diff docs/todo.rst @ 14:628f82e72d72

Version as released on PyPI 0.1.0

--- a/docs/todo.rst	Fri Aug 21 12:37:54 2015 +0100
+++ b/docs/todo.rst	Wed Aug 26 16:37:10 2015 +0100
@@ -1,38 +1,6 @@
-Outline
--------
-Log information by default
-Errors to stderr
+Todo
+----
+* No way to check if input BAM is RNA-Seq/Ribo-Seq (plot will still be generated in either case).
+* Check if BAM is sorted.
 
 
-Arguments
----------
--b ribo_file
--f transcriptome_fasta 
--t transcript_name
--n rna_file
--l read_length
--s read_offset
--m html_file
--o output_path
--d debug
-
-Tests
------
-
-Check arguments
-...............
-* BAM file valid (should be indexed for fetch to work)
-* FASTA file should be valid
-* Transcript name should exist in both BAM and FASTA (riboplot: yes, ribocount: no).
-* If RNA file is provided, bedtools should exist in PATH
-* Read length should be a valid integer (must exist in BAM)
-* Read offset - positive integer (can't exceed ?)
-* Should be possible to get codon positions.
-
-
-Notes
------
-* No way to check if input BAM is RNA-Seq/Ribo-Seq (plot will still be generated in either case)
-* No way to check if BAM is sorted
-
-