Linx: renamed from sv-linx

README.md

@@ -9,7 +9,7 @@ More detailed descriptions of the following algorithms are available from the li
  - [COBALT](./cobalt/README.md)
  - [GRIPSS](./gripss/README.md)
  - [PURPLE](./purple/README.md)
- - [Linx](./sv-linx/README.md)
+ - [Linx](./linx/README.md)
  - [Isofox](./isofox/README.md)
  - [SERVE](./serve/README.md)
  - [PROTECT](./protect/README.md)

isofox/README.md

@@ -195,7 +195,7 @@ The output file is approximately 120MB.
 To annotate SVs with gene information and to support fusion detection, ISOFOX uses gene, transcript, exon and protein domain information from the Ensembl database. 
 To improve performance, this data is first extracted into 4 CSV data files and then loaded into memory each time ISOFOX runs.
 
-These files can be downloaded from the Hartwig resources page, or generated using the Hartwig LINX application (see https://github.com/hartwigmedical/hmftools/blob/master/sv-linx/README.md for instructions).
+These files can be downloaded from the Hartwig resources page, or generated using the Hartwig LINX application (see https://github.com/hartwigmedical/hmftools/blob/master/linx/README.md for instructions).
 
 Note that the ensembl gene cache currently generates for standard autosomes and sex chromosomes only (alt contigs and MT chromosomes are excluded).
 

sv-linx/README.md → linx/README.md

@@ -100,7 +100,7 @@ log_debug | logs in debug mode
 Single sample - Load SVs and purple data from file, upload Linx results to database:
 
 ```
-java -jar sv-linx.jar 
+java -jar linx.jar 
     -sample SAMPLE_ID 
     -ref_genome_version 37
     -sv_vcf /path_to_purple_vcf/
@@ -121,7 +121,7 @@ java -jar sv-linx.jar
 Single sample - query SVs and purple data from database, upload Linx results to database:
 
 ```
-java -jar sv-linx.jar 
+java -jar linx.jar 
     -sample SAMPLE_ID 
     -db_url [db_url] -db_user [username] -db_pass [password] 
     -output_dir /path_to_sample_data/ 
@@ -141,7 +141,7 @@ Cohort analysis - run all samples by sampleId in provided file, query SVs and pu
 Write Linx results to cohort files, no upload to database:
 
 ```
-java -jar sv-linx.jar 
+java -jar linx.jar 
     -sample cohort_sample_ids.csv
     -db_url [db_url] -db_user [username] -db_pass [password] 
     -output_dir /path_to_sample_data/ 
@@ -162,7 +162,7 @@ To improve performance, this data is first extracted into 4 CSV data files and t
 To generate these 4 data files, first run Linx with these command line options:
 
 ```
-java -cp sv-linx.jar com.hartwig.hmftools.linx.gene.GenerateEnsemblDataCache
+java -cp linx.jar com.hartwig.hmftools.linx.gene.GenerateEnsemblDataCache
     -ensembl_db [see below] -ensembl_user "anonymous" -ensembl_pass "" 
     -output_dir /path_to_write_data_files/ -ref_genome_version [37 or 38]
 ```

sv-linx/pom.xml → linx/pom.xml

@@ -8,9 +8,9 @@
         <version>local-SNAPSHOT</version>
     </parent>
 
-    <artifactId>sv-linx</artifactId>
+    <artifactId>linx</artifactId>
     <packaging>jar</packaging>
-    <version>${sv-linx.version}</version>
+    <version>${linx.version}</version>
     <name>HMF Tools - Linx</name>
 
     <dependencies>

pom.xml

@@ -23,7 +23,7 @@
         <module>cobalt</module>
         <module>purple</module>
         <module>sage</module>
-        <module>sv-linx</module>
+        <module>linx</module>
         <module>sv-tools</module>
         <module>virus-interpreter</module>
         <module>neo</module>
@@ -63,7 +63,7 @@
         <purple.version>3.1</purple.version>
         <gripss.version>1.11</gripss.version>
         <lilac.version>1.0</lilac.version>
-        <sv-linx.version>1.16</sv-linx.version>
+        <linx.version>1.16</linx.version>
         <sv-tools.version>1.0</sv-tools.version>
         <virus-interpreter.version>1.0</virus-interpreter.version>
         <health-checker.version>3.2</health-checker.version>
@@ -196,8 +196,8 @@
             </dependency>
             <dependency>
                 <groupId>com.hartwig</groupId>
-                <artifactId>sv-linx</artifactId>
-                <version>${sv-linx.version}</version>
+                <artifactId>linx</artifactId>
+                <version>${linx.version}</version>
             </dependency>
             <dependency>
                 <groupId>com.hartwig</groupId>

protect/README.md

@@ -35,12 +35,12 @@ gene inactivation is considered applicable in case of a deletion.
 
 #### Homozygous disruptions
 
-When a gene has been homozygously disrupted according to [LINX](../sv-linx/README.md), evidence is applicable when it has been defined 
+When a gene has been homozygously disrupted according to [LINX](../linx/README.md), evidence is applicable when it has been defined 
 on a gene level with event either inactivation, deletion or any mutation. 
 
 #### Fusions
 
-For fusions that are deemed reportable according to [LINX](../sv-linx/README.md) the following matching is performed:
+For fusions that are deemed reportable according to [LINX](../linx/README.md) the following matching is performed:
  - Evidence defined on a promiscuous gene level is always considered applicable if a fusion with that gene is reported either in 5' or 3' 
  position.
  - Evidence that is applicable on an exact fusion pair has to match with the actual fusion pair, and also has to match the (optional) 

purple/DriverCatalog.md

@@ -2,7 +2,7 @@
 
 If a gene panel is configured, PURPLE will compile a catalog of drivers including point mutations and copy number events.  To include point mutations in the driver catalog, the somatic VCF must be annotated with SnpEff.
 
-Running [LINX](https://github.com/hartwigmedical/hmftools/tree/master/sv-linx) enriches the PURPLE driver catalog with the addition of both homozygous disruption drivers and fusions
+Running [LINX](https://github.com/hartwigmedical/hmftools/tree/master/linx) enriches the PURPLE driver catalog with the addition of both homozygous disruption drivers and fusions
 
 ## Gene Panel Configuration
 

sv-tools/pom.xml

@@ -24,7 +24,7 @@
         </dependency>
         <dependency>
             <groupId>com.hartwig</groupId>
-            <artifactId>sv-linx</artifactId>
+            <artifactId>linx</artifactId>
         </dependency>
         <dependency>
             <groupId>org.jooq</groupId>