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docs/index.md

@@ -47,17 +47,17 @@ The usage can be provided by passing `-h` at the command line.
 ```
 A fast, accurate and versatile tool for long-read transcript quantification.
 
-Usage: oarfish [OPTIONS] --alignments <ALIGNMENTS> --output <OUTPUT>
+Usage: oarfish [OPTIONS] --output <OUTPUT> <--alignments <ALIGNMENTS>|--reads <READS>>
 
 Options:
       --quiet
           be quiet (i.e. don't output log messages that aren't at least warnings)
       --verbose
           be verbose (i.e. output all non-developer logging messages)
-  -a, --alignments <ALIGNMENTS>
-          path to the file containing the input alignments
   -o, --output <OUTPUT>
           location where output quantification file should be written
+      --single-cell
+          input is assumed to be a single-cell BAM and to have the `CB:z` tag for all read records
   -j, --threads <THREADS>
           maximum number of cores that the oarfish can use to obtain binomial probability [default: 1]
       --num-bootstraps <NUM_BOOTSTRAPS>
@@ -67,21 +67,43 @@ Options:
   -V, --version
           Print version
 
+alignment mode:
+  -a, --alignments <ALIGNMENTS>  path to the file containing the input alignments
+
+raw read mode:
+      --reads <READS>          path to the file containing the input reads
+      --reference <REFERENCE>  path to the file containing the reference transcriptome (or existing index) against which to map
+      --index-out <INDEX_OUT>  path where minimap2 index will be written (if provided)
+      --seq-tech <SEQ_TECH>    sequencing technology in which to expect reads if using mapping based mode [possible values: ont-cdna, ont-drna, pac-bio, pac-bio-hifi]
+      --best-n <BEST_N>        maximum number of secondary mappings to consider when mapping reads to the transcriptome [default: 100]
+
 filters:
       --filter-group <FILTER_GROUP>
           [possible values: no-filters, nanocount-filters]
   -t, --three-prime-clip <THREE_PRIME_CLIP>
-          maximum allowable distance of the right-most end of an alignment from the 3' transcript end [default: 4294967295]
+          maximum allowable distance of the right-most end of an alignment from the 3' transcript end [default: *4294967295]
   -f, --five-prime-clip <FIVE_PRIME_CLIP>
-          maximum allowable distance of the left-most end of an alignment from the 5' transcript end [default: 4294967295]
+          maximum allowable distance of the left-most end of an alignment from the 5' transcript end [default: *4294967295]
   -s, --score-threshold <SCORE_THRESHOLD>
-          fraction of the best possible alignment score that a secondary alignment must have for consideration [default: 0.95]
+          fraction of the best possible alignment score that a secondary alignment must have for consideration [default: *0.95]
   -m, --min-aligned-fraction <MIN_ALIGNED_FRACTION>
-          fraction of a query that must be mapped within an alignemnt to consider the alignemnt valid [default: 0.5]
+          fraction of a query that must be mapped within an alignemnt to consider the alignemnt valid [default: *0.5]
   -l, --min-aligned-len <MIN_ALIGNED_LEN>
-          minimum number of nucleotides in the aligned portion of a read [default: 50]
+          minimum number of nucleotides in the aligned portion of a read [default: *50]
   -d, --strand-filter <STRAND_FILTER>
           only alignments to this strand will be allowed; options are (fw /+, rc/-, or both/.) [default: .]
+
+coverage model:
+      --model-coverage         apply the coverage model
+  -b, --bin-width <BIN_WIDTH>  width of the bins used in the coverage model [default: 100]
+
+EM:
+      --max-em-iter <MAX_EM_ITER>
+          maximum number of iterations for which to run the EM algorithm [default: 1000]
+      --convergence-thresh <CONVERGENCE_THRESH>
+          maximum number of iterations for which to run the EM algorithm [default: 0.001]
+  -q, --short-quant <SHORT_QUANT>
+          location of short read quantification (if provided)
 ```
 
 ## Input to `oarfish`