Merge pull request #20 from vivekbhr/master

updates for conda

CHANGELOG.md

@@ -1,3 +1,7 @@
+## v0.3.4 (25 May 2018)
+ - made the installation changes for conda
+ - fixed --dir name in tag2sort
+
 ## v0.3.3_dev (04 Sept 2017)]
 
 - Fixed output-path handling for paired-end and Hi-C mode (was only working for single-end files).
@@ -13,8 +17,8 @@
 
 - In certain cases, specific SNPs were only used for the allele assignment if they were methylated. In more detail: In cases where the SNP was either C/G (REF/ALT) or G/C (REF/ALT), and the read was on the opposing strand, only the methylated form of the C on the reverse strand had previously been allowed as a valid expected base. This has now been changed so that both G and A are considered valid for the strain containing a G at the SNP position (see also this [issue](https://github.com/FelixKrueger/SNPsplit/issues/11)).
 
-- Changed the way in which C>T SNPs are handled in the allele-tagging report (note that this was merely a report/interpretation thing and did not have any effect the on the actual results). Previously, reads without a call for genome 1 or genome 2 had been listed as: 
-_reads did not contain one of the expected bases at known SNP positions_. 
+- Changed the way in which C>T SNPs are handled in the allele-tagging report (note that this was merely a report/interpretation thing and did not have any effect the on the actual results). Previously, reads without a call for genome 1 or genome 2 had been listed as:
+_reads did not contain one of the expected bases at known SNP positions_.
 In a bisulfite setting this also included C>T SNPs however, and hence the number could have been rather high (>10%). I have now changed this so that reads which had at least one C>T SNP and were unassignable at the same time are scored differently:
 _reads that were unassignable contained C>T SNPs preventing the assignment_
 
@@ -26,7 +30,7 @@ _reads that were unassignable contained C>T SNPs preventing the assignment_
 #### SNPsplit
 -----
 
-- Changed the `samtools` command throughout SNPsplit to now correctly use the path supplied by the user with `--samtools_path`. Thanks to Kenzo Hillion for spotting this (see [here](https://github.com/FelixKrueger/SNPsplit/commit/77286e1e1ad686ef5e6efcdbda826fcd5e4a5ce2)). 
+- Changed the `samtools` command throughout SNPsplit to now correctly use the path supplied by the user with `--samtools_path`. Thanks to Kenzo Hillion for spotting this (see [here](https://github.com/FelixKrueger/SNPsplit/commit/77286e1e1ad686ef5e6efcdbda826fcd5e4a5ce2)).
 
 - Option `--genome_build [NAME]` should now work as intended (used to be `--build` only).
 
@@ -59,7 +63,7 @@ _reads that were unassignable contained C>T SNPs preventing the assignment_
 
 - Option `--genome_build [NAME]` should now work as intended (used to be `--build` only).
 
-- Added a new version of the genome preparation script that can deal with the latest version of the VCF file for the old NCBIM37 genome build (`mgp.v2.snps.annot.reformat.vcf.gz`). The script is called `SNPsplit_genome_preparation_v2VCF` and may be found in the folder `outdated_VCF_versions` on Github. 
+- Added a new version of the genome preparation script that can deal with the latest version of the VCF file for the old NCBIM37 genome build (`mgp.v2.snps.annot.reformat.vcf.gz`). The script is called `SNPsplit_genome_preparation_v2VCF` and may be found in the folder `outdated_VCF_versions` on Github.
 
 
 ## v0.3.1 (18 Jul 2016)
@@ -125,4 +129,3 @@ SNPsplit_genome_preparation may be run in two different modes:
 
 
 Feedback or bugs can be sent to: [email protected]
-