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Use allele instead of gene where appropriate (doc fix only) #38

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Use allele instead of gene where appropriate (doc fix only) #38

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16 changes: 8 additions & 8 deletions bwakit/typeHLA.js
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Original file line number Diff line number Diff line change
Expand Up @@ -61,7 +61,7 @@ while ((c = getopt(arguments, "vdl:n:f:")) != null) {
if (arguments.length == getopt.ind) {
print("");
print("Usage: k8 typeHLA.js [options] <exon-to-contig.sam>\n");
print("Options: -n INT drop a contig if the edit distance to the closest gene is >INT ["+thres_nm+"]");
print("Options: -n INT drop a contig if the edit distance to the closest allele is >INT ["+thres_nm+"]");
print(" -l INT drop a contig if its match too short ["+thres_len+"]");
print(" -f FLOAT drop inconsistent contigs if their length <FLOAT fraction of total length ["+thres_ratio.toFixed(2)+"]");
print(" -d output extra info for debugging");
Expand Down Expand Up @@ -126,11 +126,11 @@ file.close();
* Prepare data structures for typing *
**************************************/

// identify the primary exons, the exons associated with most genes
// identify the primary exons, the exons associated with most alleles
var pri_exon = [], n_pri_exons;
{
var cnt = [], max = 0;
// count the number of genes per exon and track the max
// count the number of alleles per exon and track the max
for (var e = 0; e < gcnt.length; ++e) {
if (gcnt[e] != null) {
var c = 0, h = gcnt[e];
Expand All @@ -139,7 +139,7 @@ var pri_exon = [], n_pri_exons;
max = max > c? max : c;
} else cnt[e] = 0;
}
warn("- Number of genes for each exon: [" +cnt.join(",") + "]");
warn("- Number of alleles for each exon: [" +cnt.join(",") + "]");
// find primary exons
var pri_list = [];
for (var e = 0; e < cnt.length; ++e) {
Expand Down Expand Up @@ -229,7 +229,7 @@ var perf_genes = [];
for (var g in pg_aux_cnt)
if (pg_aux_cnt[g] == n_pri_exons)
perf_genes.push(parseInt(g));
warn("- Found " +perf_genes.length+ " genes fully covered by perfect matches on the primary exon(s)");
warn("- Found " +perf_genes.length+ " alleles fully covered by perfect matches on the primary exon(s)");

var h_perf_genes = {};
for (var i = 0; i < perf_genes.length; ++i) {
Expand Down Expand Up @@ -277,7 +277,7 @@ for (var c = 0; c < clist.length; ++c)
if (flt_flag[c]&2) l_cons += ovlp_len[c];
else if (flt_flag[c] == 1) l_incons += ovlp_len[c];

warn("- Total length of contigs consistent/inconsistent with perfect genes: " +l_cons+ "/" +l_incons);
warn("- Total length of contigs consistent/inconsistent with perfect alleles: " +l_cons+ "/" +l_incons);
var attempt_perf = (l_incons/(l_cons+l_incons) < thres_frac);

/********************************
Expand Down Expand Up @@ -323,7 +323,7 @@ function type_gene(perf_mode)
score[e] = []; ctg[e] = [];
if (exons[e] == null) return;
var ee = exons[e], is_pri = pri_exon[e]? 1 : 0;
// find contigs and genes associated with the current exon
// find contigs and alleles associated with the current exon
var ch = {}, gh = {};
for (var i = 0; i < ee.length; ++i)
if (elist[ee[i][1]][e] != null)
Expand All @@ -333,7 +333,7 @@ function type_gene(perf_mode)
for (var g in gh) ga.push(parseInt(g));
var named_ca = [];
for (var i = 0; i < ca.length; ++i) named_ca.push(clist[ca[i]]);
warn(" - Processing exon "+(e+1)+" (" +ga.length+ " genes; " +ca.length+ " contigs: [" +named_ca.join(", ")+ "])...");
warn(" - Processing exon "+(e+1)+" (" +ga.length+ " alleles; " +ca.length+ " contigs: [" +named_ca.join(", ")+ "])...");
// set unmapped entries to high mismatch
var sc = score[e];
for (var k = 0; k < ga.length; ++k) {
Expand Down
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