# HG changeset patch
# User charles-bernard
# Date 1476191639 14400
# Node ID 136bcda2a3de40c3795e8b9f6b53bcd839425cff
# Parent  f1b2c73cc9c1e13cf1e4009d6027ec211e9d43a8
Uploaded

diff -r f1b2c73cc9c1 -r 136bcda2a3de test-data/alfa_toy-Biofeatures Distribution.pdf
Binary file test-data/alfa_toy-Biofeatures Distribution.pdf has changed
diff -r f1b2c73cc9c1 -r 136bcda2a3de test-data/alfa_toy.bam
Binary file test-data/alfa_toy.bam has changed
diff -r f1b2c73cc9c1 -r 136bcda2a3de test-data/alfa_toy.bedgraph
--- a/test-data/alfa_toy.bedgraph	Tue Oct 11 09:13:18 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
-Chr1	149	199	2
-Chr1	299	349	1
-Chr1	499	549	6
-Chr1	1099	1149	1
diff -r f1b2c73cc9c1 -r 136bcda2a3de test-data/alfa_toy.categories_counts
--- a/test-data/alfa_toy.categories_counts	Tue Oct 11 09:13:18 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,5 +0,0 @@
-#Category,biotype	Counts_in_bam	Size_in_genome
-CDS,protein_coding	300.0	624.0
-five_prime_utr,protein_coding	75.0	250.5
-three_prime_utr,protein_coding	25.0	126.5
-intergenic,intergenic	100.0	249.0
diff -r f1b2c73cc9c1 -r 136bcda2a3de test-data/alfa_toy.gtf
--- a/test-data/alfa_toy.gtf	Tue Oct 11 09:13:18 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-Chr1	ensembl_havana	gene	250	1250	.	+	.	gene_id "ENSMUSG00000051951"; gene_biotype "protein_coding";
-Chr1	ensembl_havana	transcript	250	1250	.	+	.	gene_id "ENSMUSG00000051951"; gene_biotype "protein_coding";
-Chr1	ensembl_havana	exon	375	1000	.	+	.	gene_id "ENSMUSG00000051951"; gene_biotype "protein_coding";
-Chr1	ensembl_havana	CDS	375	1000	.	+	0	gene_id "ENSMUSG00000051951"; gene_biotype "protein_coding";
-Chr1	ensembl_havana	five_prime_utr	250	375	.	-	.	gene_id "ENSMUSG00000051951"; gene_biotype "protein_coding";
-Chr1	ensembl_havana	three_prime_utr	1000	1250	.	-	.	gene_id "ENSMUSG00000051951"; gene_biotype "protein_coding";
diff -r f1b2c73cc9c1 -r 136bcda2a3de test-data/alfa_toy.stranded.index
--- a/test-data/alfa_toy.stranded.index	Tue Oct 11 09:13:18 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,11 +0,0 @@
-#Chr1	1250
-Chr1	249	374	+	protein_coding:gene,transcript
-Chr1	249	374	-	protein_coding:five_prime_utr
-Chr1	374	375	+	protein_coding:exon,CDS
-Chr1	374	375	-	protein_coding:five_prime_utr,three_prime_utr
-Chr1	375	999	+	protein_coding:exon,CDS
-Chr1	375	999	-	antisense
-Chr1	999	1000	+	protein_coding:exon,CDS
-Chr1	999	1000	-	protein_coding:three_prime_utr
-Chr1	1000	1250	+	protein_coding:gene,transcript
-Chr1	1000	1250	-	protein_coding:five_prime_utr,three_prime_utr,exon,CDS
diff -r f1b2c73cc9c1 -r 136bcda2a3de test-data/alfa_toy.unstranded.index
--- a/test-data/alfa_toy.unstranded.index	Tue Oct 11 09:13:18 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-#Chr1	1250
-Chr1	249	374	.	protein_coding:five_prime_utr,gene,transcript
-Chr1	374	375	.	protein_coding:five_prime_utr,three_prime_utr,exon,CDS
-Chr1	375	999	.	protein_coding:exon,CDS
-Chr1	999	1000	.	protein_coding:three_prime_utr,exon,CDS
-Chr1	1000	1250	.	protein_coding:five_prime_utr,exon,CDS,three_prime_utr,gene,transcript
diff -r f1b2c73cc9c1 -r 136bcda2a3de tool-data/alfa_genomes_indexes.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/alfa_genomes_indexes.loc.sample	Tue Oct 11 09:13:59 2016 -0400
@@ -0,0 +1,5 @@
+#<species>	<version>	<release>	<value>	<dbkey>	<name>	<prefix>
+Arabidopsis_thaliana	TAIR10	30	Arabidopsis_t_TAIR10_30	Arabidopsis_t_TAIR10_30	Arabidopsis thaliana: TAIR10	<path_to_alfa_indexes>/Arabidopsis_thaliana.TAIR10.30
+Drosophila_melanogaster	dm6	30	Drosophila_m_dm6_30	Drosophila_m_dm6_30	Drosophila melanogaster: dm6	<path_to_alfa_indexes>/Drosophila_melanogaster.BDGP6.30
+Homo_sapiens	v38	82	Homo_s_v38_82	Homo_s_v38_82	Homo sapiens: v38	<path_to_alfa_indexes>/Homo_sapiens.GRCh38.82
+Mus_musculus	v38	83	Mus_m_v38_83	Mus_m_v38_83	Mus musculus: v38 	<path_to_alfa_indexes>/Mus_musculus.GRCm38.83.chr
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