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pre release changes (#127)
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* pre release changes

* building docker images

* changing version in dockerfile

* automatic version_number population to Dockerfile
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agaszmurlo authored and mwiewior committed Oct 31, 2018
1 parent e2e5708 commit 8be2b00
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Showing 8 changed files with 19 additions and 14 deletions.
4 changes: 2 additions & 2 deletions Docker/bdg-sequila/Dockerfile
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Expand Up @@ -8,10 +8,10 @@ RUN useradd -m tempuser
# Spark related variables.
##COMPONENT_VERSION variable will be replaced during the build process

ARG BDG_VERSION=0.4.1-SNAPSHOT
ARG BDG_VERSION

####set variable used in all shell scritps for downloading jars
ENV BDG_VERSION=0.4.1-SNAPSHOT
ENV BDG_VERSION=$BDG_VERSION



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2 changes: 1 addition & 1 deletion Docker/bdg-sequila/version
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@@ -1 +1 @@
0.3-SNAPSHOT
0.5
2 changes: 1 addition & 1 deletion Jenkinsfile
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Expand Up @@ -138,7 +138,7 @@ node {
stage('Building Docker images') {

echo 'Building Docker images....'
//sh './build.sh'
sh './build.sh'

}

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2 changes: 1 addition & 1 deletion build.sbt
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Expand Up @@ -2,7 +2,7 @@ import scala.util.Properties

name := """bdg-sequila"""

version := "0.4.1-SNAPSHOT"
version := "0.5"

organization := "org.biodatageeks"

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4 changes: 2 additions & 2 deletions build.sh
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Expand Up @@ -37,9 +37,9 @@ do
#if [ $diffTs -lt $MAX_COMMIT_TS_DIFF ]; then
cd $dir
if [[ ${BUILD_MODE} != "local" ]]; then
docker build --no-cache -t $image:$version .
docker build --no-cache --build-arg BDG_VERSION=${version} -t $image:$version .
else
docker build --no-cache -t $image:$version .
docker build --no-cache --build-arg BDG_VERSION=${version} -t $image:$version .
fi
docker build -t $image:latest .
if [[ ${BUILD_MODE} != "local" ]]; then
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6 changes: 3 additions & 3 deletions docs/source/function/function.rst
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Expand Up @@ -254,7 +254,7 @@ bdg_coverage is a function that calculates depth of coverage for specified sampl
//CALCULATE COVERAGE - FIXED LENGTH WINDOWS
ss.sql(s"SELECT * FROM bdg_coverage('${tableNameBAM}','NA12878.chr21', '', 100)").show(5)
ss.sql(s"SELECT * FROM bdg_coverage('${tableNameBAM}','NA12878.chr21', 'blocks', 100)").show(5)
+----------+-----+---+--------+
|contigName|start|end|coverage|
+----------+-----+---+--------+
Expand All @@ -267,8 +267,8 @@ bdg_coverage is a function that calculates depth of coverage for specified sampl
+----------+-----+---+--------+
Parameters for bdg_coverage functions:
resultType - blocks/bases
target - fixed-length windows/regions from bed file
resultType - blocks or bases (blocks by default)
target - size of fixed-length windows
ShowAllPositions - true/false. When set to true returns all positions in contig.


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11 changes: 8 additions & 3 deletions docs/source/index.rst
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Expand Up @@ -6,16 +6,16 @@
SeQuiLa User Guide
====================

SeQuiLa is an ANSI-SQL compliant solution for efficient genomic intervals querying and processing built on top of `Apache Spark`_. Range joins are bread and butter for NGS analysis but the high volume of data make them execute very slowly or even failing to compute.
SeQuiLa is an ANSI-SQL compliant solution for efficient genomic intervals querying and processing built on top of `Apache Spark`_. Range joins and depth of coverage computations are bread and butter for NGS analysis but the high volume of data make them execute very slowly or even failing to compute.

.. _Apache Spark: https://spark.apache.org/

* SeQuiLa is fast:

- genome-wide analyses in several minutes
- genome-wide analyses in less than a minute (for depth of coverage calculations) and several minutes (for range joins)
- 22x+ speedup over Spark default join operation
- up to 100x+ speedup for interval queries for BAM datasource using indexes (>= 0.4.1)
- 100% accuracy in functional tests against GRanges
- 100% accuracy in functional tests against GRanges and samtools

* SeQuiLa is elastic:

Expand Down Expand Up @@ -85,6 +85,11 @@ Example.scala
.. rubric:: Release notes:

0.5

- new result type (fixed lenght windows) for depth of coverage calculations


0.4.1

- a new highly-optimized `mosdepth <https://github.com/brentp/mosdepth>`_ distributed implementation for depth of coverage calculations
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Expand Up @@ -86,7 +86,7 @@ class CoverageTestSuite extends FunSuite with DataFrameSuiteBase with BeforeAndA
SequilaRegister.register(session)

val windowLength = 100
val bdg = session.sql(s"SELECT * FROM bdg_coverage('${tableNameMultiBAM}','NA12878', '', '${windowLength}')")
val bdg = session.sql(s"SELECT * FROM bdg_coverage('${tableNameMultiBAM}','NA12878', 'blocks', '${windowLength}')")

assert (bdg.count == 267)
assert (bdg.first().getInt(1) % windowLength == 0) // check for fixed window start position
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