compomics-utilities

compomics-utilities copied to clipboard

WaveletTree CPU usage

2

WaveletTree.rangeQuery regularly uses excessive CPU time (10+ cores used when calling with -threads 1), I believe due to JVM overhead in handling the recursion. Is it possible to rewrite this...

heckendorfc

The batch loading from the database has been removed, which makes the loading of many object very slow, which for example impacts the exports for large projects as they are...

hbarsnes

PhosphoRS score without Annotations

1

Hi @mvaudel do you think would be possible to implement phosphoRS without the fragment annotations. That means if I give you a peptide sequence, spectrum, modification, and positions. ?

ypriverol

Semi-specific digestion in the IteratorFactory

6

Is there a way to do semi-tryptic digestion using the getSequenceIterator function from IteratorFactory?

wenbostar

PeptideMapper does not report peptide hits, but protein hits

1

given: a `peptide.csv` as > DKEKEK EKEKEK and a `protein.fasta` (expected hit in second line) as ``` >sp|Q95283|COX41_PIG Cytochrome c oxidase subunit 4 isoform 1, mitochondrial (Fragment) OS=Sus scrofa OX=9823...

cbielow

PeptideMapper crashes when peptide input file contains empty lines

1

Hi, invoking PeptideMapper with a peptide file with empty lines causes: ``` Start mapping using 1 threads 0% 10% 30% 50% 60%Error: mapping went wrong Exception in thread "main" java.lang.NullPointerException...

cbielow

PeptideMapper's result size varies from run to run with multiple threads

1

Hi, this is not necessarily a bug, but somewhat surprising nonetheless: invoking PeptideMapper without the `-c` option (which will use all CPU cores of the system) results in different output...

cbielow

PeptideMapper does not find occurences with more than one 'X'

1

Hi, I'm doing some testing for PeptideMapper and found a restriction, namely it seems to consider at most one 'X' per match. Here is a small demo: Given proteins `PEPTIDEMAPPER_TEST.fasta`:...

cbielow