From ad5076149bb99ab4deae15e3a478c89e20bf6b00 Mon Sep 17 00:00:00 2001
From: pmitev <pmitev@gmail.com>
Date: Thu, 1 Sep 2022 08:29:16 +0200
Subject: [PATCH] Fixes after the last workshop

---
 docs/1.Simple_example.md              | 2 +-
 docs/3.Shell_we_awk.md                | 2 +-
 docs/6.One_line_programs.md           | 2 +-
 docs/Case_studies/manipulating_vcf.md | 2 ++
 4 files changed, 5 insertions(+), 3 deletions(-)

diff --git a/docs/1.Simple_example.md b/docs/1.Simple_example.md
index 18aedd4f..05fff8e2 100644
--- a/docs/1.Simple_example.md
+++ b/docs/1.Simple_example.md
@@ -153,7 +153,7 @@ $ awk ' /pattern/ {action} ' file1 file2 ... fileN
     - remove the minus sign in the `%-8s` formatting to see the effect.
     - more string manipulations [exercises](Exercises/String_manipulation.md)
 
-More on format modifiers: [gawk documentation](https://https://www.gnu.org/software/gawk/manual/html_node/Format-Modifiers.html#Format-Modifiers)
+More on format modifiers: [gawk documentation](https://www.gnu.org/software/gawk/manual/html_node/Format-Modifiers.html#Format-Modifiers)
 
 !!! example "Files"
     * [coins.txt](data/coins.txt)
diff --git a/docs/3.Shell_we_awk.md b/docs/3.Shell_we_awk.md
index 36a7ff9c..af72f6ae 100644
--- a/docs/3.Shell_we_awk.md
+++ b/docs/3.Shell_we_awk.md
@@ -90,7 +90,7 @@ Let's use the output from the Gaussian code as an example (*something from my re
  2O,std. LJ params. for H2O, MC/QM\\-1,1\O,0,0.,0.,0.\H,0,-0.836605,-0.
   . . . ( more lines ) . . .
 ```
-The numbers that I am interested in are in bold. There are **56 such pairs** in the whole file. I need them tabulated in simple, two-column file that is easy to read, analyze and plot. Here I will not discuss other solutions. Instead, here is a possible awk solution:
+The numbers that I am interested in are in bold. There are **56 such pairs** in the whole [file](https://github.com/pmitev/to-awk-or-not/raw/master/docs/data/gaussian.out). I need them tabulated in simple, two-column file that is easy to read, analyze and plot. Here I will not discuss other solutions. Instead, here is a possible awk solution:
 
 ``` awk title="extract-gaussian.awk"
 #!/usr/bin/awk -f
diff --git a/docs/6.One_line_programs.md b/docs/6.One_line_programs.md
index dc534c15..a9a143cf 100644
--- a/docs/6.One_line_programs.md
+++ b/docs/6.One_line_programs.md
@@ -5,6 +5,6 @@ Many useful awk programs are as short as just a line or two. Here is a collectio
 Here I realized that it is better to post some links and just mention some of my favorites, perhaps.
 
 * [The best AWK one-liners](http://tuxgraphics.org/~guido/scripts/awk-one-liner.html)
-* [AWK one-liners](http://www.softpanorama.org/Tools/Awk/awk_one_liners.shtml) by Softpanorama
 * [awk one-liners](https://nixshell.wordpress.com/2009/04/01/awk-one-liners/) by *nix shell
+* [Handy One-line Scripts for AWK](https://www.pement.org/awk/awk1line.txt) compiled by Eric Pement
 
diff --git a/docs/Case_studies/manipulating_vcf.md b/docs/Case_studies/manipulating_vcf.md
index 623bdaa5..2cf155bb 100644
--- a/docs/Case_studies/manipulating_vcf.md
+++ b/docs/Case_studies/manipulating_vcf.md
@@ -117,6 +117,8 @@ Count and sort the different genomic features in chromosome 4 by number.
         }
         ```
 
+    ??? "_Solution_ proposed by Loïs Rancilhac - 2022.08.30"
+        `awk '/_SNP/ {SNP++; print $0 > "chr4_SNPs.vcf"} /_DEL/ {DEL++; print $0 > "chr4_DEL.vcf"; LENGTH=length($4)-length($5); print LENGTH > "Deletions_lengths.txt"} /_INS/ {INS++; print $0 > "chr4_INS.vcf"; LENGTH=length($5)-length($4); print LENGTH > "Insertions_lengths.txt"} END{print "SNPs: "SNP"\nInsertions: "INS"\nDeletions: "DEL}' chr4.vcf`
 
 #### *Follow-up task:* 
 Print nucleotide substitution that these SNPs introduce sorted by number. Remember the coins...