Refactor: Use only local files. Use chr19 in test_files.

Change config.yaml, prepare.smk, genome_process.sh and filter_anno_gtf.sh to use local files.
Add new annotation test files for chr19.
Change .md5 to these new outputs.

Closes #34

RUNS/JOB/map/intermediate_files.txt

-results/small_input/formatted.fasta
-results/small_input/header_sorted_catMappings.sam
-results/small_input/fa/reads.fa
-results/small_input/GenomeMappings.sam
-results/small_input/segemehlTranscriptome_map.sam
-results/small_input/noheader_GenomeMappings.sam
-results/small_input/oligoGenome_map.fa
-results/small_input/cutted.fasta
-results/small_input/segemehlGenome_map.sam
-results/small_input/oligoTranscriptome_converted.sam
-results/small_input/nhfiltered_GenomeMappings.sam
-results/small_input/oligoTranscriptome_map.fa
-results/small_input/oligoTranscriptome_report.txt
-results/small_input/TransToGen.sam
-results/small_input/concatenated_header_catMappings.sam
-results/small_input/oligoGenome_converted.sam
-results/small_input/TranscriptomeMappings.sam
-results/small_input/noheader_TranscriptomeMappings.sam
-results/small_input/oligoTranscriptome_sorted.fa
-results/small_input/collapsed.fasta
-results/small_input/catMappings.sam
-results/small_input/filtered_for_oligomap.fasta
-results/small_input/oligoGenome_sorted.fa
-results/small_input/nhfiltered_TranscriptomeMappings.sam
-results/small_input/oligoGenome_report.txt
\ No newline at end of file
+results/test_lib/formatted.fasta
+results/test_lib/header_sorted_catMappings.sam
+results/test_lib/fa/reads.fa
+results/test_lib/GenomeMappings.sam
+results/test_lib/segemehlTranscriptome_map.sam
+results/test_lib/noheader_GenomeMappings.sam
+results/test_lib/oligoGenome_map.fa
+results/test_lib/cutted.fasta
+results/test_lib/segemehlGenome_map.sam
+results/test_lib/oligoTranscriptome_converted.sam
+results/test_lib/nhfiltered_GenomeMappings.sam
+results/test_lib/oligoTranscriptome_map.fa
+results/test_lib/oligoTranscriptome_report.txt
+results/test_lib/TransToGen.sam
+results/test_lib/concatenated_header_catMappings.sam
+results/test_lib/oligoGenome_converted.sam
+results/test_lib/TranscriptomeMappings.sam
+results/test_lib/noheader_TranscriptomeMappings.sam
+results/test_lib/oligoTranscriptome_sorted.fa
+results/test_lib/collapsed.fasta
+results/test_lib/catMappings.sam
+results/test_lib/filtered_for_oligomap.fasta
+results/test_lib/oligoGenome_sorted.fa
+results/test_lib/nhfiltered_TranscriptomeMappings.sam
+results/test_lib/oligoGenome_report.txt
\ No newline at end of file