File Changes for angie

v251_preview to v251_preview2 (2011-04-26 to 2011-05-03) v251

• src/hg/hgTracks/variation.c
  • lines changed 2, context: html, text, full: html, text
    Bug #3765 (buffer overflow error in Common SNP (132)): plugged up hole in snp125ValidFilter logic that allowed use of NULL var.
• src/hg/hgTracks/vcfTrack.c
  • lines changed 302, context: html, text, full: html, text
    Feature #3711 (vcfTabix: center-weighted haplotype sorting for display of phased genotypes):Now using hacTree to cluster haplotypes as David suggested, instead of sorting by genotypes which was a mess. Performance could be improved: the tree from hacTree ends up very lopsided when there are many identical haplotypes, so perhaps hacTree could optionally begin by sorting items (if a cmp function is passed in) and pre-clustering runs of identical items. When there are a lot of identicals, that would reduce the initial number of items that we generate all possible pairs from. Might also consider general balanced insertion schemes. Another issue: with the current alpha of 0.5, the signal vanishes once you get a certain distance away from the center variant. Make alpha depend on #variants? Or just make it larger?
• src/hg/lib/liftOver.c
  • lines changed 1, context: html, text, full: html, text
    Fix for something caught only by Ubuntu gcc's more conservative warnings:lineFileOpen's second argument is a bool, but a quoted string was passed in.
• src/inc/common.h
  • lines changed 1, context: html, text, full: html, text
    Added new lib module hacTree (Hierarchical Agglomerative Clustering),which takes an slList of items and a couple user-defined functions, and returns a binary tree of clusters, with the leaf nodes containing the original input items. The user-defined functions do the interesting parts: computing distance between two items and/or clusters, and merging two items and/or clusters into a new cluster. This is motivated by work on Feature #3711 (vcfTabix: center-weighted haplotype sorting for display of phased genotypes), but I'm hoping it might have other uses.
• src/inc/hacTree.h
  • lines changed 69, context: html, text, full: html, text
    Added new lib module hacTree (Hierarchical Agglomerative Clustering),which takes an slList of items and a couple user-defined functions, and returns a binary tree of clusters, with the leaf nodes containing the original input items. The user-defined functions do the interesting parts: computing distance between two items and/or clusters, and merging two items and/or clusters into a new cluster. This is motivated by work on Feature #3711 (vcfTabix: center-weighted haplotype sorting for display of phased genotypes), but I'm hoping it might have other uses.
• src/lib/common.c
  • lines changed 1, context: html, text, full: html, text
    Added new lib module hacTree (Hierarchical Agglomerative Clustering),which takes an slList of items and a couple user-defined functions, and returns a binary tree of clusters, with the leaf nodes containing the original input items. The user-defined functions do the interesting parts: computing distance between two items and/or clusters, and merging two items and/or clusters into a new cluster. This is motivated by work on Feature #3711 (vcfTabix: center-weighted haplotype sorting for display of phased genotypes), but I'm hoping it might have other uses.
• src/lib/hacTree.c
  • lines changed 114, context: html, text, full: html, text
    Added new lib module hacTree (Hierarchical Agglomerative Clustering),which takes an slList of items and a couple user-defined functions, and returns a binary tree of clusters, with the leaf nodes containing the original input items. The user-defined functions do the interesting parts: computing distance between two items and/or clusters, and merging two items and/or clusters into a new cluster. This is motivated by work on Feature #3711 (vcfTabix: center-weighted haplotype sorting for display of phased genotypes), but I'm hoping it might have other uses.
• src/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    Added new lib module hacTree (Hierarchical Agglomerative Clustering),which takes an slList of items and a couple user-defined functions, and returns a binary tree of clusters, with the leaf nodes containing the original input items. The user-defined functions do the interesting parts: computing distance between two items and/or clusters, and merging two items and/or clusters into a new cluster. This is motivated by work on Feature #3711 (vcfTabix: center-weighted haplotype sorting for display of phased genotypes), but I'm hoping it might have other uses.
• src/lib/tests/expected/hacTreeTest.out
  • lines changed 49, context: html, text, full: html, text
    Added new lib module hacTree (Hierarchical Agglomerative Clustering),which takes an slList of items and a couple user-defined functions, and returns a binary tree of clusters, with the leaf nodes containing the original input items. The user-defined functions do the interesting parts: computing distance between two items and/or clusters, and merging two items and/or clusters into a new cluster. This is motivated by work on Feature #3711 (vcfTabix: center-weighted haplotype sorting for display of phased genotypes), but I'm hoping it might have other uses.
  • lines changed 15, context: html, text, full: html, text
    Better hacTree test: instead of using a dumb contrived example, useDavid's clustering example from email.
• src/lib/tests/hacTreeTest.c
  • lines changed 205, context: html, text, full: html, text
    Added new lib module hacTree (Hierarchical Agglomerative Clustering),which takes an slList of items and a couple user-defined functions, and returns a binary tree of clusters, with the leaf nodes containing the original input items. The user-defined functions do the interesting parts: computing distance between two items and/or clusters, and merging two items and/or clusters into a new cluster. This is motivated by work on Feature #3711 (vcfTabix: center-weighted haplotype sorting for display of phased genotypes), but I'm hoping it might have other uses.
  • lines changed 68, context: html, text, full: html, text
    Better hacTree test: instead of using a dumb contrived example, useDavid's clustering example from email.
• src/lib/tests/input/hacTreeTest.txt
  • lines changed 7, context: html, text, full: html, text
    Added new lib module hacTree (Hierarchical Agglomerative Clustering),which takes an slList of items and a couple user-defined functions, and returns a binary tree of clusters, with the leaf nodes containing the original input items. The user-defined functions do the interesting parts: computing distance between two items and/or clusters, and merging two items and/or clusters into a new cluster. This is motivated by work on Feature #3711 (vcfTabix: center-weighted haplotype sorting for display of phased genotypes), but I'm hoping it might have other uses.
  • lines changed 7, context: html, text, full: html, text
    Better hacTree test: instead of using a dumb contrived example, useDavid's clustering example from email.
• src/lib/tests/makefile
  • lines changed 12, context: html, text, full: html, text
    Added new lib module hacTree (Hierarchical Agglomerative Clustering),which takes an slList of items and a couple user-defined functions, and returns a binary tree of clusters, with the leaf nodes containing the original input items. The user-defined functions do the interesting parts: computing distance between two items and/or clusters, and merging two items and/or clusters into a new cluster. This is motivated by work on Feature #3711 (vcfTabix: center-weighted haplotype sorting for display of phased genotypes), but I'm hoping it might have other uses.