FastSort/src/sort/sort_impl.cpp

#include <htslib/sam.h>
#include <spdlog/spdlog.h>
#include <stdint.h>
#include <stdio.h>

#include "sort_impl.h"

int ks_radixsort(size_t n, OneBam* buf, const sam_hdr_t* h, int tid) {
    if (tid == 0) spdlog::info("sort in thread, {} {}", tid, n);

    int curr = 0, ret = -1;
    ssize_t i;
    OneBam *buf_ar2[2], *bam_a, *bam_b;
    uint64_t max_pos = 1;
    uint32_t max_tid = 1, tid_bytes = 0, pos_bytes = 0, byte = 0;
    uint32_t tid_shift_l, tid_shift_r;
    int nref = sam_hdr_nref(h);

    //if (tid == 0)
        //spdlog::info("Before: {} {} {} {} {} {} {} {} {} {}", buf[0].pos, buf[1].pos, buf[2].pos, buf[3].pos, buf[4].pos, buf[5].pos, buf[6].pos,
                     //buf[7].pos, buf[8].pos, buf[9].pos);
    // spdlog::info("name: {}", std::string(buf[0].qnameAddr, buf[0].qnameLen));
    // spdlog::info("name addr: {}", (uint64_t)buf[0].qnameLen);
    // std::sort(buf, buf + n, [](const OneBam& b1, const OneBam& b2) { return b1.pos < b2.pos; });
    std::sort(buf, buf + n, [](const OneBam& b1, const OneBam& b2) {
        int cmp = 0;
        strncmp((char*)(b1.blockThread->blockArr[b1.blockIdx].data + b1.offset + OneBam::QnameOffset),
                (char*)(b2.blockThread->blockArr[b2.blockIdx].data + b2.offset + OneBam::QnameOffset), std::min(b1.qnameLen, b2.qnameLen));
        if (cmp == 0)
            return b1.qnameLen < b2.qnameLen;
        return cmp < 0;
    });
    if (tid == 0) {
        //std::string s1 = (char*)(buf[0].blockThread->blockArr[buf[0].blockIdx].data + buf[0].offset + OneBam::QnameOffset);
        //std::string s2 = (char*)(buf[1].blockThread->blockArr[buf[1].blockIdx].data + buf[1].offset + OneBam::QnameOffset);
        //spdlog::info("After: {} {} {} {} {} {} {} {} {} {}", s1, s2, buf[2].pos, buf[3].pos, buf[4].pos, buf[5].pos, buf[6].pos, buf[7].pos,
                     //buf[8].pos, buf[9].pos);
        }

    return 0;
}