Phelimb
commented
9 years ago The offending / missing line looks like this in src/predictor/core/file_reader.c.
-bash-4.1$ git diff src/predictor/core/file_reader.c diff --git a/src/predictor/core/file_reader.c b/src/predictor/core/file_reader.c index 6f8246b..c6ccb5f 100644 --- a/src/predictor/core/file_reader.c +++ b/src/predictor/core/file_reader.c @@ -1397,7 +1397,7 @@ void load_se_filelist_into_graph_colour(
{
- qual_thresh += ascii_fq_offset;
-
// qual_thresh += ascii_fq_offset;
/* COMMENT_OUT_DURING_TESTS printf(is_colour_list ? "Load single-ended sequence colour list\n" -bash-4.1$
qual_thresh += ascii_fq_offset; occurs in load_se_filelist_into_graph_colour()
but not in load_se_seq_data_into_graph_colour.
Options to make consistent would be either comment out the line in load_se_filelist_into_graph_colour() and optionally add to load_se_seq_data_into_graph_colour().
iqbal-lab
--file Command: /home/phelimb/myKrobe-predictor/bin/Mykrobe.predictor.staph --file /Net/wombat/dipro/mmm/gorm/v3/dat/Saur/stampy/00003000/C00003100_R00000022.bam --install_dir /home/phelimb/myKrobe-predictor --format JSON Start to load bin at Mon Sep 22 15:06:41 2014 Finished to load bin Mon Sep 22 15:06:42 2014 Start to load data Mon Sep 22 15:06:42 2014 Finished load data Mon Sep 22 15:08:01 2014 Got 4.000000 percent of cat, median covg 44.000000 { "species": { "S.aureus": "Major" }, "susceptibility" :{ "Gentamicin": "S", "Penicillin": "R", "Methicillin": "R", "Trimethoprim": "S", "Erythromycin": "S", "FusidicAcid": "S", "Ciprofloxacin": "R", "Rifampicin": "S", "Tetracycline": "S", "Vancomycin": "S", "Mupirocin": "S", "Clindamycin": "S" }, "called_variants" :{ "gyrA_S84L" :{ "R_cov": "100", "S_cov": "0" }, }, "called_genes" :{ "blaZ" :{ "cov": "65" }, "mecA" :{ "cov": "99" }, }, "virulence_toxins" :{ "PVL": "negative" } }
--list
Command: /home/phelimb/myKrobe-predictor/bin/Mykrobe.predictor.staph --list /data2/users/zam/staph_amr/filelists/C00003100.filelist --install_dir /home/phelimb/myKrobe-predictor/ --format JSON Start to load bin at Mon Sep 22 15:06:33 2014 Finished to load bin Mon Sep 22 15:06:34 2014 Start to load data Mon Sep 22 15:06:34 2014
Finished load data Mon Sep 22 15:07:51 2014 Got 4.000000 percent of cat, median covg 43.000000 { "species": { "S.aureus": "Major" }, "susceptibility" :{ "Gentamicin": "S", "Penicillin": "R", "Methicillin": "R", "Trimethoprim": "S", "Erythromycin": "S", "FusidicAcid": "Inconclusive", "Ciprofloxacin": "R", "Rifampicin": "S", "Tetracycline": "S", "Vancomycin": "S", "Mupirocin": "S", "Clindamycin": "S" }, "called_variants" :{ "gyrA_S84L" :{ "R_cov": "100", "S_cov": "0" }, }, "called_genes" :{ "blaZ" :{ "cov": "64" }, "mecA" :{ "cov": "99" }, }, "virulence_toxins" :{ "PVL": "negative" } }
/Net/wombat/dipro/mmm/gorm/v3/dat/Saur/stampy/00003000/C00003100_R00000022.bam