From a72a8a2fb897358927d8b6d2a4dc8afd4fde6c7b Mon Sep 17 00:00:00 2001 From: Johan Nystrom Date: Mon, 13 Feb 2023 10:21:50 +0900 Subject: [PATCH 1/2] Set version to 3.0.1 --- CHANGES | 6 ++++++ README.md | 2 +- build.sbt | 2 +- discount-aws.sh | 4 ++-- discount-gcloud.sh | 2 +- discount-shell.sh | 2 +- discount.sh | 2 +- notebooks/Discount k-mer counter.zpln | 2 +- 8 files changed, 14 insertions(+), 8 deletions(-) diff --git a/CHANGES b/CHANGES index addf92bd..dd54c332 100644 --- a/CHANGES +++ b/CHANGES @@ -1,3 +1,9 @@ +3.0.1 + + Bugfix for self-union or self-intersection of indexes (caused +a cartesian product). + Additional convenience methods for Index, e.g. unionLeft, unionRight, etc. + 3.0.0 Support for indexes (k-mer databases) written as parquet files. diff --git a/README.md b/README.md index 50d9d979..df10cbdb 100644 --- a/README.md +++ b/README.md @@ -280,7 +280,7 @@ For both notebook and REPL use, it is recommended to consult the API docs You can add Discount as a dependency using the following syntax (SBT): ` - libraryDependencies += "com.jnpersson" %% "discount" % "3.0.0" + libraryDependencies += "com.jnpersson" %% "discount" % "3.0.1" ` Please note that Discount is still under heavy development and the API may change slightly even between minor versions. diff --git a/build.sbt b/build.sbt index a69178b1..e2e4c2cf 100644 --- a/build.sbt +++ b/build.sbt @@ -1,6 +1,6 @@ name := "Discount" -version := "3.0.0" +version := "3.0.1" scalaVersion := "2.12.16" diff --git a/discount-aws.sh b/discount-aws.sh index aa085da5..b3ff3a14 100755 --- a/discount-aws.sh +++ b/discount-aws.sh @@ -12,7 +12,7 @@ BUCKET=s3://my-bucket/discount DISCOUNT_HOME="$(dirname -- "$(readlink "${BASH_SOURCE}")")" -aws s3 cp "$DISCOUNT_HOME/target/scala-2.12/Discount-assembly-3.0.0.jar" $BUCKET/ +aws s3 cp "$DISCOUNT_HOME/target/scala-2.12/Discount-assembly-3.0.1.jar" $BUCKET/ #aws s3 sync "$DISCOUNT_HOME/resources/PASHA" $BUCKET/PASHA/ @@ -23,7 +23,7 @@ aws s3 cp "$DISCOUNT_HOME/target/scala-2.12/Discount-assembly-3.0.0.jar" $BUCKET #To set SPLIT or other variables, uncomment below. COMMAND=( \ # --conf $SPLIT \ - --class com.jnpersson.discount.spark.Discount $BUCKET/Discount-assembly-3.0.0.jar $*) + --class com.jnpersson.discount.spark.Discount $BUCKET/Discount-assembly-3.0.1.jar $*) #Turn off paging for output export AWS_PAGER="" diff --git a/discount-gcloud.sh b/discount-gcloud.sh index cd130734..87a9977b 100755 --- a/discount-gcloud.sh +++ b/discount-gcloud.sh @@ -33,6 +33,6 @@ PROPERTIES=$MAXRES DISCOUNT_HOME="$(dirname -- "$(readlink "${BASH_SOURCE}")")" exec gcloud --verbosity=info dataproc jobs submit spark --region $REGION --cluster $CLUSTER \ - --class com.jnpersson.discount.spark.Discount --jars "$DISCOUNT_HOME/target/scala-2.12/Discount-assembly-3.0.0.jar" \ + --class com.jnpersson.discount.spark.Discount --jars "$DISCOUNT_HOME/target/scala-2.12/Discount-assembly-3.0.1.jar" \ --properties $PROPERTIES -- "$@" diff --git a/discount-shell.sh b/discount-shell.sh index 90851cd9..047aac9a 100755 --- a/discount-shell.sh +++ b/discount-shell.sh @@ -25,4 +25,4 @@ exec $SPARK/bin/spark-shell \ --master $MASTER \ --conf $MEMORY \ --conf $LOCAL_DIR \ - --jars "$DISCOUNT_HOME/target/scala-2.12/Discount-assembly-3.0.0.jar" + --jars "$DISCOUNT_HOME/target/scala-2.12/Discount-assembly-3.0.1.jar" diff --git a/discount.sh b/discount.sh index 119bee59..0629fec7 100755 --- a/discount.sh +++ b/discount.sh @@ -32,4 +32,4 @@ exec $SPARK/bin/spark-submit \ --conf $MEMORY \ --conf $LOCAL_DIR \ --master $MASTER \ - --class com.jnpersson.discount.spark.Discount "$DISCOUNT_HOME/target/scala-2.12/Discount-assembly-3.0.0.jar" $* + --class com.jnpersson.discount.spark.Discount "$DISCOUNT_HOME/target/scala-2.12/Discount-assembly-3.0.1.jar" $* diff --git a/notebooks/Discount k-mer counter.zpln b/notebooks/Discount k-mer counter.zpln index 28738c64..99093071 100644 --- a/notebooks/Discount k-mer counter.zpln +++ b/notebooks/Discount k-mer counter.zpln @@ -47,7 +47,7 @@ }, { "title": "Spark settings", - "text": "%spark.conf\n\n#Path to Discount jar\nspark.jars /path/to/Discount/target/scala-2.12/Discount-assembly-3.0.0.jar\n\n#If running a local Spark installation (not in a cloud), increase this setting as much as possible\nspark.driver.memory 16g\n\n#For local Spark, set the path to a Spark 3.0+ installation (if not configured elsewhere)\nSPARK_HOME /path/to/spark-3.1.2-bin-hadoop3.2\n\n#For local spark, it is helpful to set a path to a SSD drive or other fast filesystem (for temporary files)\n#Note that this directory can get large. It will be cleared when you stop or restart the Spark interpreter in Zeppelin.\nspark.local.dir /fast/spark\n\n\n", + "text": "%spark.conf\n\n#Path to Discount jar\nspark.jars /path/to/Discount/target/scala-2.12/Discount-assembly-3.0.1.jar\n\n#If running a local Spark installation (not in a cloud), increase this setting as much as possible\nspark.driver.memory 16g\n\n#For local Spark, set the path to a Spark 3.0+ installation (if not configured elsewhere)\nSPARK_HOME /path/to/spark-3.1.2-bin-hadoop3.2\n\n#For local spark, it is helpful to set a path to a SSD drive or other fast filesystem (for temporary files)\n#Note that this directory can get large. It will be cleared when you stop or restart the Spark interpreter in Zeppelin.\nspark.local.dir /fast/spark\n\n\n", "user": "anonymous", "dateUpdated": "2023-01-13T15:15:55+0900", "progress": 0, From f93da3269bb27c2aafbee9d2a825d59b49d29134 Mon Sep 17 00:00:00 2001 From: Johan Nystrom Date: Mon, 13 Feb 2023 10:23:41 +0900 Subject: [PATCH 2/2] Update API docs for 3.0.1 --- .../discount/bucket/BucketStats$.html | 8 +- .../discount/bucket/BucketStats.html | 8 +- .../discount/bucket/CountReducer.html | 8 +- .../bucket/CountersSubtractReducer.html | 12 +- .../jnpersson/discount/bucket/KmerBucket.html | 8 +- .../discount/bucket/KmerSubtractReducer.html | 11 +- .../discount/bucket/LeftReducer.html | 8 +- .../jnpersson/discount/bucket/MaxReducer.html | 8 +- .../jnpersson/discount/bucket/MinReducer.html | 8 +- .../jnpersson/discount/bucket/Reducer$.html | 8 +- .../jnpersson/discount/bucket/Reducer.html | 8 +- .../discount/bucket/ReducibleBucket$.html | 8 +- .../discount/bucket/ReducibleBucket.html | 8 +- .../discount/bucket/RightReducer.html | 8 +- .../jnpersson/discount/bucket/SumReducer.html | 8 +- docs/com/jnpersson/discount/bucket/index.html | 23 ++- docs/com/jnpersson/discount/spark/Index.html | 179 +++++++++++++++++- docs/index.js | 2 +- 18 files changed, 257 insertions(+), 74 deletions(-) diff --git a/docs/com/jnpersson/discount/bucket/BucketStats$.html b/docs/com/jnpersson/discount/bucket/BucketStats$.html index 961079f2..fd27886c 100644 --- a/docs/com/jnpersson/discount/bucket/BucketStats$.html +++ b/docs/com/jnpersson/discount/bucket/BucketStats$.html @@ -144,16 +144,16 @@

Packages

CountReducer
  • - - CountersSubtractReducer + + CountersSubtractReducer
  • KmerBucket
  • - - KmerSubtractReducer + + KmerSubtractReducer
  • diff --git a/docs/com/jnpersson/discount/bucket/BucketStats.html b/docs/com/jnpersson/discount/bucket/BucketStats.html index a9046c9e..03fbe7ec 100644 --- a/docs/com/jnpersson/discount/bucket/BucketStats.html +++ b/docs/com/jnpersson/discount/bucket/BucketStats.html @@ -144,16 +144,16 @@

    Packages

    CountReducer
  • - - CountersSubtractReducer + + CountersSubtractReducer
  • KmerBucket
  • - - KmerSubtractReducer + + KmerSubtractReducer
  • diff --git a/docs/com/jnpersson/discount/bucket/CountReducer.html b/docs/com/jnpersson/discount/bucket/CountReducer.html index 0093a1cd..f4916f95 100644 --- a/docs/com/jnpersson/discount/bucket/CountReducer.html +++ b/docs/com/jnpersson/discount/bucket/CountReducer.html @@ -144,16 +144,16 @@

    Packages

    CountReducer
  • - - CountersSubtractReducer + + CountersSubtractReducer
  • KmerBucket
  • - - KmerSubtractReducer + + KmerSubtractReducer
  • diff --git a/docs/com/jnpersson/discount/bucket/CountersSubtractReducer.html b/docs/com/jnpersson/discount/bucket/CountersSubtractReducer.html index 6699da55..c167797a 100644 --- a/docs/com/jnpersson/discount/bucket/CountersSubtractReducer.html +++ b/docs/com/jnpersson/discount/bucket/CountersSubtractReducer.html @@ -144,16 +144,16 @@

    Packages

    CountReducer
  • - - CountersSubtractReducer + + CountersSubtractReducer
  • KmerBucket
  • - - KmerSubtractReducer + + KmerSubtractReducer
  • @@ -210,7 +210,9 @@

    -

    Implements the com.jnpersson.discount.spark.Rule.CountersSubtract reduction rule

    +

    Implements the com.jnpersson.discount.spark.Rule.CountersSubtract reduction rule. +For each k-mer we calculate count_1 - count_2 and set the result to this value. +Only positive counts are preserved in the output.

    Linear Supertypes diff --git a/docs/com/jnpersson/discount/bucket/KmerBucket.html b/docs/com/jnpersson/discount/bucket/KmerBucket.html index 5b793695..2f8fc343 100644 --- a/docs/com/jnpersson/discount/bucket/KmerBucket.html +++ b/docs/com/jnpersson/discount/bucket/KmerBucket.html @@ -144,16 +144,16 @@

    Packages

    CountReducer
  • - - CountersSubtractReducer + + CountersSubtractReducer
  • KmerBucket
  • - - KmerSubtractReducer + + KmerSubtractReducer
  • diff --git a/docs/com/jnpersson/discount/bucket/KmerSubtractReducer.html b/docs/com/jnpersson/discount/bucket/KmerSubtractReducer.html index bc9507e6..d16f8254 100644 --- a/docs/com/jnpersson/discount/bucket/KmerSubtractReducer.html +++ b/docs/com/jnpersson/discount/bucket/KmerSubtractReducer.html @@ -144,16 +144,16 @@

    Packages

    CountReducer
  • - - CountersSubtractReducer + + CountersSubtractReducer
  • KmerBucket
  • - - KmerSubtractReducer + + KmerSubtractReducer
  • @@ -210,7 +210,8 @@

    -

    Implements the com.jnpersson.discount.spark.Rule.KmersSubtract reduction rule

    +

    Implements the com.jnpersson.discount.spark.Rule.KmersSubtract reduction rule. +k-mers are kept if they existed in bucket A, but not in bucket B.

    Linear Supertypes diff --git a/docs/com/jnpersson/discount/bucket/LeftReducer.html b/docs/com/jnpersson/discount/bucket/LeftReducer.html index 6dc8702d..0afade01 100644 --- a/docs/com/jnpersson/discount/bucket/LeftReducer.html +++ b/docs/com/jnpersson/discount/bucket/LeftReducer.html @@ -144,16 +144,16 @@

    Packages

    CountReducer
  • - - CountersSubtractReducer + + CountersSubtractReducer
  • KmerBucket
  • - - KmerSubtractReducer + + KmerSubtractReducer
  • diff --git a/docs/com/jnpersson/discount/bucket/MaxReducer.html b/docs/com/jnpersson/discount/bucket/MaxReducer.html index 7e7c5c1a..a89f890c 100644 --- a/docs/com/jnpersson/discount/bucket/MaxReducer.html +++ b/docs/com/jnpersson/discount/bucket/MaxReducer.html @@ -144,16 +144,16 @@

    Packages

    CountReducer
  • - - CountersSubtractReducer + + CountersSubtractReducer
  • KmerBucket
  • - - KmerSubtractReducer + + KmerSubtractReducer
  • diff --git a/docs/com/jnpersson/discount/bucket/MinReducer.html b/docs/com/jnpersson/discount/bucket/MinReducer.html index a12d4e35..3aed337f 100644 --- a/docs/com/jnpersson/discount/bucket/MinReducer.html +++ b/docs/com/jnpersson/discount/bucket/MinReducer.html @@ -144,16 +144,16 @@

    Packages

    CountReducer
  • - - CountersSubtractReducer + + CountersSubtractReducer
  • KmerBucket
  • - - KmerSubtractReducer + + KmerSubtractReducer
  • diff --git a/docs/com/jnpersson/discount/bucket/Reducer$.html b/docs/com/jnpersson/discount/bucket/Reducer$.html index 1021a5c9..7b3d0399 100644 --- a/docs/com/jnpersson/discount/bucket/Reducer$.html +++ b/docs/com/jnpersson/discount/bucket/Reducer$.html @@ -144,16 +144,16 @@

    Packages

    CountReducer
  • - - CountersSubtractReducer + + CountersSubtractReducer
  • KmerBucket
  • - - KmerSubtractReducer + + KmerSubtractReducer
  • diff --git a/docs/com/jnpersson/discount/bucket/Reducer.html b/docs/com/jnpersson/discount/bucket/Reducer.html index 9d3fb50f..1ecc051f 100644 --- a/docs/com/jnpersson/discount/bucket/Reducer.html +++ b/docs/com/jnpersson/discount/bucket/Reducer.html @@ -144,16 +144,16 @@

    Packages

    CountReducer
  • - - CountersSubtractReducer + + CountersSubtractReducer
  • KmerBucket
  • - - KmerSubtractReducer + + KmerSubtractReducer
  • diff --git a/docs/com/jnpersson/discount/bucket/ReducibleBucket$.html b/docs/com/jnpersson/discount/bucket/ReducibleBucket$.html index e5610577..5bcd692f 100644 --- a/docs/com/jnpersson/discount/bucket/ReducibleBucket$.html +++ b/docs/com/jnpersson/discount/bucket/ReducibleBucket$.html @@ -144,16 +144,16 @@

    Packages

    CountReducer
  • - - CountersSubtractReducer + + CountersSubtractReducer
  • KmerBucket
  • - - KmerSubtractReducer + + KmerSubtractReducer
  • diff --git a/docs/com/jnpersson/discount/bucket/ReducibleBucket.html b/docs/com/jnpersson/discount/bucket/ReducibleBucket.html index 22d14e71..f8b0576e 100644 --- a/docs/com/jnpersson/discount/bucket/ReducibleBucket.html +++ b/docs/com/jnpersson/discount/bucket/ReducibleBucket.html @@ -144,16 +144,16 @@

    Packages

    CountReducer
  • - - CountersSubtractReducer + + CountersSubtractReducer
  • KmerBucket
  • - - KmerSubtractReducer + + KmerSubtractReducer
  • diff --git a/docs/com/jnpersson/discount/bucket/RightReducer.html b/docs/com/jnpersson/discount/bucket/RightReducer.html index b742daca..5c4a0cae 100644 --- a/docs/com/jnpersson/discount/bucket/RightReducer.html +++ b/docs/com/jnpersson/discount/bucket/RightReducer.html @@ -144,16 +144,16 @@

    Packages

    CountReducer
  • - - CountersSubtractReducer + + CountersSubtractReducer
  • KmerBucket
  • - - KmerSubtractReducer + + KmerSubtractReducer
  • diff --git a/docs/com/jnpersson/discount/bucket/SumReducer.html b/docs/com/jnpersson/discount/bucket/SumReducer.html index 60487996..fb8ff873 100644 --- a/docs/com/jnpersson/discount/bucket/SumReducer.html +++ b/docs/com/jnpersson/discount/bucket/SumReducer.html @@ -144,16 +144,16 @@

    Packages

    CountReducer
  • - - CountersSubtractReducer + + CountersSubtractReducer
  • KmerBucket
  • - - KmerSubtractReducer + + KmerSubtractReducer
  • diff --git a/docs/com/jnpersson/discount/bucket/index.html b/docs/com/jnpersson/discount/bucket/index.html index 1f5000ac..af136cc9 100644 --- a/docs/com/jnpersson/discount/bucket/index.html +++ b/docs/com/jnpersson/discount/bucket/index.html @@ -144,16 +144,16 @@

    Packages

    CountReducer
  • - - CountersSubtractReducer + + CountersSubtractReducer
  • KmerBucket
  • - - KmerSubtractReducer + + KmerSubtractReducer
  • @@ -364,7 +364,7 @@

    Type Members

    A reducer that handles k-mer count values stored in the longsForK(k) + 1 tag position.

    -
  • +
  • @@ -376,10 +376,12 @@

    Type Members

    case class     - CountersSubtractReducer(k: Int, forwardOnly: Boolean, intersect: Boolean) extends CountReducer with Product with Serializable + CountersSubtractReducer(k: Int, forwardOnly: Boolean, intersect: Boolean) extends CountReducer with Product with Serializable -

    Implements the com.jnpersson.discount.spark.Rule.CountersSubtract reduction rule

    +

    Implements the com.jnpersson.discount.spark.Rule.CountersSubtract reduction rule.

    Implements the com.jnpersson.discount.spark.Rule.CountersSubtract reduction rule. +For each k-mer we calculate count_1 - count_2 and set the result to this value. +Only positive counts are preserved in the output.

  • @@ -397,7 +399,7 @@

    Type Members

    A bucket that maintains some number of super-mers and associated tags (e.g.

    A bucket that maintains some number of super-mers and associated tags (e.g. counts) of each k-mer.

    -
  • +
  • @@ -409,10 +411,11 @@

    Type Members

    case class     - KmerSubtractReducer(k: Int, forwardOnly: Boolean) extends CountReducer with Product with Serializable + KmerSubtractReducer(k: Int, forwardOnly: Boolean) extends CountReducer with Product with Serializable -

    Implements the com.jnpersson.discount.spark.Rule.KmersSubtract reduction rule

    +

    Implements the com.jnpersson.discount.spark.Rule.KmersSubtract reduction rule.

    Implements the com.jnpersson.discount.spark.Rule.KmersSubtract reduction rule. +k-mers are kept if they existed in bucket A, but not in bucket B.

  • diff --git a/docs/com/jnpersson/discount/spark/Index.html b/docs/com/jnpersson/discount/spark/Index.html index 69a6ba7b..326cb642 100644 --- a/docs/com/jnpersson/discount/spark/Index.html +++ b/docs/com/jnpersson/discount/spark/Index.html @@ -404,6 +404,22 @@

    Value Members
    Definition Classes
    AnyRef → Any
    +
  • + + + + + + + + + def + + + add(other: Index): Index + + +

    Convenience method for union using Rule.Sum

  • @@ -716,6 +732,22 @@

    Value Members

    Intersect this index with another one, combining the k-mers using the given reducer type.

    Intersect this index with another one, combining the k-mers using the given reducer type. A k-mer is kept after an intersection operation if it is present in both of the input indexes, and passes any other rules that the reducer implements.

    +
  • + + + + + + + + + def + + + intersectLeft(other: Index): Index + + +

    Convenience method for intersection using Rule.Left

  • @@ -732,6 +764,54 @@

    Value Members

    Intersect this index with a series of indexes using the given reducer type.

    +
  • + + + + + + + + + def + + + intersectMax(other: Index): Index + + +

    Convenience method for intersection using Rule.Max

    +
  • + + + + + + + + + def + + + intersectMin(other: Index): Index + + +

    Convenience method for intersection using Rule.Min

    +
  • + + + + + + + + + def + + + intersectRight(other: Index): Index + + +

    Convenience method for intersection using Rule.Right

  • @@ -974,8 +1054,41 @@

    Value Members

    Subtract another index from this one, using e.g.

    Subtract another index from this one, using e.g. Rule.KmersSubtract or -Rule.CountersSubtract. Subtraction is implemented as a union, but the reducer makes it non-commutative. +Rule.CountersSubtract. Subtraction is implemented as a union, but this is not a commutative operation +due to how the rules are implemented.

    +
  • + + + + + + + + + def + + + subtractCounts(other: Index): Index + + +

    Convenience method for subtraction using Rule.CountersSubtract

    +
  • + + + + + + + + + def + + + subtractKmers(other: Index): Index + + +

    Convenience method for subtraction using Rule.KmersSubtract

  • @@ -1044,6 +1157,22 @@

    Value Members

    Union this index with another one, combining the k-mers using the given reducer type.

    Union this index with another one, combining the k-mers using the given reducer type. A k-mer is kept after a union operation if it is present in either of the input indexes, and passes any other rules that the reducer implements.

    +
  • + + + + + + + + + def + + + unionLeft(other: Index): Index + + +

    Convenience method for union using Rule.Left

  • @@ -1060,6 +1189,54 @@

    Value Members

    Union this index with a series of indexes using the given reducer type.

    +
  • + + + + + + + + + def + + + unionMax(other: Index): Index + + +

    Convenience method for union using Rule.Max

    +
  • + + + + + + + + + def + + + unionMin(other: Index): Index + + +

    Convenience method for union using Rule.Min

    +
  • + + + + + + + + + def + + + unionRight(other: Index): Index + + +

    Convenience method for union using Rule.Right

  • diff --git a/docs/index.js b/docs/index.js index 52a5c2c9..d2071231 100644 --- a/docs/index.js +++ b/docs/index.js @@ -1 +1 @@ -Index.PACKAGES = {"com.jnpersson" : [], "com.jnpersson.discount.bucket" : [{"name" : "com.jnpersson.discount.bucket.BucketStats", "shortDescription" : "Statistics for a single bin\/bucket.", "object" : "com\/jnpersson\/discount\/bucket\/BucketStats$.html", "members_object" : [{"label" : "collectFromCounts", "tail" : "(id: String, counts: Array[Array[Int]]): BucketStats", "member" : "com.jnpersson.discount.bucket.BucketStats.collectFromCounts", "link" : "com\/jnpersson\/discount\/bucket\/BucketStats$.html#collectFromCounts(id:String,counts:Array[Array[Int]]):com.jnpersson.discount.bucket.BucketStats", "kind" : "def"}, {"label" : "synchronized", "tail" : "(arg0: ⇒ T0): T0", "member" : "scala.AnyRef.synchronized", "link" : "com\/jnpersson\/discount\/bucket\/BucketStats$.html#synchronized[T0](x$1:=>T0):T0", "kind" : "final def"}, {"label" : "##", "tail" : "(): 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