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Correct errors in output and documentation

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efischer
2022-02-20 20:13:38 -06:00
parent 410f0ae547
commit 7558455f39
3 changed files with 10 additions and 11 deletions
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out/artifacts/BiGpairSEQ_Sim_jar/BiGpairSEQ_Sim.jar
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20
readme.md
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@@ -94,7 +94,7 @@ Options when making a Cell Sample file:
Files are in CSV format. Rows are distinct T cells, columns are sequences within the cells. Files are in CSV format. Rows are distinct T cells, columns are sequences within the cells.
Comments are preceded by `#` Comments are preceded by `#`
Structure: Structure example:
--- ---
# Sample contains 1 unique CDR1 for every 4 unique CDR3s. # Sample contains 1 unique CDR1 for every 4 unique CDR3s.
@@ -136,20 +136,20 @@ Every column represents an individual cell, containing four sequences, represent
Notice that the Alpha CDR1 is missing in the cell above, due to sequence dropout. Notice that the Alpha CDR1 is missing in the cell above, due to sequence dropout.
Dropouts are represented by replacing sequences with the value `-1`. Comments are preceded by `#` Dropouts are represented by replacing sequences with the value `-1`. Comments are preceded by `#`
Structure: Structure Example:
--- ---
``` ```
# Cell source file name: # Cell source file name: 4MilCells.csv
# Each row represents one well on the plate # Plate size: 96
# Plate size: # Error rate: 0.1
# Concentrations: # Concentrations: 10000 5000 500
# Lambda: # Lambda: 0.6
``` ```
| Well 1, cell 1 | Well 1, cell 2 | Well 1, cell 3| ... | | well 1 | well 2 | well 3| ... |
|---|---|---|---| |---|---|---|---|
| **Well 2, cell 1** | **Well 2, cell 2** | **Well 2, cell 3**| ... | | [105383, 786528, 959247, 925928] | [525902, 791533, -1, 866282] | [409236, 132303, 804465, 942261]| ... |
| **Well 3, cell 1** | **Well 3, cell 2** | **Well 3, cell 3**| ... | | [249930, 301502, 970003, 881099] | [523787, 552952, 997194, 970507]| [425363, 417411, 845399, -1]| ... |
| ... | ... | ... | ... | | ... | ... | ... | ... |
--- ---

1
src/main/java/PlateFileWriter.java
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@@ -89,7 +89,6 @@ public class PlateFileWriter {
CSVPrinter printer = new CSVPrinter(writer, plateFileFormat); CSVPrinter printer = new CSVPrinter(writer, plateFileFormat);
){ ){
printer.printComment("Cell source file name: " + sourceFileName); printer.printComment("Cell source file name: " + sourceFileName);
printer.printComment("Each row represents one well on the plate.");
printer.printComment("Plate size: " + size); printer.printComment("Plate size: " + size);
printer.printComment("Error rate: " + error); printer.printComment("Error rate: " + error);
printer.printComment("Concentrations: " + concenString); printer.printComment("Concentrations: " + concenString);