From e31a699d953f891d6b7d9ed164418573e0684647 Mon Sep 17 00:00:00 2001 From: GitHub Action Date: Mon, 14 Oct 2024 09:32:09 +0000 Subject: [PATCH] Update latest documentation --- latest/examples/gwas_tutorial.html | 685 +++++++++--------- latest/examples/relatedness_tutorial.html | 52 +- .../sgkit.variables.call_dosage_spec.html | 2 +- ...t.variables.interval_contig_name_spec.html | 2 +- .../sgkit.variables.parent_id_spec.html | 2 +- .../sgkit.variables.sample_id_spec.html | 2 +- .../sgkit.variables.stat_Fst_spec.html | 2 +- .../sgkit.variables.stat_Tajimas_D_spec.html | 2 +- .../sgkit.variables.stat_divergence_spec.html | 2 +- .../sgkit.variables.stat_diversity_spec.html | 2 +- ...les.stat_observed_heterozygosity_spec.html | 2 +- .../sgkit.variables.stat_pbs_spec.html | 2 +- .../sgkit.variables.variant_allele_spec.html | 2 +- .../sgkit.variables.variant_contig_spec.html | 2 +- ...variables.variant_genotype_count_spec.html | 2 +- .../sgkit.variables.variant_id_spec.html | 2 +- latest/searchindex.js | 2 +- latest/user_guide.html | 4 +- 18 files changed, 385 insertions(+), 386 deletions(-) diff --git a/latest/examples/gwas_tutorial.html b/latest/examples/gwas_tutorial.html index 574e315b3..98366fec5 100644 --- a/latest/examples/gwas_tutorial.html +++ b/latest/examples/gwas_tutorial.html @@ -604,7 +604,7 @@

Importing data from VCF
    Scan:   0%|          | 0.00/1.00 [00:00<?, ?files/s]
     Scan:   0%|          | 0.00/1.00 [00:00<?, ?files/s]
     Scan:   0%|          | 0.00/1.00 [00:00<?, ?files/s]
-    Scan: 100%|██████████| 1.00/1.00 [00:00<00:00, 1.55files/s]
+    Scan: 100%|██████████| 1.00/1.00 [00:00<00:00, 1.54files/s]
 
 Explode:   0%|          | 0.00/10.9k [00:00<?, ?vars/s]
@@ -615,88 +615,87 @@ 
Importing data from VCF
 
 Explode:   0%|          | 0.00/10.9k [00:00<?, ?vars/s]
  Explode:   0%|          | 0.00/10.9k [00:00<?, ?vars/s]
- Explode:   0%|          | 48.0/10.9k [00:00<00:22, 475vars/s]
- Explode:   2%|▏         | 258/10.9k [00:00<00:08, 1.32kvars/s]
- Explode:   4%|▍         | 467/10.9k [00:00<00:06, 1.59kvars/s]
- Explode:   6%|▌         | 673/10.9k [00:00<00:05, 1.72kvars/s]
- Explode:   8%|▊         | 858/10.9k [00:01<00:05, 1.75kvars/s]
- Explode:   9%|▉         | 988/10.9k [00:02<00:18, 541vars/s]  
- Explode:  11%|█         | 1.20k/10.9k [00:02<00:14, 656vars/s]
- Explode:  13%|█▎        | 1.42k/10.9k [00:02<00:12, 766vars/s]
- Explode:  15%|█▍        | 1.62k/10.9k [00:02<00:10, 860vars/s]
- Explode:  16%|█▌        | 1.76k/10.9k [00:03<00:17, 533vars/s]
- Explode:  18%|█▊        | 1.97k/10.9k [00:03<00:14, 608vars/s]
- Explode:  20%|██        | 2.19k/10.9k [00:03<00:12, 688vars/s]
- Explode:  22%|██▏       | 2.40k/10.9k [00:03<00:11, 765vars/s]
- Explode:  24%|██▎       | 2.56k/10.9k [00:04<00:15, 553vars/s]
- Explode:  25%|██▌       | 2.72k/10.9k [00:04<00:13, 594vars/s]
- Explode:  26%|██▋       | 2.87k/10.9k [00:05<00:14, 544vars/s]
- Explode:  28%|██▊       | 3.09k/10.9k [00:05<00:12, 608vars/s]
- Explode:  30%|██▉       | 3.23k/10.9k [00:05<00:14, 518vars/s]
- Explode:  32%|███▏      | 3.44k/10.9k [00:06<00:12, 578vars/s]
- Explode:  34%|███▎      | 3.67k/10.9k [00:06<00:11, 641vars/s]
- Explode:  35%|███▌      | 3.83k/10.9k [00:07<00:13, 507vars/s]
- Explode:  37%|███▋      | 4.05k/10.9k [00:07<00:12, 564vars/s]
- Explode:  39%|███▉      | 4.27k/10.9k [00:07<00:10, 622vars/s]
- Explode:  41%|████      | 4.45k/10.9k [00:07<00:09, 667vars/s]
- Explode:  42%|████▏     | 4.62k/10.9k [00:08<00:11, 540vars/s]
- Explode:  44%|████▍     | 4.83k/10.9k [00:08<00:10, 594vars/s]
- Explode:  46%|████▌     | 5.00k/10.9k [00:08<00:09, 630vars/s]
- Explode:  47%|████▋     | 5.15k/10.9k [00:09<00:10, 531vars/s]
- Explode:  49%|████▉     | 5.37k/10.9k [00:09<00:09, 586vars/s]
- Explode:  51%|█████     | 5.51k/10.9k [00:10<00:11, 465vars/s]
- Explode:  53%|█████▎    | 5.73k/10.9k [00:10<00:10, 514vars/s]
- Explode:  54%|█████▍    | 5.92k/10.9k [00:10<00:08, 555vars/s]
- Explode:  56%|█████▌    | 6.08k/10.9k [00:11<00:09, 496vars/s]
- Explode:  58%|█████▊    | 6.30k/10.9k [00:11<00:08, 546vars/s]
- Explode:  59%|█████▉    | 6.45k/10.9k [00:11<00:07, 579vars/s]
- Explode:  61%|██████    | 6.60k/10.9k [00:12<00:08, 497vars/s]
- Explode:  63%|██████▎   | 6.82k/10.9k [00:12<00:07, 549vars/s]
- Explode:  65%|██████▍   | 7.02k/10.9k [00:12<00:06, 596vars/s]
- Explode:  66%|██████▌   | 7.17k/10.9k [00:13<00:07, 505vars/s]
- Explode:  68%|██████▊   | 7.39k/10.9k [00:13<00:06, 556vars/s]
- Explode:  70%|██████▉   | 7.59k/10.9k [00:13<00:05, 603vars/s]
- Explode:  71%|███████   | 7.75k/10.9k [00:14<00:06, 513vars/s]
- Explode:  73%|███████▎  | 7.92k/10.9k [00:14<00:05, 550vars/s]
- Explode:  74%|███████▍  | 8.08k/10.9k [00:14<00:05, 501vars/s]
- Explode:  76%|███████▌  | 8.22k/10.9k [00:15<00:05, 472vars/s]
- Explode:  77%|███████▋  | 8.35k/10.9k [00:15<00:05, 448vars/s]
- Explode:  79%|███████▊  | 8.57k/10.9k [00:15<00:04, 497vars/s]
- Explode:  80%|███████▉  | 8.70k/10.9k [00:16<00:04, 452vars/s]
- Explode:  82%|████████▏ | 8.91k/10.9k [00:16<00:03, 501vars/s]
- Explode:  83%|████████▎ | 9.04k/10.9k [00:17<00:04, 449vars/s]
- Explode:  85%|████████▌ | 9.26k/10.9k [00:17<00:03, 498vars/s]
- Explode:  86%|████████▌ | 9.38k/10.9k [00:18<00:03, 450vars/s]
- Explode:  88%|████████▊ | 9.60k/10.9k [00:18<00:02, 500vars/s]
- Explode:  90%|████████▉ | 9.74k/10.9k [00:18<00:02, 463vars/s]
- Explode:  92%|█████████▏| 9.96k/10.9k [00:18<00:01, 513vars/s]
- Explode:  93%|█████████▎| 10.1k/10.9k [00:19<00:01, 467vars/s]
- Explode:  95%|█████████▍| 10.3k/10.9k [00:19<00:01, 510vars/s]
- Explode:  96%|█████████▌| 10.4k/10.9k [00:20<00:01, 466vars/s]
- Explode:  97%|█████████▋| 10.5k/10.9k [00:20<00:00, 443vars/s]
- Explode:  98%|█████████▊| 10.7k/10.9k [00:20<00:00, 418vars/s]
- Explode: 100%|█████████▉| 10.9k/10.9k [00:21<00:00, 468vars/s]
- Explode: 100%|██████████| 10.9k/10.9k [00:21<00:00, 511vars/s]
+ Explode:   0%|          | 53.0/10.9k [00:00<00:20, 524vars/s]
+ Explode:   2%|▏         | 255/10.9k [00:00<00:08, 1.30kvars/s]
+ Explode:   4%|▍         | 466/10.9k [00:00<00:06, 1.59kvars/s]
+ Explode:   6%|▌         | 679/10.9k [00:00<00:05, 1.74kvars/s]
+ Explode:   8%|▊         | 891/10.9k [00:01<00:05, 1.82kvars/s]
+ Explode:   9%|▉         | 1.01k/10.9k [00:02<00:17, 559vars/s]
+ Explode:  11%|█▏        | 1.23k/10.9k [00:02<00:14, 673vars/s]
+ Explode:  13%|█▎        | 1.44k/10.9k [00:02<00:12, 781vars/s]
+ Explode:  15%|█▌        | 1.66k/10.9k [00:02<00:10, 885vars/s]
+ Explode:  17%|█▋        | 1.81k/10.9k [00:03<00:16, 546vars/s]
+ Explode:  19%|█▊        | 2.03k/10.9k [00:03<00:14, 622vars/s]
+ Explode:  21%|██        | 2.24k/10.9k [00:03<00:12, 698vars/s]
+ Explode:  23%|██▎       | 2.46k/10.9k [00:03<00:10, 776vars/s]
+ Explode:  24%|██▍       | 2.62k/10.9k [00:04<00:14, 558vars/s]
+ Explode:  26%|██▌       | 2.77k/10.9k [00:05<00:15, 515vars/s]
+ Explode:  28%|██▊       | 3.00k/10.9k [00:05<00:13, 577vars/s]
+ Explode:  29%|██▉       | 3.13k/10.9k [00:05<00:12, 608vars/s]
+ Explode:  30%|███       | 3.29k/10.9k [00:05<00:14, 530vars/s]
+ Explode:  32%|███▏      | 3.51k/10.9k [00:06<00:12, 591vars/s]
+ Explode:  34%|███▍      | 3.73k/10.9k [00:06<00:10, 654vars/s]
+ Explode:  36%|███▌      | 3.88k/10.9k [00:07<00:13, 518vars/s]
+ Explode:  38%|███▊      | 4.10k/10.9k [00:07<00:11, 574vars/s]
+ Explode:  40%|███▉      | 4.32k/10.9k [00:07<00:10, 632vars/s]
+ Explode:  41%|████      | 4.49k/10.9k [00:08<00:12, 505vars/s]
+ Explode:  43%|████▎     | 4.70k/10.9k [00:08<00:11, 557vars/s]
+ Explode:  45%|████▌     | 4.92k/10.9k [00:08<00:09, 611vars/s]
+ Explode:  47%|████▋     | 5.07k/10.9k [00:09<00:11, 514vars/s]
+ Explode:  49%|████▊     | 5.29k/10.9k [00:09<00:09, 566vars/s]
+ Explode:  50%|█████     | 5.44k/10.9k [00:10<00:10, 499vars/s]
+ Explode:  51%|█████▏    | 5.58k/10.9k [00:10<00:11, 481vars/s]
+ Explode:  53%|█████▎    | 5.79k/10.9k [00:10<00:09, 530vars/s]
+ Explode:  55%|█████▍    | 5.93k/10.9k [00:11<00:10, 468vars/s]
+ Explode:  57%|█████▋    | 6.15k/10.9k [00:11<00:09, 517vars/s]
+ Explode:  59%|█████▊    | 6.37k/10.9k [00:11<00:07, 568vars/s]
+ Explode:  60%|█████▉    | 6.51k/10.9k [00:12<00:09, 484vars/s]
+ Explode:  62%|██████▏   | 6.73k/10.9k [00:12<00:07, 534vars/s]
+ Explode:  64%|██████▍   | 6.95k/10.9k [00:12<00:06, 585vars/s]
+ Explode:  65%|██████▌   | 7.10k/10.9k [00:13<00:07, 493vars/s]
+ Explode:  67%|██████▋   | 7.32k/10.9k [00:13<00:06, 542vars/s]
+ Explode:  69%|██████▉   | 7.54k/10.9k [00:13<00:05, 593vars/s]
+ Explode:  71%|███████   | 7.69k/10.9k [00:14<00:06, 505vars/s]
+ Explode:  73%|███████▎  | 7.91k/10.9k [00:14<00:05, 554vars/s]
+ Explode:  74%|███████▍  | 8.06k/10.9k [00:15<00:05, 501vars/s]
+ Explode:  75%|███████▌  | 8.21k/10.9k [00:15<00:05, 473vars/s]
+ Explode:  77%|███████▋  | 8.34k/10.9k [00:16<00:05, 451vars/s]
+ Explode:  79%|███████▊  | 8.56k/10.9k [00:16<00:04, 499vars/s]
+ Explode:  80%|███████▉  | 8.68k/10.9k [00:16<00:04, 453vars/s]
+ Explode:  82%|████████▏ | 8.90k/10.9k [00:16<00:03, 502vars/s]
+ Explode:  83%|████████▎ | 9.04k/10.9k [00:17<00:04, 456vars/s]
+ Explode:  85%|████████▌ | 9.26k/10.9k [00:17<00:03, 504vars/s]
+ Explode:  86%|████████▋ | 9.39k/10.9k [00:18<00:03, 459vars/s]
+ Explode:  88%|████████▊ | 9.60k/10.9k [00:18<00:02, 507vars/s]
+ Explode:  90%|████████▉ | 9.75k/10.9k [00:18<00:02, 466vars/s]
+ Explode:  92%|█████████▏| 9.96k/10.9k [00:18<00:01, 514vars/s]
+ Explode:  93%|█████████▎| 10.1k/10.9k [00:19<00:01, 468vars/s]
+ Explode:  95%|█████████▍| 10.3k/10.9k [00:19<00:01, 507vars/s]
+ Explode:  96%|█████████▌| 10.4k/10.9k [00:20<00:00, 466vars/s]
+ Explode:  97%|█████████▋| 10.5k/10.9k [00:20<00:00, 441vars/s]
+ Explode:  98%|█████████▊| 10.7k/10.9k [00:21<00:00, 417vars/s]
+ Explode: 100%|█████████▉| 10.9k/10.9k [00:21<00:00, 461vars/s]
+ Explode: 100%|██████████| 10.9k/10.9k [00:21<00:00, 506vars/s]
 

 

 
  Encode:   0%|          | 0.00/28.2M [00:00<?, ?B/s]
   Encode:   0%|          | 0.00/28.2M [00:00<?, ?B/s]
   Encode:   0%|          | 0.00/28.2M [00:00<?, ?B/s]
   Encode:   0%|          | 0.00/28.2M [00:00<?, ?B/s]
-  Encode:   0%|          | 90.0k/28.2M [00:00<00:31, 888kB/s]
-  Encode:   1%|          | 270k/28.2M [00:00<00:22, 1.23MB/s]
-  Encode:   1%|          | 350k/28.2M [00:00<00:25, 1.08MB/s]
-  Encode:  21%|██▏       | 6.03M/28.2M [00:01<00:02, 7.86MB/s]
-  Encode:  31%|███▏      | 8.87M/28.2M [00:01<00:02, 9.38MB/s]
-  Encode:  42%|████▏     | 11.7M/28.2M [00:01<00:01, 10.4MB/s]
-  Encode:  62%|██████▏   | 17.4M/28.2M [00:01<00:00, 11.9MB/s]
-  Encode:  92%|█████████▏| 25.9M/28.2M [00:01<00:00, 17.8MB/s]
-  Encode: 100%|██████████| 28.2M/28.2M [00:02<00:00, 15.8MB/s]
-  Encode: 100%|██████████| 28.2M/28.2M [00:02<00:00, 12.4MB/s]
+  Encode:   0%|          | 90.0k/28.2M [00:00<00:31, 890kB/s]
+  Encode:   1%|          | 270k/28.2M [00:00<00:25, 1.08MB/s]
+  Encode:   1%|          | 350k/28.2M [00:00<00:28, 986kB/s] 
+  Encode:  21%|██▏       | 6.03M/28.2M [00:01<00:02, 7.41MB/s]
+  Encode:  31%|███▏      | 8.87M/28.2M [00:01<00:02, 8.76MB/s]
+  Encode:  42%|████▏     | 11.7M/28.2M [00:01<00:01, 9.68MB/s]
+  Encode:  62%|██████▏   | 17.4M/28.2M [00:01<00:00, 11.2MB/s]
+  Encode:  92%|█████████▏| 25.9M/28.2M [00:02<00:00, 16.9MB/s]
+  Encode: 100%|██████████| 28.2M/28.2M [00:02<00:00, 14.9MB/s]
+  Encode: 100%|██████████| 28.2M/28.2M [00:02<00:00, 11.8MB/s]
 

 

 
Finalise:   0%|          | 0.00/13.0 [00:00<?, ?array/s]
-Finalise: 100%|██████████| 13.0/13.0 [00:00<00:00, 1.25karray/s]
+Finalise: 100%|██████████| 13.0/13.0 [00:00<00:00, 1.26karray/s]
@@ -1112,7 +1111,7 @@

Getting to know our data @@ -1192,7 +1191,7 @@

Getting to know our data @@ -1248,7 +1247,7 @@

Getting to know our data @@ -1304,7 +1303,7 @@

Getting to know our data @@ -1384,7 +1383,7 @@

Getting to know our data @@ -1464,7 +1463,7 @@

Getting to know our data @@ -1520,7 +1519,7 @@

Getting to know our data @@ -1575,7 +1574,7 @@

Getting to know our data @@ -1630,7 +1629,7 @@

Getting to know our data @@ -1685,7 +1684,7 @@

Getting to know our data @@ -1740,7 +1739,7 @@

Getting to know our data @@ -1796,7 +1795,7 @@

Getting to know our data @@ -1852,7 +1851,7 @@

Getting to know our data @@ -1908,7 +1907,7 @@

Getting to know our data @@ -1964,7 +1963,7 @@

Getting to know our data @@ -2020,7 +2019,7 @@

Getting to know our data @@ -2076,7 +2075,7 @@

Getting to know our data @@ -2132,7 +2131,7 @@

Getting to know our data