update readme

new histograms and note on --ubam
wdecoster · Sep 5, 2023 · 435ff1f · 435ff1f
1 parent 45aeb6b
commit 435ff1f
Showing 1 changed file with 78 additions and 31 deletions.
diff --git a/README.md b/README.md
@@ -51,7 +51,7 @@ Path    alignment/example.cram
 Creation time   09/09/2022 10:53:36
 ```
 
-A 140Gbase bam file is processed in 12 minutes, using <1Gbyte of memory. Note that the identity score above is defined as the [gap-compressed identity](https://lh3.github.io/2018/11/25/on-the-definition-of-sequence-identity).
+A 140Gbase bam file is processed in 12 minutes, using <1Gbyte of memory. Note that the identity score above is defined as the [gap-compressed identity](https://lh3.github.io/2018/11/25/on-the-definition-of-sequence-identity). The `--ubam` flag will provide metrics for all reads in the file, regardless of whether they are aligned or not.
 
 ### Optional output
 
@@ -60,38 +60,85 @@ A 140Gbase bam file is processed in 12 minutes, using <1Gbyte of memory. Note th
 * calculating a normalised number of reads per chromosome, e.g. to determine the sex or aneuploidies (`--karyotype`)
 * information about the phase blocks. (`--phased`)
 * information about number of splice sites. (`--spliced`)
-* histograms of read lengths and read identities, as below. (`--hist`)
+* histograms of read lengths and read identities, as below. (`--hist`). With `--phased`, also a histogram of phase block lengths. Please let me know if the histograms look inappropriately scaled for your data.
 
 ```text
- 70.97195691947476 ..  71.97292392225151 [  122235 ]: ∎∎
- 71.97292392225151 ..  72.97389092502823 [  136051 ]: ∎∎∎
- 72.97389092502823 ..  73.97485792780498 [  145876 ]: ∎∎∎
- 73.97485792780498 ..   74.9758249305817 [  157751 ]: ∎∎∎
-  74.9758249305817 ..  75.97679193335844 [  179551 ]: ∎∎∎∎
- 75.97679193335844 ..  76.97775893613516 [  171769 ]: ∎∎∎∎
- 76.97775893613516 ..   77.9787259389119 [  159340 ]: ∎∎∎
-  77.9787259389119 ..  78.97969294168863 [  151355 ]: ∎∎∎
- 78.97969294168863 ..  79.98065994446536 [  146207 ]: ∎∎∎
- 79.98065994446536 ..  80.98162694724209 [  142832 ]: ∎∎∎
- 80.98162694724209 ..  81.98259395001882 [  140902 ]: ∎∎∎
- 81.98259395001882 ..  82.98356095279556 [  143909 ]: ∎∎∎
- 82.98356095279556 ..  83.98452795557229 [  149142 ]: ∎∎∎
- 83.98452795557229 ..  84.98549495834902 [  158386 ]: ∎∎∎
- 84.98549495834902 ..  85.98646196112576 [  176819 ]: ∎∎∎∎
- 85.98646196112576 ..  86.98742896390249 [  199558 ]: ∎∎∎∎
- 86.98742896390249 ..  87.98839596667922 [  234573 ]: ∎∎∎∎∎
- 87.98839596667922 ..  88.98936296945595 [  280849 ]: ∎∎∎∎∎∎
- 88.98936296945595 ..  89.99032997223267 [  348535 ]: ∎∎∎∎∎∎∎∎
- 89.99032997223267 ..   90.9912969750094 [  445640 ]: ∎∎∎∎∎∎∎∎∎∎
-  90.9912969750094 ..  91.99226397778614 [  583424 ]: ∎∎∎∎∎∎∎∎∎∎∎∎∎
- 91.99226397778614 ..  92.99323098056287 [  776111 ]: ∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎
- 92.99323098056287 ..   93.9941979833396 [ 1051370 ]: ∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎
-  93.9941979833396 ..  94.99516498611634 [ 1414103 ]: ∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎
- 94.99516498611634 ..  95.99613198889307 [ 1833438 ]: ∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎
- 95.99613198889307 ..   96.9970989916698 [ 2084833 ]: ∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎
-  96.9970989916698 ..  97.99806599444653 [ 1620179 ]: ∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎
- 97.99806599444653 ..  98.99903299722327 [  416669 ]: ∎∎∎∎∎∎∎∎∎
- 98.99903299722327 ..                100 [   39254 ]:
+# Histogram for read lengths:
+     0-2000 ∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎
+  2000-4000 ∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎
+  4000-6000 ∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎
+  6000-8000 ∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎
+ 8000-10000 ∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎
+10000-12000 ∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎
+12000-14000 ∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎
+14000-16000 ∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎
+16000-18000 ∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎
+18000-20000 ∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎
+20000-22000 ∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎
+22000-24000 ∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎
+24000-26000 ∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎
+26000-28000 ∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎
+28000-30000 ∎∎∎∎∎∎∎∎∎∎∎∎
+30000-32000 ∎∎∎∎∎∎∎∎∎
+32000-34000 ∎∎∎∎∎∎
+34000-36000 ∎∎∎∎
+36000-38000 ∎∎
+38000-40000 ∎
+40000-42000 ∎
+42000-44000 ∎
+44000-46000 
+46000-48000 
+48000-50000 
+50000-52000 
+52000-54000 
+54000-56000 
+56000-58000 
+58000-60000 
+     60000+ 
+
+
+# Histogram for Phred-scaled accuracies:
+  Q0-1 
+  Q1-2 
+  Q2-3 
+  Q3-4 
+  Q4-5 
+  Q5-6 ∎∎∎
+  Q6-7 ∎∎∎∎∎∎∎∎∎∎∎∎
+  Q7-8 ∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎
+  Q8-9 ∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎
+ Q9-10 ∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎
+Q10-11 ∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎
+Q11-12 ∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎
+Q12-13 ∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎
+Q13-14 ∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎
+Q14-15 ∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎
+Q15-16 ∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎
+Q16-17 ∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎
+Q17-18 ∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎∎
+Q18-19 ∎∎∎∎
+Q19-20 ∎
+Q20-21 
+Q21-22 
+Q22-23 
+Q23-24 
+Q24-25 
+Q25-26 
+Q26-27 
+Q27-28 
+Q28-29 
+Q29-30 
+Q30-31 
+Q31-32 
+Q32-33 
+Q33-34 
+Q34-35 
+Q35-36 
+Q36-37 
+Q37-38 
+Q38-39 
+Q39-40 
+  Q40+ 
 ```
 
 ## CITATION