git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@69141 bc3139a8-67e5-0310-9ffc-ced21a209358
Michael Lawrence authored on 06/09/2012 12:02:00
| ... | ... |
@@ -44,26 +44,39 @@ setMethod("gsnap", c("character", "characterORNULL", "GsnapParam"),
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| 44 | 44 |
### |
| 45 | 45 |
|
| 46 | 46 |
.gsnap <- function(db, dir = NULL, part = NULL, input_buffer_size = 1000L, |
| 47 |
- barcode_length = 0L, pc_linefeeds = FALSE, |
|
| 48 |
- orientation = c("FR", "RF", "FF"), gunzip = FALSE,
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|
| 47 |
+ barcode_length = 0L, |
|
| 48 |
+ orientation = c("FR", "RF", "FF"),
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|
| 49 |
+ fastq_id_start = NULL, fastq_id_end = NULL, |
|
| 50 |
+ filter_chastity = c("off", "either", "both"),
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|
| 51 |
+ gunzip = FALSE, |
|
| 49 | 52 |
batch = c("2", "0", "1", "3", "4"), max_mismatches = NULL,
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| 50 | 53 |
query_unk_mismatch = 0L, genome_unk_mismatch = 1L, |
| 54 |
+ terminal_threshold = 2L, |
|
| 51 | 55 |
indel_penalty = 2L, |
| 52 | 56 |
indel_endlength = 4L, max_middle_insertions = 9L, |
| 53 | 57 |
max_middle_deletions = 30L, max_end_insertions = 3L, |
| 54 | 58 |
max_end_deletions = 6L, suboptimal_levels = 0L, |
| 55 | 59 |
adapter_string = NULL, |
| 56 |
- trim_mismatch_score = -3L, snpsdir = NULL, use_snps = NULL, |
|
| 60 |
+ trim_mismatch_score = -3L, trim_indel_score = -4L, |
|
| 61 |
+ snpsdir = NULL, use_snps = NULL, |
|
| 57 | 62 |
cmetdir = NULL, atoidir = NULL, |
| 58 |
- mode = c("standard", "cmet", "atoi"),
|
|
| 59 |
- tallydir = NULL, use_tally = NULL, nthreads = NULL, |
|
| 60 |
- novelsplicing = FALSE, splicing = NULL, |
|
| 61 |
- novel_doublesplices = FALSE, localsplicedist = 200000L, |
|
| 63 |
+ mode = c("standard", "cmet-stranded", "cmet-nonstranded",
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|
| 64 |
+ "atoi-stranded", "atoi-nonstranded"), |
|
| 65 |
+ tallydir = NULL, use_tally = NULL, |
|
| 66 |
+ use_runlength = NULL, nthreads = NULL, |
|
| 67 |
+ gmap_mode = "pairsearch,terminal,improve", |
|
| 68 |
+ trigger_score_for_gmap = 5L, max_gmap_pairsearch = 3L, |
|
| 69 |
+ max_gmap_improvement = 3L, microexon_spliceprob = 0.90, |
|
| 70 |
+ novelsplicing = FALSE, splicingdir = NULL, |
|
| 71 |
+ use_splicing = NULL, ambig_splice_noclip = FALSE, |
|
| 72 |
+ localsplicedist = 200000L, |
|
| 62 | 73 |
local_splice_penalty = 0L, distant_splice_penalty = 3L, |
| 63 | 74 |
distant_splice_endlength = 16L, |
| 64 | 75 |
shortend_splice_endlength = 2L, |
| 76 |
+ distant_splice_identity = 0.95, |
|
| 77 |
+ antistranded_penalty = 0L, merge_distant_samechr = FALSE, |
|
| 65 | 78 |
pairmax_dna = 1000L, |
| 66 |
- pairmax_rna = 200000L, pairexpect = 200L, |
|
| 79 |
+ pairmax_rna = 200000L, pairexpect = 200L, pairdev = 25L, |
|
| 67 | 80 |
quality_protocol = c("sanger", "illumina"),
|
| 68 | 81 |
quality_zero_score = 33L, quality_print_shift = 0L, |
| 69 | 82 |
mapq_unique_score = NULL, npaths = 100L, |
| ... | ... |
@@ -71,9 +84,12 @@ setMethod("gsnap", c("character", "characterORNULL", "GsnapParam"),
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| 71 | 84 |
show_rediff = FALSE, clip_overlap = FALSE, |
| 72 | 85 |
print_snps = FALSE, failsonly = FALSE, |
| 73 | 86 |
nofails = FALSE, fails_as_input = FALSE, |
| 74 |
- format = NULL, split_output = NULL, no_sam_headers = FALSE, |
|
| 87 |
+ format = NULL, split_output = NULL, |
|
| 88 |
+ output_buffer_size = 1000L, |
|
| 89 |
+ no_sam_headers = FALSE, |
|
| 75 | 90 |
sam_headers_batch = NULL, read_group_id = NULL, |
| 76 |
- read_group_name = NULL, version = FALSE, |
|
| 91 |
+ read_group_name = NULL, read_group_library = NULL, |
|
| 92 |
+ read_group_platform = NULL, version = FALSE, |
|
| 77 | 93 |
.input_a = NULL, .input_b = NULL, |
| 78 | 94 |
.redirect = NULL ## e.g., > gsnap.sam |
| 79 | 95 |
) |