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annabelperry
annabelperry
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I am using htslib/sam.h to write a C++ program. As part of this program, I must extract reads occurring on specific scaffolds in specific regions from a bam file. Essentially, I want to perform the following samtools command in C++:

samtools view name.bam -o name.sam scaffold:pos-pos

Since I must extract reads from thousands of regions, I do not want to iterate through the whole bam file each time I extract reads from a region. I am wondering if HTSlib can extract reads occurring in a specified scaffold and range without iterating through the whole bam. I found the function bam_itr_querys() in the htslib/sam.h documentation on GitHub, but don't know how to format the inputs for this function, or what the "idx" input is. I also saw somewhere that I would need to pair this function with bam_itr_next(), but don't know the format to do so.

EDIT: My bam files are sorted and indexed, if that matters.

I am using htslib/sam.h to write a C++ program. As part of this program, I must extract reads occurring on specific scaffolds in specific regions from a bam file. Essentially, I want to perform the following samtools command in C++:

samtools view name.bam -o name.sam scaffold:pos-pos

Since I must extract reads from thousands of regions, I do not want to iterate through the whole bam file each time I extract reads from a region. I am wondering if HTSlib can extract reads occurring in a specified scaffold and range without iterating through the whole bam. I found the function bam_itr_querys() in the htslib/sam.h documentation on GitHub, but don't know how to format the inputs for this function, or what the "idx" input is. I also saw somewhere that I would need to pair this function with bam_itr_next(), but don't know the format to do so.

I am using htslib/sam.h to write a C++ program. As part of this program, I must extract reads occurring on specific scaffolds in specific regions from a bam file. Essentially, I want to perform the following samtools command in C++:

samtools view name.bam -o name.sam scaffold:pos-pos

Since I must extract reads from thousands of regions, I do not want to iterate through the whole bam file each time I extract reads from a region. I am wondering if HTSlib can extract reads occurring in a specified scaffold and range without iterating through the whole bam. I found the function bam_itr_querys() in the htslib/sam.h documentation on GitHub, but don't know how to format the inputs for this function, or what the "idx" input is. I also saw somewhere that I would need to pair this function with bam_itr_next(), but don't know the format to do so.

EDIT: My bam files are sorted and indexed, if that matters.

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annabelperry
annabelperry
  • 319
  • 2
  • 10

Can HTSlib extract bam reads occurring in a specific region without iterating through the whole file?

I am using htslib/sam.h to write a C++ program. As part of this program, I must extract reads occurring on specific scaffolds in specific regions from a bam file. Essentially, I want to perform the following samtools command in C++:

samtools view name.bam -o name.sam scaffold:pos-pos

Since I must extract reads from thousands of regions, I do not want to iterate through the whole bam file each time I extract reads from a region. I am wondering if HTSlib can extract reads occurring in a specified scaffold and range without iterating through the whole bam. I found the function bam_itr_querys() in the htslib/sam.h documentation on GitHub, but don't know how to format the inputs for this function, or what the "idx" input is. I also saw somewhere that I would need to pair this function with bam_itr_next(), but don't know the format to do so.