tinyRNA provides an all-in-one solution for precision analysis of sRNA-seq data. At the core of tinyRNA is a highly flexible counting utility, tiny-count, that allows for hierarchical assignment of reads to features based on positional information, extent of feature overlap, 5’ nucleotide, length, and strandedness.
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tiny-count: minor consistency changes in outputs #316
Improved Auto-documentation during tiny-count Standalone Runs
File outputs produced by tiny-count are now stored in a timestamped run directory during standalone runs. Outputs produced during pipeline runs with tinyRNA, on the other hand, remain unchanged by this PR and continue to be written to the working directory. The run directory is named tiny-count_{timestamp} where {timestamp} is the date and time at the start of the run. Within the run directory is a config subdirectory which holds a copy of the configuration files for auto-documentation. Paths in these files are selectively updated just as they are during end-to-end runs with tinyRNA. These changes make tiny-count standalone outputs more consistent with those produced during tinyRNA pipeline runs.
Note: If the string {timestamp} is passed via tiny-count's --out-prefix argument, it is no longer substituted with the run's date and time due to the changes above
Decollapsed SAM File Compatibility
If the user requests decollapsed outputs, the QNAME field of each alignment will have the sequence's count stripped so that it remains compatible with tiny-count. The use of decollapsed outputs as inputs to tiny-count is inadvisable since it would increase runtimes with no added benefit, but we wanted to ensure it is possible nonetheless.
Improved Auto-documentation during tiny-count Standalone Runs
File outputs produced by tiny-count are now stored in a timestamped run directory during standalone runs. Outputs produced during pipeline runs with tinyRNA, on the other hand, remain unchanged by this PR and continue to be written to the working directory. The run directory is named
tiny-count_{timestamp}where{timestamp}is the date and time at the start of the run. Within the run directory is aconfigsubdirectory which holds a copy of the configuration files for auto-documentation. Paths in these files are selectively updated just as they are during end-to-end runs with tinyRNA. These changes make tiny-count standalone outputs more consistent with those produced during tinyRNA pipeline runs.Decollapsed SAM File Compatibility
If the user requests decollapsed outputs, the QNAME field of each alignment will have the sequence's count stripped so that it remains compatible with tiny-count. The use of decollapsed outputs as inputs to tiny-count is inadvisable since it would increase runtimes with no added benefit, but we wanted to ensure it is possible nonetheless.
Closes #310