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bitseq 0.7.5+dfsg-5
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0.7.5
Improvements:
- parseAlignment adding option to mateNamesDiffer [!! add note that this can't be used with mixed alignments !!]

Bug fixes:
- estimateExpression didn't use more cores when number of chains was changed in parameters file.

0.7.4
[0.7.3] (bug in copying alignment)
[0.7.2]
[0.7.1]:
Improvements:
- parseAlignment can use *.m_alphas files generated by estimateVBExpression for expression estimates
- estimateHyperPar forces smoothing of hyperparameters by default
- enable excluding singletons (half alignments of paired reads) in parseAlignment[0.7.3]
- .prob file contains number of transcripts so estimateExpression does not need .tr file for correct transcript count[0.7.3]

Bug fixes:
- fixing problems related to parsing FASTA reads
  (and correctly assigning additional mismatches)
- fixed problem with half alignments being omitted from read distribution estimation[0.7.2]

0.7.0:
Improvements:
- estimateVBexpression provides new expression inference method using fast collapsed VB
- adding --unstranded flag to parseAlignment, to allow read pairs with various directions to be used
- changing computation of Rhat to produce better estimates

Bug fixes:
- adding -lpthread option for parseAlignment compilation, so that samtools links even without -fopenmp

[0.6.1]
0.6.0:
Improvements:
- thetaMeans contains variance of theta
- proper handling of bad alignments
- major speed improvement for parseAlignment on multiple CPUs
- getGeneExpression and getWithinGene expression can use 'external' TR->GE mapping or gene list
- getWithinGene changed so that transcripts keep order unless --groupByGene
- getGeneExpression produces gene info file with list of genes
- increased output precision in gGE and gWGE

Bug fixes:
- fixed major bug in getGeneExpression and getWithinGeneExpression
- fixed occasional underflow in effective length computation

0.5.3:
Improvements:
- parseAlignment should be compatible with bowtie 2 output + new flag (-l/--limit) to limit maximum number of alignments
- parseAlignment tries to determine input type based on extension (no need to use --format parameter in most cases)
- more helpful error messages in get[Within]GeneExpression programs

Bug fixes:
- fixed broken extractTranscriptInfo.py and added new 'type' that looks for "gene=<gene name>"

Internals:
- replacing Boost headers with the latest stable version 1.53.0
- replacing samtools API with the latest stable version 0.1.19
- parseAlignment saves probabilities in log scale

0.5.0:
Improvements:
- parse alignment can extract and save gene names from Ensembl type reference
- estimateDE now produces comparison for all condition pairs when used with more than 2 conditions
- added --seed option to estimateHyperPar and estimateDE
- estimateHyperPar works in log scale only (it accepts only mean logged expression in --meanFile; and logs expression samples automatically when needed)

Bug fixes:
- fixed output of estimateDE: fold change with confidence intervals are in log2 scale, mean expression in natural log scale
   + changed flag confidencePerc to confidenceInterval and default value to 95
- changed getPPLR so that it produces PPLR comparison in the same "direction" as estimateDE
- fixed problem with long lines in reference sequence file in parseAlignment

Deprecation:
- drop obsolete parseAlignment.py

0.4.3:
- changed order in estimateDE output (logFC ConfidenceLow ConfidenceHigh)
   -> rename to credible intervals ?
- added normalization for getV. estimateDE estimateHP
- estimateE
   - new format in thetaMeans
   - set seed
   - doMax
- drop example.html
- bugfix for parseAlignment