A mutable bi-directional map. There is a 1:1 mapping between keys and values. */
class BiMap[K, V]() extends mutable.Map[K, V]
  with mutable.MapOps[K, V, mutable.Map, BiMap[K, V]]
  with StrictOptimizedIterableOps[(K, V), mutable.Iterable, BiMap[K, V]]  {
  private val forward = mutable.HashMap.empty[K, V]

clintval

Rasterize Recursively

 ❯ parallel -j4 convert -density 400 +antialias {} {.}.raster.pdf ::: **/*.pdf