|
file | adapters.c |
| sequence manipulation for alignment
|
|
file | bloom.c |
| functions that implement the bloom filter
|
|
file | city.c |
| functions for hashin strings, C translation of cityhash (C++, google)
|
|
file | fa_read.c |
| reads in and stores fasta files
|
|
file | fopen_gen.c |
| Uncompress/compress input/output files using pipes.
|
|
file | fq_read.c |
| fastq entries manipulations (read/write)
|
|
file | init_makeBloom.c |
| Help dialog for makeBloom and initialization of the command line arguments.
|
|
file | init_makeTree.c |
| Help dialog for makeTree and initialization of the command line arguments.
|
|
file | init_Qreport.c |
| Help dialog for Qreport and initialization of the command line arguments.
|
|
file | init_Sreport.c |
| Help dialog for Sreport and initialization of the command line arguments.
|
|
file | init_trimFilter.c |
| help dialog for trimFilter and initialization of the command line arguments.
|
|
file | init_trimFilterDS.c |
| help dialog for trimFilterDS and initialization of the command line arguments.
|
|
file | io_trimFilter.c |
| buffer fq output, write summary file
|
|
file | Lmer.c |
| Manipulation of Lmers and sequences.
|
|
file | makeBloom.c |
| makeBloom main function
|
|
file | makeTree.c |
| makeTree main function
|
|
file | Qreport.c |
| QReport main function.
|
|
file | Rcommand_Qreport.c |
| get Rscript command for Qreport
|
|
file | Rcommand_Sreport.c |
| get Rscript command for Sreport
|
|
file | Sreport.c |
| Sreport main function.
|
|
file | stats_info.c |
| Construct the quality report variables and update them.
|
|
file | str_manip.c |
| functions that do string manipulation
|
|
file | struct_trimFilter.c |
| function that frees the memory of parTF (structure storing the trimFilter/trimFilterDS input arguments).
|
|
file | tree.c |
| Construction of tree, check paths, write tree, read in tree.
|
|
file | trim.c |
| trims/filter sequences after Quality, N's contaminations.
|
|
file | trimDS.c |
| trim adapters from double stranded data
|
|
file | trimFilter.c |
| trimFilter main function
|
|
file | trimFilterDS.c |
| trimFilterDS main function
|
|