Release 0.8 alpha

.gitignore

@@ -1,9 +1,9 @@
 bin
 manual/sondovac_manual.brf
 manual/sondovac_manual.kilepr
-manual/sondovac_manual.tex.backup
 pkgs/linux32b
 pkgs/linux64b
 pkgs/macosx
 src
 *~
+*.backup

.info

@@ -1,2 +1,2 @@
-CURRENTVERSION=0.7
-NEWVERSION=https://github.com/V-Z/sondovac/releases/download/v0.7-alpha/sondovac-0.7-alpha.zip
+CURRENTVERSION=0.8
+NEWVERSION=https://github.com/V-Z/sondovac/releases/download/v0.8-alpha/sondovac-0.8-alpha.zip

CHANGELOG

@@ -1,30 +1,30 @@
 Sondovač changelog
 
-Version 0.8 alpha release 2015-09-09
+Version 0.8 alpha released 2015-10-09
 ================================================================================
 
 * Usage of mitochondrial reference sequence is optional
 * Better formatting of script messages
 * Various fixes and enhancements
 
 
-Version 0.7 alpha release 2015-09-06
+Version 0.7 alpha released 2015-10-06
 ================================================================================
 
 * Fixed reported problems with sed differences among Linux and Mac OS X
 * Added more exhaustive documentation
 * Various fixes and enhancements
 
 
-Version 0.6 alpha release 2015-08-10
+Version 0.6 alpha released 2015-08-10
 ================================================================================
 
 * Fixed problems with some versions of output of Geneious
 * Better compilation and installation of required additional software packages
 * Various fixes and enhancements
 
 
-Version 0.5 alpha release 2015-07-24
+Version 0.5 alpha released 2015-07-24
 ================================================================================
 
 * First public release, early alpha stage

INSTALL

@@ -1,4 +1,4 @@
-Sondovač 0.6 Install instructions
+Sondovač 0.8 Install instructions
 
 Requirements to run Sondovač
 ================================================================================

LICENSE

@@ -1,4 +1,4 @@
-Sondovač 0.6 Licenses
+Sondovač 0.8 Licenses
 
 The set of BASH scripts Sondovač is licensed under GNU General Public License
 version 3. List of licenses of included software is in following table (see

README

@@ -1,7 +1,8 @@
-Sondovač 0.6 Basic help
+Sondovač 0.8 Basic help
 
-Sondovač is a script to create orthologous low-copy nuclear probes from 
-transcriptome and genome skim data for target enrichment.
+Sondovač (English pronunciation is "Sondovach".) is a script to create 
+orthologous low-copy nuclear probes from transcriptome and genome skim data for 
+target enrichment.
 
 
 Script summary
@@ -333,8 +334,10 @@ Script sondovac_part_a.sh creates the following files:
       of plastid origin)
 4)  *_genome_skim_data_no_cp_reads* - Genome skim data without cpDNA reads
 5)  *_genome_skim_data_no_cp_no_mt_reads.bam - SAM converted to BAM (removal of 
-      reads of mitochondrial origin)
-6)  *_genome_skim_data_no_cp_no_mt_reads* - Genome skim data without mtDNA reads
+      reads of mitochondrial origin) - only if mitochondriome reference 
+      sequence was used
+6)  *_genome_skim_data_no_cp_no_mt_reads* - Genome skim data without mtDNA 
+      reads - only if mitochondriome reference sequence was used
 7)  *_combined_reads_co_cp_no_mt_reads* - Combined paired-end genome skim reads
 8)  *_blat_unique_transcripts_versus_genome_skim_data.pslx - Output of BLAT 
       (matching of the unique transcripts and the filtered, combined genome 
@@ -364,7 +367,7 @@ Script sondovac_part_b.sh creates following files:
 2) *_similarity_test2 - Contigs that comprise exons ≥ bait length and have a 
      certain total locus length (in the Oxalis case ≥600 bp)
 3) *_target_enrichment_probe_sequences.fasta - Probes in FASTA
-4) *.target_enrichment_probe_sequences_final.pslx - Final probes ready for bait 
+4) *.possible_cp_dna_genes_in_probe_set.pslx - Final probes ready for bait 
      synthesis
 
 
@@ -409,6 +412,20 @@ Leebens-Mack J and Wong G K-S (2014) Data access for the 1,000 Plants (1KP)
 project. GigaScience 3:17, http://www.gigasciencejournal.com/content/3/1/17/
 
 
+Record output of Sondovač
+================================================================================
+
+To record whole output of Sondovač script (regardless parameters used) use 
+utility "tee". It will produce plain text output with everything printed to the 
+screen. It can be useful for reference or explorations is something went wrong. 
+Use it as follows:
+
+./sondovac_part_a.sh | tee records.log
+
+You can use any command line arguments, script will behave as usually. Plain 
+text file "records.log" will then contain all its output.
+
+
 License
 ================================================================================
 

geneious_column_separator.pl

@@ -9,6 +9,7 @@
 # Read provided file name
 my $GENEIOUSFILE = $ARGV[0];
 my $GENEIOUSFILENAME = basename($GENEIOUSFILE, ".tsv");
+
 # Check if it is readable
 open(FH, "< $GENEIOUSFILE") || die "Cannot open $GENEIOUSFILE for reading: $!";
 my @array = <FH>;