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…rtial) Partial documentation pass — initial completed files from parallel agents. Remaining files will follow in subsequent commits. https://claude.ai/code/session_01CVzyi7WGAKyTJzbmnSNF6r
…ules Documents the following modules: - algorithms.py: UnionFind, Rect, QuadTree, binsearch - blockIt.py: makeBlockItInsert, printBlockIt - bwa.py: SAMAlignment, SAMReader, parseSAMString, joinSAMIntervals, all submit functions - clustering.py: Point, Cluster, kmeans, getDistance, makeRandomPoint - converters.py: bed2GTF - GTFlib.py: Error, ParsingError, GTF_Entry, GTFIterator - intervallib.py: Interval and all methods - JensenShannon.py: js_div_matrix, make_probs, js_div, kl_div and helpers - misc.py: Annot, seq2nuID, nuID2seq and all utilities - myDataTypes.py: Stack, BinaryTree, EmptyNode, BinaryNode, Graph - mySam.py: SAMAlignment, all parsing and interval functions - sequencelib.py: FastaIterator, complement, reverse_complement, Tm, GC and all utilities - smRNA.py: evaluateSequence, testCandidate, getTm, getGC, main - stats.py: all statistical functions https://claude.ai/code/session_01CVzyi7WGAKyTJzbmnSNF6r
Additional documentation from ongoing parallel agents. https://claude.ai/code/session_01CVzyi7WGAKyTJzbmnSNF6r
Documents the following modules: - Chip.py: ChipInterval, ChipData, all methods and functions - QCtools.py: makePWM, FastqIterator - bowtie.py: prepBowtie, runBowtie - bwa.py: SAMAlignment and all pipeline functions - MinerMethod.py: module docstring, CP_FDM/SDM/SPE, nthRoot - qpcrAnalysis.py: Well class and all analysis methods - gibson.py, lincClonelib.py, lincName.py, lincRNAs.py: all functions - stats.py, util.py: remaining undocumented functions https://claude.ai/code/session_01CVzyi7WGAKyTJzbmnSNF6r
Documents: - qpcr/MinerMethod.py: nthRoot, CP_FDM, CP_SDM, CP_SPE, module docstring - qpcr/util.py: uniqify, module docstring - seqlib/go.py: GoTerm, AllTerm, GoHandler and all methods - seqlib/lincName.py: remaining undocumented functions - seqlib/seqlib.py: SeqDict and all methods - seqlib/stats.py: remaining functions https://claude.ai/code/session_01CVzyi7WGAKyTJzbmnSNF6r
Documents: - Alignment.py: Alignment class and all methods - continuousData.py: ContinuousData, SimpleChIPData - seqData.py: SamData, ChromData - genomelib.py: UCSCStrandDescr, UCSCSeqIntervalRow, all functions - dbConn.py: all connection and query functions - prob.py: cumulative_sum, frequency_dic, pick_one, pick_many, gaussian - primer3lib.py: Record, Primer and all methods - shrimp.py: ShrimpRead, ProbCalcRead and all methods - stats.py: remaining functions https://claude.ai/code/session_01CVzyi7WGAKyTJzbmnSNF6r
Documents: - LSFlib.py: LSFError, LSFJob and all methods - RIPDiff.py: RIPUnit class and all methods, globalNorm, localNorm - plotting.py: chromatinAggPlots and all plotting functions - prob.py: cumulative_sum, frequency_dic, all probability functions - solid.py: CSSeq class and all methods https://claude.ai/code/session_01CVzyi7WGAKyTJzbmnSNF6r
Completes full documentation pass across all 43 modules in qpcr and seqlib. Every public function, method, and class now has a Google-style docstring. https://claude.ai/code/session_01CVzyi7WGAKyTJzbmnSNF6r
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Summary
across all 43 modules in the qpcr and seqlib packages (~120+ previously
undocumented APIs)
Created on / @authormodule headers with descriptivemodule-level docstrings
Modules documented
qpcr: abi.py, MinerMethod.py, qpcrAnalysis.py, util.py
seqlib — sequence/math: sequencelib.py, JensenShannon.py, stats.py, prob.py
seqlib — algorithms/data: algorithms.py, clustering.py, myDataTypes.py,
blockIt.py, converters.py
seqlib — bioinformatics: mySam.py, bwa.py, bowtie.py, Chip.py, QCtools.py
seqlib — genomics core: intervallib.py, GTFlib.py, util.py, seqlib.py,
genomelib.py, seqData.py, Alignment.py, continuousData.py
seqlib — legacy: misc.py, smRNA.py, gibson.py, lincRNAs.py, lincClonelib.py,
lincName.py, go.py, dbConn.py, primer3lib.py, shrimp.py, solid.py,
RIPDiff.py, plotting.py, LSFlib.py, pygrlib.py, seqstats.py
Test plan