Is there a history of merges not included in anchor_summary.txt?

[mu-bio]

Hello @mahulchak ,

I checked anchor_summary.txt to see which contigs were merged.
Then I found that the history merging a contig was not included in anchor_summary.txt, even though the contig length was increased by the merge.
May the file not contain a history of merged contigs?

The details are as follows:

The contig name is "S_5".
The line containing S_5 in the anchor_summary.txt is:

$ cat anchor_summary.txt | awk -F "\t" '$1=="S_5" || $2=="S_5" {print}'
S_5	C_4554	635863	9935	1	9935	1	9935

The S_5 length should not increase because C_4554 contains it.
However, according to the output fasta file, S_5 length increased. (S_5 length increased to 764,575 bp from 635,863 bp)

cat merged.fasta | awk '$1~">" {h=$1}; $1!~">" && h==">S_5" {print h": "length($1)}'
>S_5: 764575

Why did S_5 length increase after merging?

Incidentally, the line containing S_5 in the aln_summary.tsv is:

$ cat aln_summary.tsv | awk -F "\t" '$1=="S_5" || $2=="S_5" {print}'
S_5	C_1	635863	753307	11297	481279	1	469983
S_5	C_1	635863	753307	481349	635863	470171	624685
S_5	C_13	635863	419977	9797	11437	350194	351834
S_5	C_4554	635863	9935	1	9935	1	9935

Thanks,
Mimi

[mahulchak]

This could potentially be a bug. I'll need to check what happened. Will you be able to share your files (fasta & delta) ?

…

On Tue, Jun 22, 2021, 01:47 Mimi ***@***.***> wrote: Hello @mahulchak <https://github.com/mahulchak> , I checked anchor_summary.txt to see which contigs were merged. Then I found that the history merging a contig was not included in anchor_summary.txt, even though the contig length was increased by the merge. May the file not contain a history of merged contigs? The details are as follows: The contig name is "S_5". The line containing S_5 in the anchor_summary.txt is: $ cat anchor_summary.txt | awk -F "\t" '$1=="S_5" || $2=="S_5" {print}' S_5 C_4554 635863 9935 1 9935 1 9935 The S_5 length should not increase because C_4554 contains it. However, according to the output fasta file, S_5 length increased. (S_5 length increased to 764,575 bp from 635,863 bp) cat merged.fasta | awk '$1~">" {h=$1}; $1!~">" && h==">S_5" {print h": "length($1)}' >S_5: 764575 Why did S_5 length increase after merging? Incidentally, the line containing S_5 in the aln_summary.tsv is: $ cat aln_summary.tsv | awk -F "\t" '$1=="S_5" || $2=="S_5" {print}' S_5 C_1 635863 753307 11297 481279 1 469983 S_5 C_1 635863 753307 481349 635863 470171 624685 S_5 C_13 635863 419977 9797 11437 350194 351834 S_5 C_4554 635863 9935 1 9935 1 9935 Thanks, Mimi — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#65>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABZQH2EKYMDWLUOSW5ZUA33TUBEZ5ANCNFSM47DGYHVQ> .